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Chen Y, Zhao M, Ouyang Y, Zhang S, Liu Z, Wang K, Zhang Z, Liu Y, Yang C, Sun W, Shen J, Zhu Z. Biotemplated precise assembly approach toward ultra-scaled high-performance electronics. Nat Protoc 2023; 18:2975-2997. [PMID: 37670036 DOI: 10.1038/s41596-023-00870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/08/2023] [Indexed: 09/07/2023]
Abstract
Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 μA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.
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Affiliation(s)
- Yahong Chen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Mengyu Zhao
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yifan Ouyang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Suhui Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zhihan Liu
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Zhaoxuan Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yingxia Liu
- Department of Systems Engineering, City University of Hong Kong, Hong Kong, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
- Zhangjiang Laboratory, Shanghai, China.
| | - Jie Shen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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Brooks JF, Riggs J, Mueller JL, Mathenge R, Wholey WY, Meyer AR, Yoda ST, Vykunta VS, Nielsen HV, Cheng W, Zikherman J. Molecular basis for potent B cell responses to antigen displayed on particles of viral size. Nat Immunol 2023; 24:1762-1777. [PMID: 37653247 PMCID: PMC10950062 DOI: 10.1038/s41590-023-01597-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Multivalent viral epitopes induce rapid, robust and T cell-independent humoral immune responses, but the biochemical basis for such potency remains incompletely understood. We take advantage of a set of liposomes of viral size engineered to display affinity mutants of the model antigen (Ag) hen egg lysozyme. Particulate Ag induces potent 'all-or-none' B cell responses that are density dependent but affinity independent. Unlike soluble Ag, particulate Ag induces signal amplification downstream of the B cell receptor by selectively evading LYN-dependent inhibitory pathways and maximally activates NF-κB in a manner that mimics T cell help. Such signaling induces MYC expression and enables even low doses of particulate Ag to trigger robust B cell proliferation in vivo in the absence of adjuvant. We uncover a molecular basis for highly sensitive B cell responses to viral Ag display that is independent of encapsulated nucleic acids and is not merely accounted for by avidity and B cell receptor cross-linking.
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Affiliation(s)
- Jeremy F Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Julianne Riggs
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - James L Mueller
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Raisa Mathenge
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wei-Yun Wholey
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Alexander R Meyer
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Sekou-Tidiane Yoda
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Vivasvan S Vykunta
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Hailyn V Nielsen
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wei Cheng
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, CA, USA.
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53
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Tisza M, Lloyd R, Hoffman K, Smith D, Rewers M, Cregeen SJ, Petrosino JF. Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559994. [PMID: 37808738 PMCID: PMC10557657 DOI: 10.1101/2023.09.28.559994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial colonization proceeds through well-studied phases. However, less is known about phage communities in early human development due to small study sizes, inability to leverage large databases, and lack of appropriate bioinformatics tools. In this study, whole genome shotgun sequencing data from the TEDDY study, composed of 12,262 longitudinal samples from 887 children in 4 countries, is reanalyzed to assess phage and bacterial dynamics simultaneously. Reads from these samples were mapped to marker genes from both bacteria and a new database of tens of thousands of phage taxa from human microbiomes. We uncover that each child is colonized by hundreds of different phages during the early years, and phages are more transitory than bacteria. Participants' samples continually harbor new phage species over time whereas the diversification of bacterial species begins to saturate. Phage data improves the ability for machine learning models to discriminate samples by country. Finally, while phage populations were individual-specific, striking patterns arose from the larger dataset, showing clear trends of ecological succession amongst phages, which correlated well with putative host bacteria. Improved understanding of phage-bacterial relationships may reveal new means by which to shape and modulate the microbiome and its constituents to improve health and reduce disease, particularly in vulnerable populations where antibiotic use and/or other more drastic measures may not be advised.
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Affiliation(s)
- Michael Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Smith
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Sara Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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54
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Ramirez A, Felgner J, Jain A, Jan S, Albin TJ, Badten AJ, Gregory AE, Nakajima R, Jasinskas A, Felgner PL, Burkhardt AM, Davies DH, Wang SW. Engineering Protein Nanoparticles Functionalized with an Immunodominant Coxiella burnetii Antigen to Generate a Q Fever Vaccine. Bioconjug Chem 2023; 34:1653-1666. [PMID: 37682243 PMCID: PMC10515490 DOI: 10.1021/acs.bioconjchem.3c00317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Coxiella burnetii is the causative agent of Q fever, for which there is yet to be an FDA-approved vaccine. This bacterial pathogen has both extra- and intracellular stages in its life cycle, and therefore both a cell-mediated (i.e., T lymphocyte) and humoral (i.e., antibody) immune response are necessary for effective eradication of this pathogen. However, most proposed vaccines elicit strong responses to only one mechanism of adaptive immunity, and some can either cause reactogenicity or lack sufficient immunogenicity. In this work, we aim to apply a nanoparticle-based platform toward producing both antibody and T cell immune responses against C. burnetii. We investigated three approaches for conjugation of the immunodominant outer membrane protein antigen (CBU1910) to the E2 nanoparticle to obtain a consistent antigen orientation: direct genetic fusion, high affinity tris-NTA-Ni conjugation to polyhistidine-tagged CBU1910, and the SpyTag/SpyCatcher (ST/SC) system. Overall, we found that the ST/SC approach yielded nanoparticles loaded with the highest number of antigens while maintaining stability, enabling formulations that could simultaneously co-deliver the protein antigen (CBU1910) and adjuvant (CpG1826) on one nanoparticle (CBU1910-CpG-E2). Using protein microarray analyses, we found that after immunization, antigen-bound nanoparticle formulations elicited significantly higher antigen-specific IgG responses than soluble CBU1910 alone and produced more balanced IgG1/IgG2c ratios. Although T cell recall assays from these protein antigen formulations did not show significant increases in antigen-specific IFN-γ production compared to soluble CBU1910 alone, nanoparticles conjugated with a CD4 peptide epitope from CBU1910 generated elevated T cell responses in mice to both the CBU1910 peptide epitope and whole CBU1910 protein. These investigations highlight the feasibility of conjugating antigens to nanoparticles for tuning and improving both humoral- and cell-mediated adaptive immunity against C. burnetii.
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Affiliation(s)
- Aaron Ramirez
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Jiin Felgner
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Aarti Jain
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Sharon Jan
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Tyler J. Albin
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Alexander J. Badten
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Anthony E. Gregory
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Rie Nakajima
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Algimantas Jasinskas
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Philip L. Felgner
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Amanda M. Burkhardt
- Department
of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - D. Huw Davies
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Szu-Wen Wang
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, and Institute for Immunology, University of California, Irvine, California 92697, United States
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Andalibi A, Veneziano R, Paige M, Buschmann M, Haymond A, Espina V, Luchini A, Liotta L, Bishop B, Van Hoek M. Drug discovery efforts at George Mason University. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:270-274. [PMID: 36921802 DOI: 10.1016/j.slasd.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/14/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023]
Abstract
With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.
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Affiliation(s)
- Ali Andalibi
- School for Systems Biology, George Mason University, Manassas, VA, USA
| | - Remi Veneziano
- Department of Biomedical Engineering, College of Engineering and Computing, George Mason University, Manassas, VA, USA
| | - Mikell Paige
- Department of Chemistry, College of Science, George Mason University, Fairfax, VA, USA
| | - Michael Buschmann
- Department of Biomedical Engineering, College of Engineering and Computing, George Mason University, Manassas, VA, USA
| | - Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA; School for Systems Biology, George Mason University, Manassas, VA, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA; School for Systems Biology, George Mason University, Manassas, VA, USA
| | - Barney Bishop
- Department of Chemistry, College of Science, George Mason University, Fairfax, VA, USA
| | - Monique Van Hoek
- School for Systems Biology, George Mason University, Manassas, VA, USA
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Wang J, Li P, Wang C, Liu N, Xing D. Molecularly or atomically precise nanostructures for bio-applications: how far have we come? MATERIALS HORIZONS 2023; 10:3304-3324. [PMID: 37365977 DOI: 10.1039/d3mh00574g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
A huge variety of nanostructures are promising for biomedical applications, but only a few have been practically applied. Among the various reasons, the limited structural preciseness is a critical one, as it increases the difficulty in product quality control, accurate dosing, and ensuring the repeatability of material performance. Constructing nanoparticles with molecule-like preciseness is becoming a new research field. In this review, we focus on the artificial nanomaterials that can currently be molecularly or atomically precise, including DNA nanostructures, some metallic nanoclusters, dendrimer nanoparticles and carbon nanostructures, describing their syntheses, bio-applications and limitations, in view of up-to-date studies. A perspective on their potential for clinical translation is also given. This review is expected to provide a particular rationale for the future design of nanomedicines.
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Affiliation(s)
- Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ping Li
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ning Liu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
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Ronsard L, Yousif AS, Nait Mohamed FA, Feldman J, Okonkwo V, McCarthy C, Schnabel J, Caradonna T, Barnes RM, Rohrer D, Lonberg N, Schmidt A, Lingwood D. Engaging an HIV vaccine target through the acquisition of low B cell affinity. Nat Commun 2023; 14:5249. [PMID: 37640732 PMCID: PMC10462694 DOI: 10.1038/s41467-023-40918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Low affinity is common for germline B cell receptors (BCR) seeding development of broadly neutralizing antibodies (bnAbs) that engage hypervariable viruses, including HIV. Antibody affinity selection is also non-homogenizing, insuring the survival of low affinity B cell clones. To explore whether this provides a natural window for expanding human B cell lineages against conserved vaccine targets, we deploy transgenic mice mimicking human antibody diversity and somatic hypermutation (SHM) and immunize with simple monomeric HIV glycoprotein envelope immunogens. We report an immunization regimen that focuses B cell memory upon the conserved CD4 binding site (CD4bs) through both conventional affinity maturation and reproducible expansion of low affinity BCR clones with public patterns in SHM. In the latter instance, SHM facilitates target acquisition by decreasing binding strength. This suggests that permissive B cell selection enables the discovery of antibody epitopes, in this case an HIV bnAb site.
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Affiliation(s)
- Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Jared Feldman
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Julia Schnabel
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Timothy Caradonna
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Aaron Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA.
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Zhang K, Huang Z, Wang Y, Xue J, Liang N, Wei Z. Rapid determination of the presence of EGFR mutations with DNA-based nanocalipers. NANOSCALE 2023; 15:13834-13841. [PMID: 37580989 DOI: 10.1039/d3nr02665e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Selecting 1st-line treatment for lung cancer is currently a binary choice, either chemotherapy or targeted medicine, depending on whether EGFR mutations exist. Next-generation sequencing is fully capable of accurately identifying EGFR mutations and guiding the usage of tyrosine kinase inhibitors, but it is highly expensive. Moreover, as the sequencing is not helpful for patients with wild-type EGFR, the long wait for sequencing may delay the chemotherapy and correspondingly increase the risks of cancer progression. To address this issue, a new method for rapidly determining the presence of EGFR mutations is developed in this study. A series of DNA origami-engineered nanocalipers are designed and constructed to determine the EGFR spatial distribution of either mutated EGFR or wild-type EGFR lung cancer cells. The experimental results on cancer cell lines and 9 clinical tissue samples show that compared with wild-type EGFR cells, mutated EGFR cells have narrower EGFR spacing. Hence, the DNA nanocalipers are demonstrated to be capable of determining the presence of EGFR mutations and shrinking the detection period from weeks to hours, compared with sequencing. For determining EGFR mutation status in 9 clinical samples, DNA nanocalipers show 100% consistency with next-generation sequencing.
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Affiliation(s)
- Kexin Zhang
- Department of Biomedical Engineering, School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Zewen Wei
- Department of Biomedical Engineering, School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China.
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59
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Johnson SN, Brucks SD, Apley KD, Farrell MP, Berkland CJ. Multivalent Scaffolds to Promote B cell Tolerance. Mol Pharm 2023; 20:3741-3756. [PMID: 37410969 DOI: 10.1021/acs.molpharmaceut.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Autoimmune diseases are characterized by aberrant immune responses toward self-antigens. Current treatments lack specificity, promoting adverse effects by broadly suppressing the immune system. Therapies that specifically target the immune cells responsible for disease are a compelling strategy to mitigate adverse effects. Multivalent formats that display numerous binding epitopes off a single scaffold may enable selective immunomodulation by eliciting signals through pathways unique to the targeted immune cells. However, the architecture of multivalent immunotherapies can vary widely, and there is limited clinical data with which to evaluate their efficacy. Here, we set forth to review the architectural properties and functional mechanisms afforded by multivalent ligands and evaluate four multivalent scaffolds that address autoimmunity by altering B cell signaling pathways. First, we address both synthetic and natural polymer backbones functionalized with a variety of small molecule, peptide, and protein ligands for probing the effects of valency and costimulation. Then, we review nanoparticles composed entirely from immune signals which have been shown to be efficacious. Lastly, we outline multivalent liposomal nanoparticles capable of displaying high numbers of protein antigens. Taken together, these examples highlight the versatility and desirability of multivalent ligands for immunomodulation and illuminate strengths and weaknesses of multivalent scaffolds for treating autoimmunity.
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Affiliation(s)
- Stephanie N Johnson
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Spencer D Brucks
- Department of Chemistry, Harvey Mudd College, Claremont, California 91711, United States
| | - Kyle D Apley
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Mark P Farrell
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045, United States
- Bioengineering Program, University of Kansas, Lawrence, Kansas 66045, United States
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60
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Lee K, Davis B, Wang X, Mirg S, Wen C, Abune L, Peterson BE, Han L, Chen H, Wang H, Szczesny SE, Lei Y, Kothapalli SR, Wang Y. Nanoparticle-Decorated Biomimetic Extracellular Matrix for Cell Nanoencapsulation and Regulation. Angew Chem Int Ed Engl 2023; 62:e202306583. [PMID: 37277318 PMCID: PMC10526972 DOI: 10.1002/anie.202306583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/07/2023]
Abstract
Cell encapsulation has been studied for various applications ranging from cell transplantation to biological production. However, current encapsulation technologies focus on cell protection rather than cell regulation that is essential to most if not all cell-based applications. Here we report a method for cell nanoencapsulation and regulation using an ultrathin biomimetic extracellular matrix as a cell nanocapsule to carry nanoparticles (CN2 ). This method allows high-capacity nanoparticle retention at the vicinity of cell surfaces. The encapsulated cells maintain high viability and normal metabolism. When gold nanoparticles (AuNPs) are used as a model to decorate the nanocapsule, light irradiation transiently increases the temperature, leading to the activation of the heat shock protein 70 (HSP70) promoter and the regulation of reporter gene expression. As the biomimetic nanocapsule can be decorated with any or multiple NPs, CN2 is a promising platform for advancing cell-based applications.
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Affiliation(s)
- Kyungsene Lee
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Xuelin Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubham Mirg
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Connie Wen
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lidya Abune
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Benjamin E Peterson
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Li Han
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Haoyang Chen
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hongjun Wang
- Department of Biomedical Engineering, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Spencer E Szczesny
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuguo Lei
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sri-Rajasekhar Kothapalli
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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61
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Choi Y, Cho BK, Seok SH, Kim C, Ryu JH, Kwon IC. Controlled spatial characteristics of ligands on nanoparticles: Determinant of cellular functions. J Control Release 2023; 360:672-686. [PMID: 37437847 DOI: 10.1016/j.jconrel.2023.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/27/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Interactions of various ligands and receptors have been extensively investigated because they regulate a series of signal transduction leading to various functional cellular outcomes. The receptors on cell membrane recognize their specific ligands, resulting in specific binding between ligands and receptors. Accumulating evidence reveals that the receptors recognize the difference on the spatial characteristics of ligands as well as the types of ligands. Thus, control on spatial characteristics of multiple ligands presented on therapeutic nanoparticles is believed to impact the cellular functions. Specifically, the localized and multivalent distribution of ligands on nanoparticles can induce receptor oligomerization and receptor clustering, controlling intensity or direction of signal transduction cascades. Here, we will introduce recent studies on the use of material-based nanotechnology to control spatial characteristics of ligands and their effect on cellular functions. These therapeutic nanoparticles with controlled spatial characteristics of ligands may be a promising strategy for maximized therapeutic outcome.
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Affiliation(s)
- Youngjin Choi
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Bo Kyung Cho
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Su Hyun Seok
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Chansoo Kim
- Computational Science Centre & ASSIST, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; AI-Robot Department, University of Science and Technology, Seoul 02792, Republic of Korea
| | - Ju Hee Ryu
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
| | - Ick Chan Kwon
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea.
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62
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Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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63
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Linko V, Keller A. Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301935. [PMID: 37093216 DOI: 10.1002/smll.202301935] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.
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Affiliation(s)
- Veikko Linko
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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64
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Sun L, Shen F, Qu Y, Liu Z. Functional DNA as a Molecular Tool in Regulating Immunoreceptor-Ligand Interactions. JACS AU 2023; 3:1820-1834. [PMID: 37502159 PMCID: PMC10369416 DOI: 10.1021/jacsau.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
During immune responses, activating ligands would trigger dynamic spatiotemporal organization of immunoreceptors at the cell interface, governing the fate and effector functions of immune cells. To understand the biophysical mechanisms of immunoreceptor signaling, diverse tools, including DNA technologies, have been developed to manipulate receptor-ligand interactions during the immune activation process. With great capability in the controllable assembly of biomolecules, functional DNA-based precise arrangement of immune molecules at cell interfaces has provided a powerful means in revealing the principles of immunoreceptor triggering, even at the single-molecule level. In addition, precisely regulating immunoreceptor-ligand interactions with functional DNA has been applied in immunotherapies of major diseases. This Perspective will focus on the recent advances in exploring immunoreceptor signaling with functional DNA as the molecular tool as well as the applications of functional DNA mediated regulation of immunoreceptor activation. We also outline the challenges and opportunities of applying functional DNA in immune modulation and immunotherapy.
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Affiliation(s)
- Lele Sun
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- School
of Chemistry and Chemical Engineering, Shanghai
Jiao Tong University, Shanghai 201240, China
| | - Yanfei Qu
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Zhuang Liu
- Institute
of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab
Carbon Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
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65
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He A, Li X, Dai Z, Li Q, Zhang Y, Ding M, Wen ZF, Mou Y, Dong H. Nanovaccine-based strategies for lymph node targeted delivery and imaging in tumor immunotherapy. J Nanobiotechnology 2023; 21:236. [PMID: 37482608 PMCID: PMC10364424 DOI: 10.1186/s12951-023-01989-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/08/2023] [Indexed: 07/25/2023] Open
Abstract
Therapeutic tumor vaccines have attracted considerable attention in the past decade; they can induce tumor regression, eradicate minimal residual disease, establish lasting immune memory and avoid non-specific and adverse side effects. However, the challenge in the field of therapeutic tumor vaccines is ensuring the delivery of immune components to the lymph nodes (LNs) to activate immune cells. The clinical response rate of traditional therapeutic tumor vaccines falls short of expectations due to inadequate lymph node delivery. With the rapid development of nanotechnology, a large number of nanoplatform-based LN-targeting nanovaccines have been exploited for optimizing tumor immunotherapies. In addition, some nanovaccines possess non-invasive visualization performance, which is benefit for understanding the kinetics of nanovaccine exposure in LNs. Herein, we present the parameters of nanoplatforms, such as size, surface modification, shape, and deformability, which affect the LN-targeting functions of nanovaccines. The recent advances in nanoplatforms with different components promoting LN-targeting are also summarized. Furthermore, emerging LNs-targeting nanoplatform-mediated imaging strategies to both improve targeting performance and enhance the quality of LN imaging are discussed. Finally, we summarize the prospects and challenges of nanoplatform-based LN-targeting and /or imaging strategies, which optimize the clinical efficacy of nanovaccines in tumor immunotherapies.
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Affiliation(s)
- Ao He
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Xiaoye Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Zhuo Dai
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Qiang Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Yu Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Meng Ding
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China
| | - Zhi-Fa Wen
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, 210004, China.
| | - Yongbin Mou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
| | - Heng Dong
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, 30 Zhongyang Road, Nanjing, 210008, China.
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66
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Sentosa J, Djutanta F, Horne B, Showkeir D, Rezvani R, Leff C, Pradhan S, Hariadi RF. Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation. PLoS One 2023; 18:e0283134. [PMID: 37467178 DOI: 10.1371/journal.pone.0283134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/02/2023] [Indexed: 07/21/2023] Open
Abstract
DNA origami purification is essential for many fields, including biophysics, molecular engineering, and therapeutics. The increasing interest in DNA origami has led to the development of rate-zonal centrifugation (RZC) as a scalable, high yield, and contamination-free method for purifying DNA origami nanostructures. RZC purification uses a linear density gradient of viscous media, such as glycerol or sucrose, to separate molecules according to their mass and shape. However, many methods for creating density gradients are time-consuming because they rely on slow passive diffusion. To expedite the preparation time, we used a LEGO gradient mixer to generate rotational motion and rapidly create a quasi-continuous density gradient with a minimal layering of the viscous media. Rotating two layers of differing concentrations at an angle decreases the time needed to form the density gradient from a few hours to minutes. In this study, the density gradients created by the LEGO gradient mixer were used to purify 3 DNA origami shapes that have different aspect ratios and numbers of components, with an aspect ratio ranging from 1:1 to 1:100 and the number of components up to 2. The gradient created by our LEGO gradient mixer is sufficient to purify folded DNA origami nanostructures from excess staple strands, regardless of their aspect ratios. Moreover, the gradient was able to separate DNA origami dimers from DNA origami monomers. In light of recent advances in large-scale DNA origami production, our method provides an alternative for purifying DNA origami nanostructures in large (gram) quantities in resource-limited settings.
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Affiliation(s)
- Jason Sentosa
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Brian Horne
- Department of Physics, Arizona State University, Tempe, AZ, United States of America
| | - Dominic Showkeir
- Department of Physics, Arizona State University, Tempe, AZ, United States of America
| | - Robert Rezvani
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Chloe Leff
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Swechchha Pradhan
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Rizal F Hariadi
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
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67
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Wamhoff EC, Ronsard L, Feldman J, Knappe GA, Hauser BM, Romanov A, Lam E, Denis KS, Boucau J, Barczak AK, Balazs AB, Schmidt A, Lingwood D, Bathe M. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.08.16.504128. [PMID: 36032975 PMCID: PMC9413718 DOI: 10.1101/2022.08.16.504128] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multivalent antigen display is a well-established principle to enhance humoral immunity. Protein-based virus-like particles (VLPs) are commonly used to spatially organize antigens. However, protein-based VLPs are limited in their ability to control valency on fixed scaffold geometries and are thymus-dependent antigens that elicit neutralizing B cell memory themselves, which can distract immune responses. Here, we investigated DNA origami as an alternative material for multivalent antigen display in vivo, applied to the receptor binding domain (RBD) of SARS-CoV2 that is the primary antigenic target of neutralizing antibody responses. Icosahedral DNA-VLPs elicited neutralizing antibodies to SARS-CoV-2 in a valency-dependent manner following sequential immunization in mice, quantified by pseudo- and live-virus neutralization assays. Further, induction of B cell memory against the RBD required T cell help, but the immune sera did not contain boosted, class-switched antibodies against the DNA scaffold. This contrasted with protein-based VLP display of the RBD that elicited B cell memory against both the target antigen and the scaffold. Thus, DNA-based VLPs enhance target antigen immunogenicity without generating off-target, scaffold-directed immune memory, thereby offering a potentially important alternative material for particulate vaccine design.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Jared Feldman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Blake M. Hauser
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Evan Lam
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Kerri St. Denis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Amy K Barczak
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Alejandro B. Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Aaron Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, United States
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, United States
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68
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Torkan E, Salmani-Tehrani M. Conformational dynamics and mechanical properties of biomimetic RNA, DNA, and RNA-DNA hybrid nanotubes: an atomistic molecular dynamics study. Phys Chem Chem Phys 2023. [PMID: 37309220 DOI: 10.1039/d3cp01028g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs. Here, the simulations were carried out using the equilibrium molecular dynamics (MD) and steered molecular dynamics (SMD) approaches. Using in-house scripting, we modeled hexagonal nanotubes composed of six double-stranded molecules connected by four-way Holliday junctions. Classical MD analyses were performed on the collected trajectory data to investigate structural properties. Analyses of the microscopic structural parameters of RDHNT indicated a structural transition from the A-form to a conformation between the A- and B-forms, which may be attributable to the increased rigidity of RNA scaffolds compared to DNA staples. Comprehensive research on the elastic mechanical properties was also conducted based on spontaneous thermal fluctuations of nanotubes and employing the equipartition theorem. The Young's modulus of RDHNT (E = 165 MPa) and RNT (E = 144 MPa) was found to be almost the same and nearly half of that found for DNT (E = 325 MPa). Furthermore, the results showed that RNT was more resistant to bending, torsional, and volumetric deformations than DNT and RDHNT. We also used non-equilibrium SMD simulations to acquire comprehensive knowledge of the mechanical response of nanotubes to tensile stress.
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Affiliation(s)
- Ehsan Torkan
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Mehdi Salmani-Tehrani
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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69
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Vilcapoma J, Aliyeva A, Hayden A, Chandrasekaran AR, Zhou L, Punnoose JA, Yang D, Hansen C, Shiu SCC, Russell A, George KS, Wong WP, Halvorsen K. A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.31.23290613. [PMID: 37398235 PMCID: PMC10312858 DOI: 10.1101/2023.05.31.23290613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.
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Affiliation(s)
- Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Asmer Aliyeva
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | | | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Clinton Hansen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Simon Chi-Chin Shiu
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alexis Russell
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
| | - Kirsten St. George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY 12208
- Department of Biomedical Science, University at Albany, State University of New York, Albany, NY 12208
| | - Wesley P. Wong
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
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70
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Oktay E, Bush J, Vargas M, Scarton DV, O'Shea B, Hartman A, Green CM, Neyra K, Gomes CM, Medintz IL, Mathur D, Veneziano R. Customized Scaffolds for Direct Assembly of Functionalized DNA Origami. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37267624 DOI: 10.1021/acsami.3c05690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in a variety of biomedical applications including targeted drug delivery and vaccine development. DNA-NPs can be designed into a broad range of nanoarchitectures in one, two, and three dimensions with high structural fidelity. Moreover, the addressability of the DNA-NPs enables the precise organization of functional moieties, which improves targeting, actuation, and stability. DNA-NPs are usually functionalized via chemically modified staple strands, which can be further conjugated with additional polymers and proteins for the intended application. Although this method of functionalization is extremely efficient to control the stoichiometry and organization of functional moieties, fewer than half of the permissible sites are accessible through staple modifications. In addition, DNA-NP functionalization rapidly becomes expensive when a high number of functionalizations such as fluorophores for tracking and chemical modifications for stability that do not require spatially precise organization are used. To facilitate the synthesis of functional DNA-NPs, we propose a simple and robust strategy based on an asymmetric polymerase chain reaction (aPCR) protocol that allows direct synthesis of custom-length scaffolds that can be randomly modified and/or precisely modified via sequence design. We demonstrated the potential of our strategy by producing and characterizing heavily modified scaffold strands with amine groups for dye functionalization, phosphorothioate bonds for stability, and biotin for surface immobilization. We further validated our sequence design approach for precise conjugation of biomolecules by synthetizing scaffolds including binding loops and aptamer sequences that can be used for direct hybridization of nucleic acid tagged biomolecules or binding of protein targets.
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Affiliation(s)
- Esra Oktay
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Joshua Bush
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Merlyn Vargas
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Dylan Valerio Scarton
- College of Science, Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, Virginia 22030-4444, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Bailey O'Shea
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Amber Hartman
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Carolina M Gomes
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Remi Veneziano
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
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71
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Ricci F, Dietz H. The harmony of form and function in DNA nanotechnology. NATURE NANOTECHNOLOGY 2023; 18:541-542. [PMID: 36991158 DOI: 10.1038/s41565-023-01362-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Francesco Ricci
- Laboratory of Biosensors and Nanomachines, Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Rome, Italy.
| | - Hendrik Dietz
- Department of Biosciences and Munich Institute of Biomedical Engineering, School of Natural Sciences, Technical University of Munich, Munich, Germany.
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72
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Ma N, Cheng K, Feng Q, Liu G, Liang J, Ma X, Chen Z, Lu Y, Wang X, He W, Xu H, Wu S, Zou J, Shi Q, Nie G, Zhao X. Nanoscale Organization of TRAIL Trimers using DNA Origami to Promote Clustering of Death Receptor and Cancer Cell Apoptosis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206160. [PMID: 36890776 DOI: 10.1002/smll.202206160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/19/2023] [Indexed: 06/08/2023]
Abstract
Through inducing death receptor (DR) clustering to activate downstream signaling, tumor necrosis factor related apoptosis inducing ligand (TRAIL) trimers trigger apoptosis of tumor cells. However, the poor agonistic activity of current TRAIL-based therapeutics limits their antitumor efficiency. The nanoscale spatial organization of TRAIL trimers at different interligand distances is still challenging, which is essential for the understanding of interaction pattern between TRAIL and DR. In this study, a flat rectangular DNA origami is employed as display scaffold, and an "engraving-printing" strategy is developed to rapidly decorate three TRAIL monomers onto its surface to form DNA-TRAIL3 trimer (DNA origami with surface decoration of three TRAIL monomers). With the spatial addressability of DNA origami, the interligand distances are precisely controlled from 15 to 60 nm. Through comparing the receptor affinity, agonistic activity and cytotoxicity of these DNA-TRAIL3 trimers, it is found that ≈40 nm is the critical interligand distance of DNA-TRAIL3 trimers to induce death receptor clustering and the resulting apoptosis.Finally, a hypothetical "active unit" model is proposed for the DR5 clustering induced by DNA-TRAIL3 trimers.
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Affiliation(s)
- Nana Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Keman Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Qingqing Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Guangna Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Xiaotu Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Zhiqiang Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yichao Lu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Xinwei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Wei He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Hu Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Jiajia Zou
- Beijing Intell Nanomedicine, No. 9, Chengwan Street, Haidian District, Beijing, 100000, China
| | - Quanwei Shi
- Beijing Intell Nanomedicine, No. 9, Chengwan Street, Haidian District, Beijing, 100000, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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73
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Wassermann LM, Scheckenbach M, Baptist AV, Glembockyte V, Heuer-Jungemann A. Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212024. [PMID: 36932052 DOI: 10.1002/adma.202212024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
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Affiliation(s)
- Lea M Wassermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Anna V Baptist
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
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74
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541980. [PMID: 37292995 PMCID: PMC10245855 DOI: 10.1101/2023.05.23.541980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our "trihead" nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A. Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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75
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Wamhoff EC, Knappe GA, Burds AA, Du RR, Neun BW, Difilippantonio S, Sanders C, Edmondson EF, Matta JL, Dobrovolskaia MA, Bathe M. Evaluation of Nonmodified Wireframe DNA Origami for Acute Toxicity and Biodistribution in Mice. ACS APPLIED BIO MATERIALS 2023; 6:1960-1969. [PMID: 37040258 PMCID: PMC10189729 DOI: 10.1021/acsabm.3c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 04/12/2023]
Abstract
Wireframe DNA origami can be used to fabricate virus-like particles for a range of biomedical applications, including the delivery of nucleic acid therapeutics. However, the acute toxicity and biodistribution of these wireframe nucleic acid nanoparticles (NANPs) have not been previously characterized in animal models. In the present study, we observed no indications of toxicity in BALB/c mice following a therapeutically relevant dosage of nonmodified DNA-based NANPs via intravenous administration, based on liver and kidney histology, liver and kidney biochemistry, and body weight. Further, the immunotoxicity of these NANPs was minimal, as indicated by blood cell counts and type-I interferon and pro-inflammatory cytokines. In an SJL/J model of autoimmunity, we observed no indications of NANP-mediated DNA-specific antibody response or immune-mediated kidney pathology following the intraperitoneal administration of NANPs. Finally, biodistribution studies revealed that these NANPs accumulate in the liver within one hour, concomitant with substantial renal clearance. Our observations support the continued development of wireframe DNA-based NANPs as next-generation nucleic acid therapeutic delivery platforms.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Grant A. Knappe
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States of America
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Aurora A. Burds
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Rebecca R. Du
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Barry W. Neun
- Nanotechnology
Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Simone Difilippantonio
- Laboratory
of Animal Sciences Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Chelsea Sanders
- Laboratory
of Animal Sciences Program, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Elijah F. Edmondson
- Molecular
Histology and Pathology Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Jennifer L. Matta
- Molecular
Histology and Pathology Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Marina A. Dobrovolskaia
- Nanotechnology
Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States of America
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States of America
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76
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Tian R, Shang Y, Wang Y, Jiang Q, Ding B. DNA Nanomaterials-Based Platforms for Cancer Immunotherapy. SMALL METHODS 2023; 7:e2201518. [PMID: 36651129 DOI: 10.1002/smtd.202201518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Indexed: 05/17/2023]
Abstract
The past few decades have witnessed the evolving paradigm for cancer therapy from nonspecific cytotoxic agents to selective, mechanism-based therapeutics, especially immunotherapy. In particular, the integration of nanomaterials with immunotherapy is proven to improve the therapeutic outcome and minimize off-target toxicity in the treatment. As a novel nanomaterial, DNA-based self-assemblies featuring uniform geometries, feasible modifications, programmability, surface addressability, versatility, and intrinsic biocompatibility, are extensively exploited for innovative and effective cancer immunotherapy. In this review, the successful employment of DNA nanoplatforms for cancer immunotherapy, including the delivery of immunogenic cell death inducers, adjuvants and vaccines, immune checkpoint blockers as well as the application in immune cell engineering and adoptive cell therapy is summarized. The remaining challenges and future perspectives regarding the pharmacokinetics/pharmacodynamics, in vivo fate and immunogenicity of DNA materials, and the design of intelligent DNA nanomedicine for individualized cancer immunotherapy are also discussed.
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Affiliation(s)
- Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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77
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Obeng EM, Fulcher AJ, Wagstaff KM. Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering. Biotechnol Adv 2023; 64:108108. [PMID: 36740026 DOI: 10.1016/j.biotechadv.2023.108108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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78
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Chen F, Huang Y, Huang Z, Jiang T, Yang Z, Zeng J, Jin A, Zuo H, Huang CZ, Mao C. DNA-scaffolded multivalent vaccine against SARS-CoV-2. Acta Biomater 2023; 164:387-396. [PMID: 37088158 PMCID: PMC10122553 DOI: 10.1016/j.actbio.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
Short peptides are poor immunogens. One way to increase their immune responses is by arraying immunogens in multivalency. Simple and efficient scaffolds for spatial controlling the inter-antigen distance and enhancing immune activation are required. Here, we report a molecular vaccine design principle that maximally drives potent SARS-CoV-2 RBD subunit vaccine on DNA duplex to induce robust and efficacious immune responses in vivo. We expect that the DNA-peptide epitope platform represents a facile and generalizable strategy to enhance the immune response. STATEMENT OF SIGNIFICANCE: DNA scaffolds offer a biocompatible and convenient platform for arraying immunogens in multivalency antigenic peptides, and spatially control the inter-antigen distance. This can effectively enhance immune response. Peptide (instead of entire protein) vaccines are highly attractive. However, short peptides are poor immunogens. Our DNA scaffolded multivalent peptide immunogen system induced robust and efficacious immune response in vivo as demonstrated by the antigenic peptide against SAR-CoV-2. The present strategy could be readily generalized and adapted to prepare multivalent vaccines against other viruses or disease. Particularly, the different antigens could be integrated into one single vaccine and lead to super-vaccines that can protect the host from multiple different viruses or multiple variants of the same virus.
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Affiliation(s)
- Fangfang Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuhan Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zhengyu Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Tingting Jiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Zailin Yang
- Department of Hematology-Oncology, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Jie Zeng
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Aishun Jin
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; Department of Chemistry, Purdue University, West Lafayette 47907, IN, USA.
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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80
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Schneider L, Rabe KS, Domínguez CM, Niemeyer CM. Hapten-Decorated DNA Nanostructures Decipher the Antigen-Mediated Spatial Organization of Antibodies Involved in Mast Cell Activation. ACS NANO 2023; 17:6719-6730. [PMID: 36990450 PMCID: PMC10100567 DOI: 10.1021/acsnano.2c12647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The immunological response of mast cells is controlled by the multivalent binding of antigens to immunoglobulin E (IgE) antibodies bound to the high-affinity receptor FcεRI on the cell membrane surface. However, the spatial organization of antigen-antibody-receptor complexes at the nanometer scale and the structural constraints involved in the initial events at the cell surface are not yet fully understood. For example, it is unclear what influence the affinity and nanoscale distance between the binding partners involved have on the activation of mast cells to degranulate inflammatory mediators from storage granules. We report the use of DNA origami nanostructures (DON) functionalized with different arrangements of the haptenic 2,4-dinitrophenyl (DNP) ligand to generate multivalent artificial antigens with full control over valency and nanoscale ligand architecture. To investigate the spatial requirements for mast cell activation, the DNP-DON complexes were initially used in surface plasmon resonance (SPR) analysis to study the binding kinetics of isolated IgE under physiological conditions. The most stable binding was observed in a narrow window of approximately 16 nm spacing between haptens. In contrast, affinity studies with FcεRI-linked IgE antibodies on the surface of rat basophilic leukemia cells (RBL-2H3) indicated virtually no distance-dependent variations in the binding of the differently structured DNP-DON complexes but suggested a supramolecular oligovalent nature of the interaction. Finally, the use of DNP-DON complexes for mast cell activation revealed that antigen-directed tight assembly of antibody-receptor complexes is the critical factor for triggering degranulation, even more critical than ligand valence. Our study emphasizes the significance of DNA nanostructures for the study of fundamental biological processes.
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81
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Lolaico M, Blokhuizen S, Shen B, Wang Y, Högberg B. Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges. ACS NANO 2023; 17:6565-6574. [PMID: 36951760 PMCID: PMC10100577 DOI: 10.1021/acsnano.2c11982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.
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Affiliation(s)
- Marco Lolaico
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Sebbe Blokhuizen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Boxuan Shen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, P.O. Box 16100, 00076 Aalto, Finland
| | - Yang Wang
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Björn Högberg
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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82
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Ding F, Zhang S, Chen Q, Feng H, Ge Z, Zuo X, Fan C, Li Q, Xia Q. Immunomodulation with Nucleic Acid Nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206228. [PMID: 36599642 DOI: 10.1002/smll.202206228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
The precise regulation of interactions of specific immunological components is crucial for controllable immunomodulation, yet it remains a great challenge. With the assistance of advanced computer design, programmable nucleic acid nanotechnology enables the customization of synthetic nucleic acid nanodevices with unprecedented geometrical and functional precision, which have shown promising potential for precise immunoengineering. Notably, the inherently immunologic functions of nucleic acids endow these nucleic acid-based assemblies with innate advantages in immunomodulatory engagement. In this review, the roles of nucleic acids in innate immunity are discussed, focusing on the definition, immunologic modularity, and enhanced bioavailability of structural nucleic acid nanodevices. In light of this, molecular programming and precise organization of functional modules with nucleic acid nanodevices for immunomodulation are emphatically reviewed. At last, the present challenges and future perspectives of nucleic acid nanodevices for immunomodulation are discussed.
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Affiliation(s)
- Fei Ding
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Shuangye Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Chen
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Hao Feng
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiaolei Zuo
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- WLA Laboratories, World Laureates Association, Shanghai, 201203, P. R. China
| | - Qiang Xia
- Shanghai Institute of Transplantation, Department of Liver Surgery, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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83
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Zhao L, Meng F, Li Y, Liu S, Xu M, Chu F, Li C, Yang X, Luo L. Multivalent Nanobody Conjugate with Rigid, Reactive Oxygen Species Scavenging Scaffold for Multi-Target Therapy of Alzheimer's Disease. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210879. [PMID: 36786375 DOI: 10.1002/adma.202210879] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/08/2023] [Indexed: 05/17/2023]
Abstract
Efficient therapeutic strategies that concurrently target both Aβ aggregation and oxidative stress in the Alzheimer's disease (AD) microenvironment emerge as a cutting-edge tool to combat the intricate pathogenesis of AD. Here, a multivalent nanobody conjugate with rigid, reactive oxygen species (ROS) scavenging scaffold is developed to achieve simultaneous Aβ amyloidogenesis mitigation, ROS elimination, and Aβ plaque clearance. Grafting Aβ segment (33-GLMVGGVVIA-42) into the third complementary-determining region of a parent nanobody generates an engineered nanobody NB that can recognize Aβ and inhibit its aggregation through homotypic interactions. NB is further genetically modified with a fragment of human interleukin-1β (163-VQGEESNDK-171), so that the obtained fusion nanobody NBIL can also facilitate the Aβ clearance by microglia. Linking NBIL covalently onto a rigid, ROS scavenging scaffold poly(deca-4,6-diynedioic acid) (PDDA) creates the multivalent nanobody conjugate PNBIL, which not only boosts the binding affinity between NBIL and Aβ aggregates for nearly 100 times but also possesses a long-term capability of oxidative stress alleviation, inflammation reduction, and neuron protection. PNBIL has significantly attenuated symptoms on two AD mouse models through amyloidogenesis inhibition and AD microenvironment modulation, validating that the multivalent nanobody conjugate design based on combinatory nanobody and molecular engineering is a promising approach of multi-target therapeutic strategies.
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Affiliation(s)
- Liyuan Zhao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yingjie Li
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Sujuan Liu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Mengmeng Xu
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Fan Chu
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Chuanzhou Li
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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84
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Oktay E, Alem F, Hernandez K, Girgis M, Green C, Mathur D, Medintz IL, Narayanan A, Veneziano R. DNA origami presenting the receptor binding domain of SARS-CoV-2 elicit robust protective immune response. Commun Biol 2023; 6:308. [PMID: 36959304 PMCID: PMC10034259 DOI: 10.1038/s42003-023-04689-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases with prolonged antibody response and effective protection in the context of a viral challenge.
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Affiliation(s)
- Esra Oktay
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Farhang Alem
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Keziah Hernandez
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Michael Girgis
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Christopher Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA.
| | - Remi Veneziano
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA.
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85
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Li S, Zhang MY, Yuan J, Zhang YX. Nano-vaccines for gene delivery against HIV-1 infection. Expert Rev Vaccines 2023; 22:315-326. [PMID: 36945780 DOI: 10.1080/14760584.2023.2193266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Over the last four decades, human immunodeficiency virus type 1 (HIV-1) infection has been a major public health concern. It is acknowledged that an effective vaccine remains the best hope for eliminating the HIV-1 pandemic. The prophylaxis of HIV-1 infection remains a central theme because of the absence of an available HIV-1 vaccine. The incapability of conventional delivery strategies to induce potent immunity is a crucial task to overcome and ultimately lead to a major obstacle in HIV-1 vaccine research. AREAS COVERED The literature search was conducted in the following databases: PubMed, Web of Science, and Embase. Nano-platforms based vaccines have proven prophylaxis of various diseases for effectively activating the immune system. Nano-vaccines, including non-viral and viral vectored nano-vaccines, are in a position to improve the effectiveness of HIV-1 antigen delivery and enhance the innate and adaptive immune responses against HIV-1. Compared to traditional vaccination strategies, genetic immunization can elicit a long-term immune response to provide protective immunity for HIV-1 prevention. EXPERT OPINION The research progress on nano-vaccines for gene delivery against HIV-1 was discussed. The vaccine strategies based on nano-platforms that are being applied to stimulate effective HIV-1-specific cellular and humoral immune responses were particularly emphasized.
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Affiliation(s)
- Shuang Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jie Yuan
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
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86
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Qi L, Tian Y, Li N, Mao M, Fang X, Han D. Engineering Circular Aptamer Assemblies with Tunable Selectivity to Cell Membrane Antigens In Vitro and In Vivo. ACS APPLIED MATERIALS & INTERFACES 2023; 15:12822-12830. [PMID: 36856721 DOI: 10.1021/acsami.2c22820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The strategy of enhancing molecular recognition by improving the binding affinity of drug molecules against targets has generated a lot of successful therapeutic applications. However, one critical consequence of such affinity improvement, generally called "on-target, off-tumor" toxicity, emerged as a major obstacle limiting their clinical usage. Herein, we provide a modular assembly strategy that affords affinity-tunable DNA nanostructures allowing for immobilizing multiple aptamers that bind to the example antigen of EpCAM with different affinities. We develop a theoretical model proving that the apparent affinity of aptamer assemblies to target cells varies with antigen density as well as aptamer valency. More importantly, we demonstrate experimentally that the theoretical model can be used to predict the least valency required for discrimination between EpCAMhigh and EpCAMlow cells in vitro and in vivo. We believe that our strategy will have broad applications in an engineering nucleic acid-based delivery platform for targeted and cell therapy.
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Affiliation(s)
- Liqing Qi
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Yuan Tian
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
| | - Na Li
- National Genomics Data Center, China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Menghan Mao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
| | - Xiaohong Fang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Da Han
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, School of Medicine, Shanghai Jiao Tong University, Renji Hospital, Institute of Molecular Medicine, Shanghai 200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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87
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Brooks JF, Riggs J, Mueller JL, Mathenge R, Wholey WY, Yoda ST, Vykunta VS, Cheng W, Zikherman J. Molecular basis for potent B cell responses to antigen displayed on particles of viral size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528761. [PMID: 36824873 PMCID: PMC9949087 DOI: 10.1101/2023.02.15.528761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although it has long been appreciated that multivalent antigens - and particularly viral epitope display - produce extremely rapid, robust, and T-independent humoral immune responses, the biochemical basis for such potency has been incompletely understood. Here we take advantage of a set of neutral liposomes of viral size that are engineered to display affinity mutants of the model antigen (Ag) hen egg lysozyme at precisely varied density. We show that particulate Ag display by liposomes induces highly potent B cell responses that are dose-and density-dependent but affinity-independent. Titrating dose of particulate, but not soluble, Ag reveals bimodal Erk phosphorylation and cytosolic calcium increases. Particulate Ag induces signal amplification downstream of the B cell receptor (BCR) by selectively evading LYN-dependent inhibitory pathways, but in vitro potency is independent of CD19. Importantly, Ag display on viral-sized particles signals independently of MYD88 and IRAK1/4, but activates NF- κ B robustly in a manner that mimics T cell help. Together, such biased signaling by particulate Ag promotes MYC expression and reduces the threshold required for B cell proliferation relative to soluble Ag. These findings uncover a molecular basis for highly sensitive B cell response to viral Ag display and remarkable potency of virus-like particle vaccines that is not merely accounted for by avidity and BCR cross-linking, and is independent of the contribution of B cell nucleic acid-sensing machinery.
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88
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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Wamhoff EC, Knappe GA, Burds AA, Du RR, Neun BW, Difilippantonio S, Sanders C, Edmondson EF, Matta JL, Dobrovolskaia MA, Bathe M. Evaluation of non-modified wireframe DNA origami for acute toxicity and biodistribution in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530026. [PMID: 36909507 PMCID: PMC10002694 DOI: 10.1101/2023.02.25.530026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Wireframe DNA origami can be used to fabricate virus-like particles for a range of biomedical applications, including the delivery of nucleic acid therapeutics. However, the acute toxicity and biodistribution of these wireframe nucleic acid nanoparticles (NANPs) have not previously been characterized in animal models. In the present study, we observed no indications of toxicity in BALB/c mice following therapeutically relevant dosage of unmodified DNA-based NANPs via intravenous administration, based on liver and kidney histology, liver biochemistry, and body weight. Further, the immunotoxicity of these NANPs was minimal, as indicated by blood cell counts and type-I interferon and pro-inflammatory cytokines. In an SJL/J model of autoimmunity, we observed no indications of NANP-mediated DNA-specific antibody response or immune-mediated kidney pathology following the intraperitoneal administration of NANPs. Finally, biodistribution studies revealed that these NANPs accumulate in the liver within one hour, concomitant with substantial renal clearance. Our observations support the continued development of wireframe DNA-based NANPs as next-generation nucleic acid therapeutic delivery platforms.
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90
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Current Status of Oligonucleotide-Based Protein Degraders. Pharmaceutics 2023; 15:pharmaceutics15030765. [PMID: 36986626 PMCID: PMC10055846 DOI: 10.3390/pharmaceutics15030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Transcription factors (TFs) and RNA-binding proteins (RBPs) have long been considered undruggable, mainly because they lack ligand-binding sites and are equipped with flat and narrow protein surfaces. Protein-specific oligonucleotides have been harnessed to target these proteins with some satisfactory preclinical results. The emerging proteolysis-targeting chimera (PROTAC) technology is no exception, utilizing protein-specific oligonucleotides as warheads to target TFs and RBPs. In addition, proteolysis by proteases is another type of protein degradation. In this review article, we discuss the current status of oligonucleotide-based protein degraders that are dependent either on the ubiquitin–proteasome system or a protease, providing a reference for the future development of degraders.
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91
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Gene-encoding DNA origami for mammalian cell expression. Nat Commun 2023; 14:1017. [PMID: 36823187 PMCID: PMC9950468 DOI: 10.1038/s41467-023-36601-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
DNA origami may enable more versatile gene delivery applications through its ability to create custom nanoscale objects with specific targeting, cell-invading, and intracellular effector functionalities. Toward this goal here we describe the expression of genes folded in DNA origami objects delivered to mammalian cells. Genes readily express from custom-sequence single-strand scaffolds folded within DNA origami objects, provided that the objects can denature in the cell. We demonstrate enhanced gene expression efficiency by including and tuning multiple functional sequences and structures, including virus-inspired inverted-terminal repeat-like (ITR) hairpin motifs upstream or flanking the expression cassette. We describe gene-encoding DNA origami bricks that assemble into multimeric objects to enable stoichiometrically controlled co-delivery and expression of multiple genes in the same cells. Our work provides a framework for exploiting DNA origami for gene delivery applications.
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92
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Pezeshkian W, Grünewald F, Narykov O, Lu S, Arkhipova V, Solodovnikov A, Wassenaar TA, Marrink SJ, Korkin D. Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling. Structure 2023; 31:492-503.e7. [PMID: 36870335 DOI: 10.1016/j.str.2023.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands
| | - Oleksandr Narykov
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Senbao Lu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | | | | | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, 9747AS Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747AG Groningen, the Netherlands.
| | - Dmitry Korkin
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA 01609, USA; Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA.
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93
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Chen J, Li Y, Liu Z. Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101249. [PMID: 36714073 PMCID: PMC9869493 DOI: 10.1016/j.xcrp.2023.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.
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Affiliation(s)
- Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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94
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Shi Q, Wu Y, Xu Y, Bao M, Chen X, Huang K, Yang Q, Yang Y. Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis. ACS NANO 2023; 17:2460-2471. [PMID: 36693051 DOI: 10.1021/acsnano.2c09772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mimicking the size and shape of spherical viruses, we constructed a soccer-ball shaped virus-inspired DNA origami (ViDO) framework as a programmable non-LNP (lipid nanoparticle) gene carrier. The DNA framework was decorated with precisely controlled recognition molecules outside and loaded with adequate genetic molecules inside. Five variants were constructed to systematically investigate their cell uptake and modulated gene silencing efficiency. Cellular uptake was enhanced with an increasing number of aptamers, while with a median number of aptamer supply, dispersed distribution performed better than the clustered pattern. Intriguingly, the transfection efficiency was maximized using the ViDO with clustered five aptamers, which exhibited a competitive RNA silencing effect induced by Lipo2000 with low cytotoxicity. Our results revealed the effects of aptamer distribution patterns on endocytosis and transfection, thus providing a programmable platform for meticulous optimization of the gene delivery system.
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Affiliation(s)
- Qian Shi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanyuan Wu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Bao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao Chen
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Kui Huang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiulan Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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95
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Badten A, Ramirez A, Hernandez-Davies JE, Albin TJ, Jain A, Nakajima R, Felgner J, Davies DH, Wang SW. Protein Nanoparticle-Mediated Delivery of Recombinant Influenza Hemagglutinin Enhances Immunogenicity and Breadth of the Antibody Response. ACS Infect Dis 2023; 9:239-252. [PMID: 36607269 PMCID: PMC9926493 DOI: 10.1021/acsinfecdis.2c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Indexed: 01/07/2023]
Abstract
The vast majority of seasonal influenza vaccines administered each year are derived from virus propagated in eggs using technology that has changed little since the 1930s. The immunogenicity, durability, and breadth of response would likely benefit from a recombinant nanoparticle-based approach. Although the E2 protein nanoparticle (NP) platform has been previously shown to promote effective cell-mediated responses to peptide epitopes, it has not yet been reported to deliver whole protein antigens. In this study, we synthesized a novel maleimido tris-nitrilotriacetic acid (NTA) linker to couple protein hemagglutinin (HA) from H1N1 influenza virus to the E2 NP, and we evaluated the HA-specific antibody responses using protein microarrays. We found that recombinant H1 protein alone is immunogenic in mice but requires two boosts for IgG to be detected and is strongly IgG1 (Th2) polarized. When conjugated to E2 NPs, IgG2c is produced leading to a more balanced Th1/Th2 response. Inclusion of the Toll-like receptor 4 agonist monophosphoryl lipid A (MPLA) significantly enhances the immunogenicity of H1-E2 NPs while retaining the Th1/Th2 balance. Interestingly, broader homo- and heterosubtypic cross-reactivity is also observed for conjugated H1-E2 with MPLA, compared to unconjugated H1 with or without MPLA. These results highlight the potential of an NP-based delivery of HA for tuning the immunogenicity, breadth, and Th1/Th2 balance generated by recombinant HA-based vaccination. Furthermore, the modularity of this protein-protein conjugation strategy may have utility for future vaccine development against other human pathogens.
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Affiliation(s)
- Alexander
J. Badten
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Aaron Ramirez
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Jenny E. Hernandez-Davies
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Tyler J. Albin
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Aarti Jain
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Rie Nakajima
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Jiin Felgner
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - D. Huw Davies
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
| | - Szu-Wen Wang
- Department
of Chemical and Biomolecular Engineering, Vaccine Research and Development
Center, Department of Physiology and Biophysics, Department of Chemistry, Department of Biomedical
Engineering, Chao Family Comprehensive Cancer Center, Institute for Immunology, University of California, Irvine, California 92697, United States
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96
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Mathur D, Galvan AR, Green CM, Liu K, Medintz IL. Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art. NANOSCALE 2023; 15:2516-2528. [PMID: 36722508 PMCID: PMC10407680 DOI: 10.1039/d2nr05868e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Angelica Rose Galvan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Kevin Liu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
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97
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Yousefpour P, Ni K, Irvine DJ. Targeted modulation of immune cells and tissues using engineered biomaterials. NATURE REVIEWS BIOENGINEERING 2023; 1:107-124. [PMID: 37772035 PMCID: PMC10538251 DOI: 10.1038/s44222-022-00016-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 09/30/2023]
Abstract
Therapies modulating the immune system offer the prospect of treating a wide range of conditions including infectious diseases, cancer and autoimmunity. Biomaterials can promote specific targeting of immune cell subsets in peripheral or lymphoid tissues and modulate the dosage, timing and location of stimulation, thereby improving safety and efficacy of vaccines and immunotherapies. Here we review recent advances in biomaterials-based strategies, focusing on targeting of lymphoid tissues, circulating leukocytes, tissue-resident immune cells and immune cells at disease sites. These approaches can improve the potency and efficacy of immunotherapies by promoting immunity or tolerance against different diseases.
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Affiliation(s)
- Parisa Yousefpour
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyuan Ni
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Darrell J. Irvine
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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98
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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99
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Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
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Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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100
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Xu Y, Yang YR, Shi Q, Ward AB, Huang K, Chen X, Wang W, Yang Y. An Infectious Virus-like Particle Built on a Programmable Icosahedral DNA Framework. Angew Chem Int Ed Engl 2023; 62:e202214731. [PMID: 36377708 DOI: 10.1002/anie.202214731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Indexed: 11/16/2022]
Abstract
Viral genomes can be compressed into a near-spherical nanochamber to form infectious particles. In order to mimic the virus morphology and packaging behavior, we invented a programmable icosahedral DNA nanoframe with enhanced rigidity and encapsulated the phiX174 bacteriophage genome. The packaging efficiency could be modulated through specific anchoring strands adjustment, and the trapped phage genome remained accessible for enzymatic operations. Moreover, the packed complex could infect Escherichia coli (E. coli) cells through bacterial uptake to produce plaques. This rigid icosahedral DNA architecture demonstrated a versatile platform to develop virus mimetic particles for convenient functional nucleic acid entrapment, manipulation and delivery.
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Affiliation(s)
- Yunyun Xu
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
| | - Yuhe R Yang
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, No. 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, P.R. China.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Qian Shi
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kui Huang
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
| | - Xiao Chen
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
| | - Wei Wang
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
| | - Yang Yang
- School of Medicine, Shanghai Jiao Tong University, Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, 1630 Dongfang Road, B17-1820, Pudong, Shanghai, 200127, P.R. China
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