1
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Li S, Tian T, Zhang T, Lin Y, Cai X. A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure. Nat Protoc 2024:10.1038/s41596-024-01050-7. [PMID: 39215132 DOI: 10.1038/s41596-024-01050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/11/2024] [Indexed: 09/04/2024]
Abstract
As microRNAs (miRNA) regulate almost all physiopathological activities in the human body, miRNA therapeutics that deliver miRNA regulators have attracted considerable attention in the field of nucleic acid drug development. The use of tetrahedral DNA nanostructures to deliver miRNA regulators is promising because of their simple fabrication, enhanced cell entry, effective tissue penetration, biocompatibility and functional editability. This protocol extension builds on our previous protocol for the use of tetrahedral DNA nanostructures and was designed to establish an updated bioswitchable delivery system (BDS) for achieving controlled cargo loading and release. A ribonuclease H-sensitive sequence is designed as a bioswitchable apparatus for the targeted release of the miRNA regulator. The functional sequence of the miRNA regulator and minimal secondary structure formation tendency during annealing are two key points in cargo design. We provide two BDS design strategies; BDS-A comprises an intact DNA tetrahedron with the RNA cargo hanging outside, offering the merits of lower cost, simplicity, and more direct structural design. In the BDS-B design, the RNA regulators are embedded into the DNA tetrahedron, which is beneficial for dermal tissue permeation applications. Following sequence design in Oligo 7 and Tiamat, the BDS assembly is completed and then ribonuclease H achieves controlled release of the miRNA regulator by triggering the bioswitchable apparatus. This is verified via polyacrylamide and agarose gel electrophoresis or fluorophore modifications. Both BDSs show promising cellular membrane permeability, tissue permeability and target inhibition in vitro and in vivo. The assembly and characterization of the BDS can be completed in 4 d, and the validation time for biostability and biological applications will depend on the specific use.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
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2
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Li S, Chu Y, Guo X, Mao C, Xiao SJ. Circular RNA oligonucleotides: enzymatic synthesis and scaffolding for nanoconstruction. NANOSCALE HORIZONS 2024. [PMID: 39042106 DOI: 10.1039/d4nh00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We report the efficient synthesis of monomeric circular RNAs (circRNAs) in the size range of 16-44 nt with a novel DNA dumbbell splinting plus T4 DNA ligation strategy. Such a DNA dumbbell splinting strategy was developed by one group among ours recently for near-quantitative conversion of short linear DNAs into monomeric circular ones. Furthermore, using the 44 nt circRNA as scaffold strands, we constructed hybrid RNA:DNA and pure RNA:RNA double crossover tiles and their assemblies of nucleic acid nanotubes and flat arrays.
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Affiliation(s)
- Shijie Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yanxin Chu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xin Guo
- Bruker (Beijing) Scientific Technology Co. Ltd, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Shou-Jun Xiao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China
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3
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Sun J, Lu S, Xiao J, Xu N, Li Y, Xu J, Deng M, Xuanyuan H, Zhang Y, Wu F, Jin W, Liu K. Inhibition of SARS-CoV-2 Replication by Self-Assembled siRNA Nanoparticles Targeting Multiple Highly Conserved Viral Sequences. Viruses 2024; 16:1072. [PMID: 39066234 PMCID: PMC11281333 DOI: 10.3390/v16071072] [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: 04/28/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 07/28/2024] Open
Abstract
Coronavirus infectious disease 2019 (COVID-19), caused by severe acute respiratory virus type 2 (SARS-CoV-2), has caused a global public health crisis. As an RNA virus, the high gene mutability of SARS-CoV-2 poses significant challenges to the development of broad-spectrum vaccines and antiviral therapeutics. There remains a lack of specific therapeutics directly targeting SARS-CoV-2. With the ability to efficiently inhibit the expression of target genes in a sequence-specific way, small interfering RNA (siRNA) therapy has exhibited significant potential in antiviral and other disease treatments. In this work, we presented a highly effective self-assembled siRNA nanoparticle targeting multiple highly conserved regions of SARS-CoV-2. The siRNA sequences targeting viral conserved regions were first screened and evaluated by their thermodynamic features, off-target effects, and secondary structure toxicities. RNA motifs including siRNA sequences were then designed and self-assembled into siRNA nanoparticles. These siRNA nanoparticles demonstrated remarkable uniformity and stability and efficiently entered cells directly through cellular endocytic pathways. Moreover, these nanoparticles effectively inhibited the replication of SARS-CoV-2, exhibiting a superior inhibitory effect compared to free siRNA. These results demonstrated that these self-assembled siRNA nanoparticles targeting highly conserved regions of SARS-CoV-2 represent highly effective antiviral candidates for the treatment of infections, and are promisingly effective against current and future viral variants.
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Affiliation(s)
- Jianan Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Siya Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Jizhen Xiao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Nuo Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yingbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Jinfeng Xu
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Maohua Deng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Hanlu Xuanyuan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yushi Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Fangli Wu
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weibo Jin
- College of Life Sciences & Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Kuancheng Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
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4
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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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5
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Zhu L, Luo J, Ren K. Nucleic acid-based artificial nanocarriers for gene therapy. J Mater Chem B 2023; 11:261-279. [PMID: 36524395 DOI: 10.1039/d2tb01179d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.
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Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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6
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Danai L, Johnson MB, Afonin KA. Discriminating Immunorecognition Pathways Activated by RNA Nanostructures. Methods Mol Biol 2023; 2709:229-240. [PMID: 37572284 PMCID: PMC10482317 DOI: 10.1007/978-1-0716-3417-2_15] [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] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanoparticles (NANPs) composed of therapeutic DNA, RNA, or a hybrid of both are increasingly investigated for their targeted and tunable immunomodulatory properties. By taking advantage of the NANPs' unique and relatively straightforward self-assembling behavior, nucleic acid sequences can be designed from the bottom-up and specifically tailored to induce certain immune responses in mammalian cells (Johnson et al., Nucleic Acids Res 48:11785-11798, 2020). Although not yet used in the clinic, functionalized NANPs display promising advantages to be included in therapeutic applications. By adjusting the chemical composition of a limited selection of NANPs all sharing the same physicochemical properties, it is demonstrated how substituting RNA strands for different chemical analogs can increase the thermodynamic and enzymatic stability of NANPs. Altering the composition of NANPs also determines the cellular mechanisms which initiate immune responses, therefore impacting the subcellular targeting and delivery efficiency.
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Affiliation(s)
- Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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7
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Kasprzak WK, Shapiro BA. Application of Molecular Dynamics to Expand Docking Program's Exploratory Capabilities and to Evaluate Its Predictions. Methods Mol Biol 2023; 2568:75-101. [PMID: 36227563 DOI: 10.1007/978-1-0716-2687-0_6] [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] [Indexed: 06/16/2023]
Abstract
Recognition of the growing importance of RNA as a target for therapeutic or diagnostic ligands brings the importance of computational predictions of docking poses to such receptors to the forefront. Most docking programs have been optimized for protein targets, based on a relatively rich pool of known docked protein structures. Unfortunately, despite progress, numbers of known docked RNA complexes are low and the accuracy of the computational predictions trained on those inadequate samples lags behind that achieved for proteins. Compared to proteins, RNA structures generally have fewer docking pockets, have less diverse electrostatic surfaces, and are more flexible, raising the possibility of producing only transiently available good docking targets. We are presenting a docking prediction protocol that adds molecular dynamics simulations before and after the actual docking in order to explore the conformational space of the target RNA and then to reevaluate the stability of the predicted RNA-ligand complex. In this way we are attempting to overcome important limitations of the docking programs: the rigid (fully or mostly) target structure and imperfect nature of the docking scoring functions.
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Affiliation(s)
- Wojciech K Kasprzak
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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8
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Trammell SR. Light-Assisted Drying for the Thermal Stabilization of Nucleic Acid Nanoparticles and Other Biologics. Methods Mol Biol 2023; 2709:117-130. [PMID: 37572276 DOI: 10.1007/978-1-0716-3417-2_7] [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: 08/14/2023]
Abstract
Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Nucleic acid nanoparticles (NANPs) are an example of new biological products that require refrigerated storage. Light-assisted drying (LAD) is a new processing technique to prepare biologics for anhydrous storage in a trehalose amorphous solid matrix at ambient temperatures. Small volume samples (10 μL) containing NANPs are irradiated with a 1064 nm laser to speed the evaporation of water and create an amorphous trehalose preservation matrix. In previous studies, samples were stored for 1 month at 4 °C or 20 °C without degradation. A FLIR SC655 mid-IR camera is used to record the temperature of samples during processing. The trehalose matrix was characterized using polarized light imaging to determine if crystallization occurred during processing or storage. Damage to LAD-processed NANPs was assessed after processing and storage using gel electrophoresis.
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Affiliation(s)
- Susan R Trammell
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC, USA.
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9
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Perdomo VA, Kim T. Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures. Methods Mol Biol 2023; 2709:3-29. [PMID: 37572270 DOI: 10.1007/978-1-0716-3417-2_1] [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: 08/14/2023]
Abstract
Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.
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Affiliation(s)
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV, USA.
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10
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Radwan Y, Afonin KA, Johnson MB. Assessment of Intracellular Compartmentalization of RNA Nanostructures. Methods Mol Biol 2023; 2709:211-228. [PMID: 37572283 PMCID: PMC10482314 DOI: 10.1007/978-1-0716-3417-2_14] [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] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanoparticles (NANPs) are extensively investigated as diagnostic and therapeutic tools. These innovative particles can be composed of RNA, DNA, and/or modified nucleic acids. Due to the regulatory role of nucleic acids in the cellular system, NANPs have the ability to identify target molecules and regulate expression of genes in disease pathways. However, translation of NANPs in clinical settings is hindered due to inefficient intracellular delivery, chemical instability, and off-target immunostimulatory effects following immune recognition. The composition of nucleic acids forming NANPs has been demonstrated to influence immunorecognition, subcellular compartmentalization, and physicochemical properties of NANPs. This chapter first outlines the methods used to generate a panel of NANPs with a uniform shape, size, charge, sequence, and connectivity. This includes the procedures for replacing the RNA strands with DNA or chemical analogs in the designated NANPs. Second, this chapter will also describe experiments to assess the effect of the chemical modification on enzymatic and thermodynamic stability, delivery efficiency, and subcellular compartmentalization of NANPs.
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Affiliation(s)
- Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.
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11
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Anh Lam P, Furr DP, Tran A, McKeough RQ, Beasock D, Chandler M, Afonin KA, Trammell SR. The Application of Light-Assisted Drying to the Thermal Stabilization of Nucleic Acid Nanoparticles. Biopreserv Biobank 2022; 20:451-460. [PMID: 36067075 PMCID: PMC9603253 DOI: 10.1089/bio.2022.0035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Cold-chain storage can be challenging and expensive for the transportation and storage of biologics, especially in low-resource settings. Nucleic acid nanoparticles (NANPs) are an example of new biological products that require refrigerated storage. Light-assisted drying (LAD) is a new processing technique to prepare biologics for anhydrous storage in a trehalose amorphous solid matrix at ambient temperatures. In this study, LAD was used to thermally stabilize four types of NANPs with differing structures and melting temperatures. Methods: Small volume samples (10 μL) containing NANPs were irradiated with a 1064 nm laser to speed the evaporation of water and create an amorphous trehalose preservation matrix. Samples were then stored for 1 month at 4°C or 20°C. A FLIR C655 mid-IR camera was used to record the temperature of samples during processing. The trehalose matrix was characterized using polarized light imaging (PLI) to determine if crystallization occurred during processing or storage. Damage to LAD-processed NANPs was assessed after processing and storage using gel electrophoresis. Results: Based on the end moisture content (EMC) as a function time and the thermal histories of samples, a LAD processing time of 30 min is sufficient to achieve low EMCs for the 10 μL samples used in this study. PLI demonstrates that the trehalose matrix was resistant to crystallization during processing and after storage at 4°C and at room temperature. The native-polyacrylamide gel electrophoresis results for DNA cubes, RNA cubes, and RNA rings indicate that the main structures of these NANPs were not damaged significantly after LAD processing and being stored at 4°C or at room temperature for 1 month. Conclusions: These preliminary studies indicate that LAD processing can stabilize NANPs for dry-state storage at room temperature, providing an alternative to refrigerated storage for these nanomedicine products.
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Affiliation(s)
- Phuong Anh Lam
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Daniel P. Furr
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Allison Tran
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Riley Q. McKeough
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Damian Beasock
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Susan R. Trammell
- Department of Physics and Optical Science and University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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12
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Tran AN, Chandler M, Halman J, Beasock D, Fessler A, McKeough RQ, Lam PA, Furr DP, Wang J, Cedrone E, Dobrovolskaia MA, Dokholyan NV, Trammell SR, Afonin KA. Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104814. [PMID: 35128787 PMCID: PMC8976831 DOI: 10.1002/smll.202104814] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/17/2021] [Indexed: 05/13/2023]
Abstract
Recent advances in nanotechnology now allow for the methodical implementation of therapeutic nucleic acids (TNAs) into modular nucleic acid nanoparticles (NANPs) with tunable physicochemical properties which can match the desired biological effects, provide uniformity, and regulate the delivery of multiple TNAs for combinatorial therapy. Despite the potential of novel NANPs, the maintenance of their structural integrity during storage and shipping remains a vital issue that impedes their broader applications. Cold chain storage is required to maintain the potency of NANPs in the liquid phase, which greatly increases transportation costs. To promote long-term storage and retention of biological activities at higher temperatures (e.g., +50 °C), a panel of representative NANPs is first exposed to three different drying mechanisms-vacuum concentration (SpeedVac), lyophilization (Lyo), and light-assisted drying (LAD)-and then rehydrated and analyzed. While SpeedVac primarily operates using heat, Lyo avoids temperature increases by taking advantage of pressure reduction and LAD involves a near-infrared laser for uniform drying in the presence of trehalose. This work compares and defines refinements crucial in formulating an optimal strategy for producing stable, fully functional NANPs and presents a forward advancement in their development for clinical applications.
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Affiliation(s)
- Allison N Tran
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Adam Fessler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Riley Q McKeough
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Phuong Anh Lam
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Daniel P Furr
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Edward Cedrone
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Susan R Trammell
- Department of Physics and Optical Science, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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13
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Kim D, Han S, Ji Y, Moon S, Nam H, Lee JB. Multimeric RNAs for efficient RNA-based therapeutics and vaccines. J Control Release 2022; 345:770-785. [PMID: 35367477 PMCID: PMC8970614 DOI: 10.1016/j.jconrel.2022.03.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 11/17/2022]
Abstract
There has been a growing interest in RNA therapeutics globally, and much progress has been made in this area, which has been further accelerated by the clinical applications of RNA-based vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Following these successful clinical trials, various technologies have been developed to improve the efficacy of RNA-based drugs. Multimerization of RNA therapeutics is one of the most attractive approaches to ensure high stability, high efficacy, and prolonged action of RNA-based drugs. In this review, we offer an overview of the representative approaches for generating repetitive functional RNAs by chemical conjugation, structural self-assembly, enzymatic elongation, and self-amplification. The therapeutic and vaccine applications of engineered multimeric RNAs in various diseases have also been summarized. By outlining the current status of multimeric RNAs, the potential of multimeric RNA as a promising treatment strategy is highlighted.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sunghyun Moon
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea.
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14
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Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Adv Drug Deliv Rev 2022; 181:114081. [PMID: 34915069 PMCID: PMC8886801 DOI: 10.1016/j.addr.2021.114081] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 01/01/2023]
Abstract
With numerous recent advances, the field of therapeutic nucleic acid nanotechnology is now poised for clinical translation supported by several examples of FDA-approved nucleic acid nanoformulations including two recent mRNA-based COVID-19 vaccines. Within this rapidly growing field, a new subclass of nucleic acid therapeutics called nucleic acid nanoparticles (NANPs) has emerged in recent years, which offers several unique properties distinguishing it from traditional therapeutic nucleic acids. Key unique aspects of NANPs include their well-defined 3D structure, their tunable multivalent architectures, and their ability to incorporate conditional activations of therapeutic targeting and release functions that enable diagnosis and therapy of cancer, regulation of blood coagulation disorders, as well as the development of novel vaccines, immunotherapies, and gene therapies. However, non-consolidated research developments of this highly interdisciplinary field create crucial barriers that must be overcome in order to impact a broader range of clinical indications. Forming a consortium framework for nucleic acid nanotechnology would prioritize and consolidate translational efforts, offer several unifying solutions to expedite their transition from bench-to-bedside, and potentially decrease the socio-economic burden on patients for a range of conditions. Herein, we review the unique properties of NANPs in the context of therapeutic applications and discuss their associated translational challenges.
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Affiliation(s)
- Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Weina Ke
- Biomedical Informatics and Data Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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15
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Hill A, van Leeuwen D, Schlösser V, Behera A, Mateescu B, Hall J. Chemically synthesized, self-assembling small interfering RNA-prohead RNA molecules trigger Dicer-independent gene silencing. Chemistry 2021; 28:e202103995. [PMID: 34879171 PMCID: PMC9305526 DOI: 10.1002/chem.202103995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 11/07/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three‐way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA‐3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA‐3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA‐3WJs transfected into Dicer‐deficient cell lines trigger potent gene silencing. Interestingly, siRNA‐3WJs transfected into an Argonaute 2‐deficient cell line also retain some gene silencing activity. siRNA‐3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5′ of the 3WJ (5′‐siRNA‐3WJ) relative to 3′ of the 3WJ (3′‐siRNA‐3WJ). This work sheds light on the functional properties of siRNA‐3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.
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Affiliation(s)
- Alyssa Hill
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, SWITZERLAND
| | - Daniël van Leeuwen
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Verena Schlösser
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Alok Behera
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Bogdan Mateescu
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Jonathan Hall
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
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16
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Harvey C, Klassa S, Finol E, Hall J, Hill AC. Chimeric Flaviviral RNA-siRNA Molecules Resist Degradation by The Exoribonuclease Xrn1 and Trigger Gene Silencing in Mammalian Cells. Chembiochem 2021; 22:3099-3106. [PMID: 34431199 PMCID: PMC8596575 DOI: 10.1002/cbic.202100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 11/11/2022]
Abstract
RNA is an emerging platform for drug delivery, but the susceptibility of RNA to nuclease degradation remains a major barrier to its implementation in vivo. Here, we engineered flaviviral Xrn1-resistant RNA (xrRNA) motifs to host small interfering RNA (siRNA) duplexes. The xrRNA-siRNA molecules self-assemble in vitro, resist degradation by the conserved eukaryotic 5' to 3' exoribonuclease Xrn1, and trigger gene silencing in 293T cells. The resistance of the molecules to Xrn1 does not translate to stability in blood serum. Nevertheless, our results demonstrate that flavivirus-derived xrRNA motifs can confer Xrn1 resistance on a model therapeutic payload and set the stage for further investigations into using the motifs as building blocks in RNA nanotechnology.
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Affiliation(s)
- Cressida Harvey
- Department of BiologyETH ZürichWolfgang-Pauli-Strasse 278093ZürichSwitzerland
| | - Sven Klassa
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Esteban Finol
- Department of BiologyETH ZürichWolfgang-Pauli-Strasse 278093ZürichSwitzerland
| | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alyssa C. Hill
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
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17
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Abstract
RNA-based therapeutics have shown great promise in treating a broad spectrum of diseases through various mechanisms including knockdown of pathological genes, expression of therapeutic proteins, and programmed gene editing. Due to the inherent instability and negative-charges of RNA molecules, RNA-based therapeutics can make the most use of delivery systems to overcome biological barriers and to release the RNA payload into the cytosol. Among different types of delivery systems, lipid-based RNA delivery systems, particularly lipid nanoparticles (LNPs), have been extensively studied due to their unique properties, such as simple chemical synthesis of lipid components, scalable manufacturing processes of LNPs, and wide packaging capability. LNPs represent the most widely used delivery systems for RNA-based therapeutics, as evidenced by the clinical approvals of three LNP-RNA formulations, patisiran, BNT162b2, and mRNA-1273. This review covers recent advances of lipids, lipid derivatives, and lipid-derived macromolecules used in RNA delivery over the past several decades. We focus mainly on their chemical structures, synthetic routes, characterization, formulation methods, and structure-activity relationships. We also briefly describe the current status of representative preclinical studies and clinical trials and highlight future opportunities and challenges.
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Affiliation(s)
- Yuebao Zhang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Changzhen Sun
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chang Wang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Katarina E Jankovic
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center, Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
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18
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Ke W, Afonin KA. Exosomes as natural delivery carriers for programmable therapeutic nucleic acid nanoparticles (NANPs). Adv Drug Deliv Rev 2021; 176:113835. [PMID: 34144087 PMCID: PMC8440450 DOI: 10.1016/j.addr.2021.113835] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023]
Abstract
With recent advances in nanotechnology and therapeutic nucleic acids (TNAs), various nucleic acid nanoparticles (NANPs) have demonstrated great promise in diagnostics and therapeutics. However, the full realization of NANPs' potential necessitates the development of a safe, efficient, biocompatible, stable, tissue-specific, and non-immunogenic delivery system. Exosomes, the smallest extracellular vesicles and an endogenous source of nanocarriers, offer these advantages while avoiding complications associated with manufactured agents. The lipid membranes of exosomes surround a hydrophilic core, allowing for the simultaneous incorporation of hydrophobic and hydrophilic drugs, nucleic acids, and proteins. Additional capabilities for post-isolation exosome surface modifications with imaging agents, targeting ligands, and covalent linkages also pave the way for their diverse biomedical applications. This review focuses on exosomes: their biogenesis, intracellular trafficking, transportation capacities, and applications with emphasis on the delivery of TNAs and programmable NANPs. We also highlight some of the current challenges and discuss opportunities related to the development of therapeutic exosome-based formulations and their clinical translation.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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19
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Zhovmer AS, Chandler M, Manning A, Afonin KA, Tabdanov ED. Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102442. [PMID: 34284132 DOI: 10.1016/j.nano.2021.102442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022]
Abstract
Contractile forces within the planar interface between T cell and antigen-presenting surface mechanically stimulate T cell receptors (TCR) in the mature immune synapses. However, the origin of mechanical stimulation during the initial, i.e., presynaptic, microvilli-based TCR activation in the course of immune surveillance remains unknown and new tools to help address this problem are needed. In this work, we develop nucleic acid nanoassembly (NAN)-based technology for functionalization of hydrogels using isothermal toehold-mediated reassociation of RNA/DNA heteroduplexes. Resulting platform allows for regulation with NAN linkers of 3D force momentum along the TCR mechanical axis, whereas hydrogels contribute to modulation of 2D shear modulus. By utilizing different lengths of NAN linkers conjugated to polyacrylamide gels of different shear moduli, we demonstrate an efficient capture of human T lymphocytes and tunable activation of TCR, as confirmed by T-cell spreading and pY foci.
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Affiliation(s)
- Alexander S Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Alexis Manning
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Erdem D Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
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20
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Zhou L, Chandrasekaran AR, Yan M, Valsangkar VA, Feldblyum JI, Sheng J, Halvorsen K. A mini DNA-RNA hybrid origami nanobrick. NANOSCALE ADVANCES 2021; 3:4048-4051. [PMID: 34355117 PMCID: PMC8276786 DOI: 10.1039/d1na00026h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/04/2021] [Indexed: 05/11/2023]
Abstract
DNA origami is typically used to fold a long single-stranded DNA scaffold into nanostructures with complex geometries using many short DNA staple strands. Integration of RNA into nucleic acid nanostructures is also possible, but has been less studied. In this research, we designed and characterized a hybrid RNA-scaffolded origami nanostructure with dimensions of ∼12 nm. We used 12 DNA staple strands to fold a 401 nt RNA scaffold into a ten-helix bundle with a honeycomb cross section. We verified the construction of the nanostructure using gel electrophoresis and atomic force microscopy. The DNA-RNA hybrid origami showed higher resistance to ribonuclease compared to a DNA-RNA duplex control. Our work shows potential use in folding long RNA, such as messenger RNA, into origami nanostructures that can be delivered into targeted cells as medicine or a vaccine.
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Affiliation(s)
- Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York Albany NY, USA
| | | | - Mengwen Yan
- Department of Chemistry, University at Albany, State University of New York Albany NY USA
| | - Vibhav A Valsangkar
- The RNA Institute, University at Albany, State University of New York Albany NY, USA
- Department of Chemistry, University at Albany, State University of New York Albany NY USA
| | - Jeremy I Feldblyum
- Department of Chemistry, University at Albany, State University of New York Albany NY USA
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York Albany NY, USA
- Department of Chemistry, University at Albany, State University of New York Albany NY USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York Albany NY, USA
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22
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Gong X, Wang H, Li R, Tan K, Wei J, Wang J, Hong C, Shang J, Liu X, Liu J, Wang F. A smart multiantenna gene theranostic system based on the programmed assembly of hypoxia-related siRNAs. Nat Commun 2021; 12:3953. [PMID: 34172725 PMCID: PMC8233311 DOI: 10.1038/s41467-021-24191-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The systemic therapeutic utilisation of RNA interference (RNAi) is limited by the non-specific off-target effects, which can have severe adverse impacts in clinical applications. The accurate use of RNAi requires tumour-specific on-demand conditional activation to eliminate the off-target effects of RNAi, for which conventional RNAi systems cannot be used. Herein, a tumourous biomarker-activated RNAi platform is achieved through the careful design of RNAi prodrugs in extracellular vesicles (EVs) with cancer-specific recognition/activation features. These RNAi prodrugs are assembled by splitting and reconstituting the principal siRNAs into a hybridisation chain reaction (HCR) amplification machine. EVs facilitate the specific and efficient internalisation of RNAi prodrugs into target tumour cells, where endogenous microRNAs (miRNAs) promote immediate and autonomous HCR-amplified RNAi activation to simultaneously silence multiantenna hypoxia-related genes. With multiple guaranteed cancer recognition and synergistic therapy features, the miRNA-initiated HCR-promoted RNAi cascade holds great promise for personalised theranostics that enable reliable diagnosis and programmable on-demand therapy.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China
| | - Ruomeng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Kaiyue Tan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Chen Hong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China.
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P. R. China.
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23
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A simple screening strategy for complex RNA-DNA hybrid nanoshapes. Methods 2021; 197:106-111. [PMID: 33631308 DOI: 10.1016/j.ymeth.2021.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/11/2021] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
The design of hybrid nucleic acid nanomaterials capitalizes on the partitioning of architectural and functional roles between structurally diverse RNA modules and chemically robust DNA components. Selecting optimal combinations of RNA and DNA building blocks is the key to preparing stable polygonal RNA-DNA hybrid nanoshapes. Here, we outline a simple screening strategy by gel electrophoresis under native folding conditions to identify combinations of RNA and DNA modules that self-assemble to robust polygonal hybrid nanoshapes. As a proof of concept, we outline the preparation of RNA-DNA hybrid nanoshapes containing a set of different RNA architectural joints, including internal loop motifs and three-way junction (3WJ) folds. For each hybrid nanoshape, we demonstrate the selection process used to identify optimal DNA modules from a library of DNA connectors. The simple screening strategy outlined here provides a general robust method to identify and prepare RNA-DNA hybrid nanoshapes from diverse libraries of discrete nucleic acid building blocks.
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24
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Avila YI, Chandler M, Cedrone E, Newton HS, Richardson M, Xu J, Clogston JD, Liptrott NJ, Afonin KA, Dobrovolskaia MA. Induction of Cytokines by Nucleic Acid Nanoparticles (NANPs) Depends on the Type of Delivery Carrier. Molecules 2021; 26:652. [PMID: 33513786 PMCID: PMC7865455 DOI: 10.3390/molecules26030652] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Recent insights into the immunostimulatory properties of nucleic acid nanoparticles (NANPs) have demonstrated that variations in the shape, size, and composition lead to distinct patterns in their immunostimulatory properties. While most of these studies have used a single lipid-based carrier to allow for NANPs' intracellular delivery, it is now apparent that the platform for delivery, which has historically been a hurdle for therapeutic nucleic acids, is an additional means to tailoring NANP immunorecognition. Here, the use of dendrimers for the delivery of NANPs is compared to the lipid-based platform and the differences in resulting cytokine induction are presented.
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Affiliation(s)
- Yelixza I. Avila
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Hannah S. Newton
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Jie Xu
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Jeffrey D. Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
| | - Neill J. Liptrott
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L7 3NY, UK;
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC 28223-0001, USA; (Y.I.A.); (M.C.); (M.R.)
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21702, USA; (E.C.); (H.S.N.); (J.X.); (J.D.C.)
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25
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Mo F, Jiang K, Zhao D, Wang Y, Song J, Tan W. DNA hydrogel-based gene editing and drug delivery systems. Adv Drug Deliv Rev 2021; 168:79-98. [PMID: 32712197 DOI: 10.1016/j.addr.2020.07.018] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is a promising synthesizer for precisely constructing almost arbitrary geometry in two and three dimensions. Among various DNA-based soft materials, DNA hydrogels are comprised of hydrophilic polymeric networks of crosslinked DNA chains. For their properties of biocompatibility, porosity, sequence programmability and tunable multifunctionality, DNA hydrogels have been widely studied in bioanalysis and biomedicine. In this review, recent developments in DNA hydrogels and their applications in drug delivery systems are highlighted. First, physical and chemical crosslinking methods for constructing DNA hydrogels are introduced. Subsequently, responses of DNA hydrogels to nonbiological and biological stimuli are described. Finally, DNA hydrogel-based delivery platforms for different types of drugs are detailed. With the emergence of gene therapy, this review also gives future prospects for combining DNA hydrogels with the gene editing toolbox.
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26
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Wang J, Li Y, Nie G. Multifunctional biomolecule nanostructures for cancer therapy. NATURE REVIEWS. MATERIALS 2021; 6:766-783. [PMID: 34026278 PMCID: PMC8132739 DOI: 10.1038/s41578-021-00315-x] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 05/08/2023]
Abstract
Biomolecule-based nanostructures are inherently multifunctional and harbour diverse biological activities, which can be explored for cancer nanomedicine. The supramolecular properties of biomolecules can be precisely programmed for the design of smart drug delivery vehicles, enabling efficient transport in vivo, targeted drug delivery and combinatorial therapy within a single design. In this Review, we discuss biomolecule-based nanostructures, including polysaccharides, nucleic acids, peptides and proteins, and highlight their enormous design space for multifunctional nanomedicines. We identify key challenges in cancer nanomedicine that can be addressed by biomolecule-based nanostructures and survey the distinct biological activities, programmability and in vivo behaviour of biomolecule-based nanostructures. Finally, we discuss challenges in the rational design, characterization and fabrication of biomolecule-based nanostructures, and identify obstacles that need to be overcome to enable clinical translation.
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Affiliation(s)
- Jing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yiye Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
- GBA Research Innovation Institute for Nanotechnology, Guangdong, China
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, China
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27
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Johnson MB, Halman JR, Miller DK, Cooper JS, Khisamutdinov E, Marriott I, Afonin KA. The immunorecognition, subcellular compartmentalization, and physicochemical properties of nucleic acid nanoparticles can be controlled by composition modification. Nucleic Acids Res 2020; 48:11785-11798. [PMID: 33091133 PMCID: PMC7672449 DOI: 10.1093/nar/gkaa908] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleic acid nanoparticles (NANPs) have become powerful new platforms as therapeutic and diagnostic tools due to the innate biological ability of nucleic acids to identify target molecules or silence genes involved in disease pathways. However, the clinical application of NANPs has been limited by factors such as chemical instability, inefficient intracellular delivery, and the triggering of detrimental inflammatory responses following innate immune recognition of nucleic acids. Here, we have studied the effects of altering the chemical composition of a circumscribed panel of NANPs that share the same connectivity, shape, size, charge and sequences. We show that replacing RNA strands with either DNA or chemical analogs increases the enzymatic and thermodynamic stability of NANPs. Furthermore, we have found that such composition changes affect delivery efficiency and determine subcellular localization, effects that could permit the targeted delivery of NANP-based therapeutics and diagnostics. Importantly, we have determined that altering NANP composition can dictate the degree and mechanisms by which cell immune responses are initiated. While RNA NANPs trigger both TLR7 and RIG-I mediated cytokine and interferon production, DNA NANPs stimulate minimal immune activation. Importantly, incorporation of 2'F modifications abrogates RNA NANP activation of TLR7 but permits RIG-I dependent immune responses. Furthermore, 2'F modifications of DNA NANPs significantly enhances RIG-I mediated production of both proinflammatory cytokines and interferons. Collectively this indicates that off-target effects may be reduced and/or desirable immune responses evoked based upon NANPs modifications. Together, our studies show that NANP composition provides a simple way of controlling the immunostimulatory potential, and physicochemical and delivery characteristics, of such platforms.
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Affiliation(s)
- Morgan Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Justin R Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Daniel K Miller
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Joseph S Cooper
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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28
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Nordmeier S, Ke W, Afonin KA, Portnoy V. Exosome mediated delivery of functional nucleic acid nanoparticles (NANPs). NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 30:102285. [PMID: 32781137 PMCID: PMC7680442 DOI: 10.1016/j.nano.2020.102285] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/25/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
Abstract
RNAi-based technologies have shown biomedical potential; however, safe and efficient delivery of RNA remains a barrier for their broader clinical applications. Nucleic acid nanoparticles (NANPs) programmed to self-assemble and organize multiple therapeutic nucleic acids (TNAs) also became attractive candidates for diverse therapeutic options. Various synthetic nanocarriers are used to deliver TNAs and NANPs, but their clinical translation is limited due to immunotoxicity. Exosomes are cell-derived nanovesicles involved in cellular communication. Due to their ability to deliver biomolecules, exosomes are a novel delivery choice. In this study, we explored the exosome-mediated delivery of NANPs designed to target GFP. We assessed the intracellular uptake, gene silencing efficiency, and immunostimulation of exosomes loaded with NANPs. We also confirmed that interdependent RNA/DNA fibers upon recognition of each other after delivery, can conditionally activate NF-kB decoys and prevent pro-inflammatory cytokines. Our study overcomes challenges in TNA delivery and demonstrates future studies in drug delivery systems.
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Affiliation(s)
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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29
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Dobrovolskaia MA, Afonin KA. Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles. Nat Protoc 2020; 15:3678-3698. [PMID: 33097923 PMCID: PMC7875514 DOI: 10.1038/s41596-020-0393-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/31/2020] [Indexed: 12/21/2022]
Abstract
This protocol assesses proinflammatory properties of nucleic acid nanoparticles (NANPs) using a validated preclinical model, peripheral blood mononuclear cells (PBMCs), that is highly predictive of cytokine responses. The experimental procedure details the preparation of pyrogen-free NANPs, isolation of PBMCs from freshly collected human blood, and analysis of characteristic biomarkers (type I and III interferons) produced by PBMCs transfected with NANPs. Although representative NANPs with high and low immunostimulatory potential are used as standards throughout the procedure, this protocol can be adapted to any NANPs or therapeutic nucleic acids, irrespective of whether they are carrier based or carrier free; additional cytokine biomarkers can also be included. We test several commercial platforms and controls broadly accessible to the research community to quantify all biomarkers in either single- or multiplex format. The continuous execution of this protocol takes <48 h; when immediate analysis is not feasible, single-use aliquots of the supernatants can be frozen and stored (-20 °C; 12 months).
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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30
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Torelli E, Kozyra J, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami. ACS Synth Biol 2020; 9:1682-1692. [PMID: 32470289 DOI: 10.1021/acssynbio.0c00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in a high synthesis yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy, and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time. Our work suggests that the scaffolded origami technique is a viable, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Jerzy Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
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31
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Kasprzak WK, Ahmed NA, Shapiro BA. Modeling ligand docking to RNA in the design of RNA-based nanostructures. Curr Opin Biotechnol 2020; 63:16-25. [DOI: 10.1016/j.copbio.2019.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
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32
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Chandler M, Johnson MB, Panigaj M, Afonin KA. Innate immune responses triggered by nucleic acids inspire the design of immunomodulatory nucleic acid nanoparticles (NANPs). Curr Opin Biotechnol 2020; 63:8-15. [PMID: 31778882 PMCID: PMC7246180 DOI: 10.1016/j.copbio.2019.10.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022]
Abstract
The unknown immune stimulation by nucleic acid nanoparticles (NANPs) has become one of the major impediments to a broad spectrum of clinical developments of this novel technology. Having evolved to defend against bacterial and viral nucleic acids, mammalian cells have established patterns of recognition that are also the pathways through which NANPs can be processed. Explorations into the immune stimulation brought about by a vast diversity of known NANPs have shown that variations in design correlate with variations in immune response. Therefore, as the mechanisms of stimulation are further elucidated, these trends are now being taken into account in the design phase to allow for development of NANPs that are tailored for controlled immune activation or quiescence.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Morgan Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, 041 54, Slovak Republic
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA; The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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33
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Zakrevsky P, Kasprzak WK, Heinz WF, Wu W, Khant H, Bindewald E, Dorjsuren N, Fields EA, de Val N, Jaeger L, Shapiro BA. Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates. NANOSCALE 2020; 12:2555-2568. [PMID: 31932830 DOI: 10.1039/c9nr08197f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA interference (RNAi) substrates, allowing multiple functional entities to be combined on a single particle in a programmable fashion. Rather than employing a completely bottom-up approach to scaffold design, here multiple copies of an existing synthetic supramolecular RNA nano-architecture serve as building blocks along with additional motifs for the design of a novel truncated tetrahedral RNA scaffold, demonstrating that rationally designed RNA assemblies can themselves serve as modular pieces in the construction of larger rationally designed structures. The resulting tetrahedral scaffold displays enhanced characteristics for RNAi-substrate delivery in comparison to similar RNA-based scaffolds, as evidenced by its increased functional capacity, increased cellular uptake and ultimately an increased RNAi efficacy of its adorned Dicer substrate siRNAs. The unique truncated tetrahedral shape of the nanoparticle core appears to contribute to this particle's enhanced function, indicating the physical characteristics of RNA scaffolds merit significant consideration when designing platforms for delivery of functional RNAs via RNA nanoparticles.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Htet Khant
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eric A Fields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA and Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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34
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Halman JR, Kim KT, Gwak SJ, Pace R, Johnson MB, Chandler MR, Rackley L, Viard M, Marriott I, Lee JS, Afonin KA. A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (Nanps) for controlled gene silencing, immunostimulation, and biodistribution. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 23:102094. [PMID: 31669854 PMCID: PMC6942546 DOI: 10.1016/j.nano.2019.102094] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022]
Abstract
Programmable nucleic acid nanoparticles (NANPs) provide controlled coordination of therapeutic nucleic acids (TNAs) and other biological functionalities. Beyond multivalence, recent reports demonstrate that NANP technology can also elicit a specific immune response, adding another layer of customizability to this innovative approach. While the delivery of nucleic acids remains a challenge, new carriers are introduced and tested continuously. Polymeric platforms have proven to be efficient in shielding nucleic acid cargos from nuclease degradation while promoting their delivery and intracellular release. Here, we venture beyond the delivery of conventional TNAs and combine the stable cationic poly-(lactide-co-glycolide)-graft-polyethylenimine with functionalized NANPs. Furthermore, we compare several representative NANPs to assess how their overall structures influence their delivery with the same carrier. An extensive study of various formulations both in vitro and in vivo reveals differences in their immunostimulatory activity, gene silencing efficiency, and biodistribution, with fibrous NANPs advancing for TNA delivery.
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Affiliation(s)
- Justin R Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ki-Taek Kim
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - So-Jung Gwak
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Richard Pace
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Morgan R Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Lauren Rackley
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Jeoung Soo Lee
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA.
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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35
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Dobrovolskaia MA. Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies. Molecules 2019; 24:molecules24244620. [PMID: 31861154 PMCID: PMC6943637 DOI: 10.3390/molecules24244620] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Vaccines and immunotherapies involve a variety of technologies and act through different mechanisms to achieve a common goal, which is to optimize the immune response against an antigen. The antigen could be a molecule expressed on a pathogen (e.g., a disease-causing bacterium, a virus or another microorganism), abnormal or damaged host cells (e.g., cancer cells), environmental agent (e.g., nicotine from a tobacco smoke), or an allergen (e.g., pollen or food protein). Immunogenic vaccines and therapies optimize the immune response to improve the eradication of the pathogen or damaged cells. In contrast, tolerogenic vaccines and therapies retrain or blunt the immune response to antigens, which are recognized by the immune system as harmful to the host. To optimize the immune response to either improve the immunogenicity or induce tolerance, researchers employ different routes of administration, antigen-delivery systems, and adjuvants. Nanocarriers and adjuvants are of particular interest to the fields of vaccines and immunotherapy as they allow for targeted delivery of the antigens and direct the immune response against these antigens in desirable direction (i.e., to either enhance immunogenicity or induce tolerance). Recently, nanoparticles gained particular attention as antigen carriers and adjuvants. This review focuses on a particular subclass of nanoparticles, which are made of nucleic acids, so-called nucleic acid nanoparticles or NANPs. Immunological properties of these novel materials and considerations for their clinical translation are discussed.
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
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36
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Johnson TG, Schelch K, Mehta S, Burgess A, Reid G. Why Be One Protein When You Can Affect Many? The Multiple Roles of YB-1 in Lung Cancer and Mesothelioma. Front Cell Dev Biol 2019; 7:221. [PMID: 31632972 PMCID: PMC6781797 DOI: 10.3389/fcell.2019.00221] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/18/2019] [Indexed: 12/14/2022] Open
Abstract
Lung cancers and malignant pleural mesothelioma (MPM) have some of the worst 5-year survival rates of all cancer types, primarily due to a lack of effective treatment options for most patients. Targeted therapies have shown some promise in thoracic cancers, although efficacy is limited only to patients harboring specific mutations or target expression. Although a number of actionable mutations have now been identified, a large population of thoracic cancer patients have no therapeutic options outside of first-line chemotherapy. It is therefore crucial to identify alternative targets that might lead to the development of new ways of treating patients diagnosed with these diseases. The multifunctional oncoprotein Y-box binding protein-1 (YB-1) could serve as one such target. Recent studies also link this protein to many inherent behaviors of thoracic cancer cells such as proliferation, invasion, metastasis and involvement in cancer stem-like cells. Here, we review the regulation of YB-1 at the transcriptional, translational, post-translational and sub-cellular levels in thoracic cancer and discuss its potential use as a biomarker and therapeutic target.
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Affiliation(s)
- Thomas G Johnson
- Asbestos Diseases Research Institute, Sydney, NSW, Australia.,Cell Division Laboratory, The ANZAC Research Institute, Sydney, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia.,Sydney Catalyst Translational Cancer Research Centre, The University of Sydney, Sydney, NSW, Australia
| | - Karin Schelch
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Sunali Mehta
- Department of Pathology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre, University of Otago, Dunedin, New Zealand
| | - Andrew Burgess
- Cell Division Laboratory, The ANZAC Research Institute, Sydney, NSW, Australia.,School of Medicine, The University of Sydney, Sydney, NSW, Australia
| | - Glen Reid
- Department of Pathology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre, University of Otago, Dunedin, New Zealand
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37
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Guo S, Xu C, Yin H, Hill J, Pi F, Guo P. Tuning the size, shape and structure of RNA nanoparticles for favorable cancer targeting and immunostimulation. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1582. [PMID: 31456362 DOI: 10.1002/wnan.1582] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 12/16/2022]
Abstract
The past decade has shown exponential growth in the field of RNA nanotechnology. The rapid advances of using RNA nanoparticles for biomedical applications, especially targeted cancer therapy, suggest its potential as a new generation of drug. After the first milestone of small molecule drugs and the second milestone of antibody drugs, it was predicted that RNA drugs, either RNA itself or chemicals/ligands that target RNA, will be the third milestone in drug development. Thus, a comprehensive assessment of the current therapeutic RNA nanoparticles is urgently needed to meet the drug evaluation criteria. Specifically, the pharmacological and immunological profiles of RNA nanoparticles need to be systematically studied to provide insights in rational design of RNA-based therapeutics. By virtue of its programmability and biocompatibility, RNA molecules can be designed to construct sophisticated nanoparticles with versatile functions/applications and highly tunable physicochemical properties. This intrinsic characteristic allows the systemic study of the effects of various properties of RNA nanoparticles on their in vivo behaviors such as cancer targeting and immune responses. This review will focus on the recent progress of RNA nanoparticles in cancer targeting, and summarize the effects of common physicochemical properties such as size and shape on the RNA nanoparticles' biodistribution and immunostimulation profiles. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Diagnostic Tools > in vivo Nanodiagnostics and Imaging Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio.,Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio.,James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio.,Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio.,James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Hongran Yin
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio.,Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio.,James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio
| | | | | | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio.,Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio.,Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio.,James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio
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38
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Komura F, Takahashi Y, Inoue T, Takakura Y, Nishikawa M. Development of a Nanostructured RNA/DNA Assembly as an Adjuvant Targeting Toll-Like Receptor 7/8. Nucleic Acid Ther 2019; 29:335-342. [PMID: 31329033 DOI: 10.1089/nat.2019.0787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adjuvants are essential for efficiently inducing an antigen-specific immune response in vaccine therapy. Single-stranded RNA (ssRNA) containing guanosine- and uridine-rich sequences is recognized by Toll-like receptor (TLR)7 and/or TLR8 and induces strong immune responses; thus, the application of ssRNA as an adjuvant is desirable. The development of a ssRNA-based adjuvant, however, requires the efficient delivery of ssRNA into the endosomes of antigen-presenting cells, where the TLRs exist. To achieve this, we developed a nanostructured RNA/DNA assembly using DNA nanotechnology, which can be efficiently recognized by antigen-presenting cells. The nanostructured RNA/DNA assembly, named tetrapodRD3, was designed using a 40-mer phosphorothioate-stabilized RNA and three 40-mer phosphodiester DNAs. TetrapodRD3 was more stable than ssRNA under serum conditions. The secreted alkaline phosphatase assay using HEK-Blue hTLR cells showed that tetrapodRD3 triggered human TLR8-specific responses. Fluorescently labeled tetrapodRD3 was efficiently taken up by murine dendritic DC2.4 cells and induced a high level of tumor necrosis factor-α release from the cells. Antigen presentation by the major histocompatibility complex class I on bone marrow-derived dendritic cells was significantly increased by the addition of an antigen along with tetrapodRD3. These results indicate that tetrapodRD3 constructed using DNA nanotechnology can be a useful adjuvant targeting human TLR8.
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Affiliation(s)
- Fusae Komura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takao Inoue
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Makiya Nishikawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
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39
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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40
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Oliver RC, Rolband LA, Hutchinson-Lundy AM, Afonin KA, Krueger JK. Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E681. [PMID: 31052508 PMCID: PMC6566709 DOI: 10.3390/nano9050681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
Abstract
Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.
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Affiliation(s)
- Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Lewis A Rolband
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
| | | | - Kirill A Afonin
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
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41
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Chandler M, Afonin KA. Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E611. [PMID: 31013847 PMCID: PMC6523571 DOI: 10.3390/nano9040611] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Nucleic acids are programmable and biocompatible polymers that have beneficial uses in nanotechnology with broad applications in biosensing and therapeutics. In some cases, however, the development of the latter has been impeded by the unknown immunostimulatory properties of nucleic acid-based materials, as well as a lack of functional dynamicity due to stagnant structural design. Recent research advancements have explored these obstacles in tandem via the assembly of three-dimensional, planar, and fibrous cognate nucleic acid-based nanoparticles, called NANPs, for the conditional activation of embedded and otherwise quiescent functions. Furthermore, a library of the most representative NANPs was extensively analyzed in human peripheral blood mononuclear cells (PBMCs), and the links between the programmable architectural and physicochemical parameters of NANPs and their immunomodulatory properties have been established. This overview will cover the recent development of design principles that allow for fine-tuning of both the physicochemical and immunostimulatory properties of dynamic NANPs and discuss the potential impacts of these novel strategies.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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42
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Hong E, Halman JR, Shah A, Cedrone E, Truong N, Afonin KA, Dobrovolskaia MA. Toll-Like Receptor-Mediated Recognition of Nucleic Acid Nanoparticles (NANPs) in Human Primary Blood Cells. Molecules 2019; 24:E1094. [PMID: 30897721 PMCID: PMC6470694 DOI: 10.3390/molecules24061094] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 12/11/2022] Open
Abstract
Infusion reactions (IRs) create a translational hurdle for many novel therapeutics, including those utilizing nanotechnology. Nucleic acid nanoparticles (NANPs) are a novel class of therapeutics prepared by rational design of relatively short oligonucleotides to self-assemble into various programmable geometric shapes. While cytokine storm, a common type of IR, has halted clinical development of several therapeutic oligonucleotides, NANP technologies hold tremendous potential to bring these reactions under control by tuning the particle's physicochemical properties to the desired type and magnitude of the immune response. Recently, we reported the very first comprehensive study of the structure⁻activity relationship between NANPs' shape, size, composition, and their immunorecognition in human cells, and identified the phagolysosomal pathway as the major route for the NANPs' uptake and subsequent immunostimulation. Here, we explore the molecular mechanism of NANPs' recognition by primary immune cells, and particularly the contributing role of the Toll-like receptors. Our current study expands the understanding of the immune recognition of engineered nucleic acid-based therapeutics and contributes to the improvement of the nanomedicine safety profile.
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Affiliation(s)
- Enping Hong
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research Sponsored by The National Cancer Institute, Frederick, MD 21702, USA.
| | - Justin R Halman
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Ankit Shah
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research Sponsored by The National Cancer Institute, Frederick, MD 21702, USA.
| | - Edward Cedrone
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research Sponsored by The National Cancer Institute, Frederick, MD 21702, USA.
| | - Nguyen Truong
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research Sponsored by The National Cancer Institute, Frederick, MD 21702, USA.
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43
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Jedrzejczyk D, Chworos A. Self-Assembling RNA Nanoparticle for Gene Expression Regulation in a Model System. ACS Synth Biol 2019; 8:491-497. [PMID: 30649860 DOI: 10.1021/acssynbio.8b00319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In the search for enzymatically processed RNA fragments, we found the novel three-way junction motif. The structure prediction suggested the arrangement of helices at acute angle approx. 60°. This allows the design of a trimeric RNA nanoparticle that can be functionalized with multiple regulatory fragments. Such RNA nano-object of equilateral triangular shape was applied for gene expression regulation studies in two independent cellular systems. Biochemical and functional studies confirmed the predicted shape and structure of the nanoparticle. The regulatory siRNA fragments incorporated into the nanoparticle were effectively released and triggered gene silencing. The regulatory effect was prolonged when induced with structuralized RNA compared to unstructured siRNAs. In these studies, the enzymatic processing of the motif was utilized for function release from the nanoparticle, enabling simultaneous delivery of different regulatory functions. This methodology of sequence search, RNA structural prediction, and application for rational design opens a new way for creating enzymatically processed RNA nanoparticles.
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Affiliation(s)
- Dominika Jedrzejczyk
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , 90-363 Lodz , Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , 90-363 Lodz , Poland
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44
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Ke W, Hong E, Saito RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA. RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells. Nucleic Acids Res 2019; 47:1350-1361. [PMID: 30517685 PMCID: PMC6379676 DOI: 10.1093/nar/gky1215] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid-based assemblies that interact with each other and further communicate with the cellular machinery in a controlled manner represent a new class of reconfigurable materials that can overcome limitations of traditional biochemical approaches and improve the potential therapeutic utility of nucleic acids. This notion enables the development of novel biocompatible 'smart' devices and biosensors with precisely controlled physicochemical and biological properties. We extend this novel concept by designing RNA-DNA fibers and polygons that are able to cooperate in different human cell lines and that have defined immunostimulatory properties confirmed by ex vivo experiments. The mutual intracellular interaction of constructs results in the release of a large number of different siRNAs while giving a fluorescent response and activating NF-κB decoy DNA oligonucleotides. This work expands the possibilities of nucleic acid technologies by (i) introducing very simple design principles and assembly protocols; (ii) potentially allowing for a simultaneous release of various siRNAs together with functional DNA sequences and (iii) providing controlled rates of reassociation, stabilities in human blood serum, and immunorecognition.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Mathias Viard
- Basic Science Program, Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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45
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Kim D, Kim H, Han S, Scatena M, Kim DH, Lee JB. Immunostimulatory Effects Triggered by Self-Assembled Microspheres with Tandem Repeats of Polymerized RNA Strands. Adv Healthc Mater 2019; 8:e1801395. [PMID: 30657652 DOI: 10.1002/adhm.201801395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/08/2019] [Indexed: 12/19/2022]
Abstract
Self-assembled RNA particles have been exploited widely to maximize the therapeutic potential of RNA. However, the immune response via RNA particles is not fully understood. In addition, the investigation of the immunogenicity from RNA-based particles is required owing to inherent immunostimulatory effects of RNA for clinical translation. To examine the immune stimulating potency, rationally designed microsized RNA particles, called RNA microspheres (RMSs), are generated with single or double strands via rolling circle transcription. The RMSs show an exceptional stability in the presence of serum, while they are selectively degraded under endolysosomal conditions. With precisely controlled size, both RMSs are successfully taken up by macrophages. Unlike the nature of RNA fragments, RMSs induce only basal-level expression of inflammatory cytokines as well as type I interferon from macrophages, suggesting that RMSs are immunocompatible in the therapeutic dose range. Taken together, this study could help accelerate clinical translation and broaden the applicability of the self-assembled RNA-based particles without being limited by their potential immunotoxicity, while a systematic controllability study observing the release of RNA fragments from RMSs would provide self-assembled RNA-based structures with a great potential for immunomodulation.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
| | - Sangwoo Han
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Marta Scatena
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
- Institute of Stem Cell and Regenerative Medicine; University of Washington; Seattle WA 98109 USA
| | - Deok-Ho Kim
- Department of Bioengineering; University of Washington; Seattle WA 98195 USA
- Institute of Stem Cell and Regenerative Medicine; University of Washington; Seattle WA 98109 USA
| | - Jong Bum Lee
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
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46
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Reichel D, Tripathi M, Perez JM. Biological Effects of Nanoparticles on Macrophage Polarization in the Tumor Microenvironment. Nanotheranostics 2019; 3:66-88. [PMID: 30662824 PMCID: PMC6328304 DOI: 10.7150/ntno.30052] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/02/2018] [Indexed: 12/11/2022] Open
Abstract
Biological interactions between tumor-associated macrophages (TAMs), cancer cells and other cells within the tumor microenvironment contribute to tumorigenesis, tumor growth, metastasis and therapeutic resistance. TAMs can remodel the tumor microenvironment to reduce growth barriers such as the dense extracellular matrix and shift tumors towards an immunosuppressive microenvironment that protects cancer cells from targeted immune responses. Nanoparticles can interrupt these biological interactions within tumors by altering TAM phenotypes through a process called polarization. Macrophage polarization within tumors can shift TAMs from a growth-promoting phenotype towards a cancer cell-killing phenotype that predicts treatment efficacy. Because many types of nanoparticles have been shown to preferentially accumulate within macrophages following systemic administration, there is considerable interest in identifying nanoparticle effects on TAM polarization, evaluating nanoparticle-induced TAM polarization effects on cancer treatment using drug-loaded nanoparticles and identifying beneficial types of nanoparticles for effective cancer treatment. In this review, the macrophage polarization effects of nanoparticles will be described based on their primary chemical composition. Because of their strong macrophage-polarizing and antitumor effects compared to other types of nanoparticles, the effects of iron oxide nanoparticles on macrophages will be discussed in detail. By comparing the macrophage polarization effects of various nanoparticle treatments reported in the literature, this review aims to both elucidate nanoparticle material effects on macrophage polarization and to provide insight into engineering nanoparticles with more beneficial immunological responses for cancer treatment.
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Affiliation(s)
- Derek Reichel
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Manisha Tripathi
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Current Address: Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - J. Manuel Perez
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
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47
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Cultrara CN, Shah S, Kozuch SD, Patel MR, Sabatino D. Solid phase synthesis and self-assembly of higher-order siRNAs and their bioconjugates. Chem Biol Drug Des 2018; 93:999-1010. [PMID: 30480355 DOI: 10.1111/cbdd.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/10/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
New methods for the synthesis of higher-order siRNA motifs and their bioconjugates have recently gained widespread attention in the development of new and improved gene therapeutics. Our efforts aim to produce new chemical tools and protocols for the generation of modified siRNAs that screen for important oncogene targets as well as silence their activity for effective gene therapy in cancer models. More specifically, we have developed an efficient solution-phase synthesis for the production of a ribouridine branchpoint synthon that can be effectively incorporated by solid phase synthesis within higher-order RNA structures, including those adopting V-, and Y- and >-< shape RNA templates. Self-assembly of complementary RNA to the template strands produced higher-order siRNA nanostructures that were characterized by a combination of PAGE, DLS, and TEM techniques. In an effort to extend the repertoire of functionally diverse siRNAs, we have also developed solid phase bioconjugation strategies for incorporating bio-active probes such as fatty acid appendages and fluorescent reporters. Taken together, these methods highlight the ability to generate higher-order siRNAs and their bioconjugates for exploring the influence of modified siRNA structure on anti-cancer activity.
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Affiliation(s)
- Christopher N Cultrara
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | - Sunil Shah
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | - Stephen D Kozuch
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
| | | | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey
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48
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Sajja S, Chandler M, Fedorov D, Kasprzak WK, Lushnikov A, Viard M, Shah A, Dang D, Dahl J, Worku B, Dobrovolskaia MA, Krasnoslobodtsev A, Shapiro BA, Afonin KA. Dynamic Behavior of RNA Nanoparticles Analyzed by AFM on a Mica/Air Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15099-15108. [PMID: 29669419 PMCID: PMC6207479 DOI: 10.1021/acs.langmuir.8b00105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
RNA is an attractive biopolymer for engineering self-assembling materials suitable for biomedical applications. Previously, programmable hexameric RNA rings were developed for the controlled delivery of up to six different functionalities. To increase the potential for functionalization with little impact on nanoparticle topology, we introduce gaps into the double-stranded regions of the RNA rings. Molecular dynamic simulations are used to assess the dynamic behavior and the changes in the flexibility of novel designs. The changes suggested by simulations, however, cannot be clearly confirmed by the conventional techniques such as nondenaturing polyacrylamide gel electrophoresis (native-PAGE) and dynamic light scattering (DLS). Also, an in vitro analysis in primary cultures of human peripheral blood mononuclear cells does not reveal any discrepancy in the immunological recognition of new assemblies. To address these deficiencies, we introduce a computer-assisted quantification strategy. This strategy is based on an algorithmic atomic force microscopy (AFM)-resolved deformation analysis of the RNA nanoparticles studied on a mica/air interface. We validate this computational method by manual image analysis and fitting it to the simulation-predicted results. The presented nanoparticle modification strategy and subsequent AFM-based analysis are anticipated to provide a broad spectrum approach for the future development of nucleic acid-based nanotechnology.
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Affiliation(s)
- Sameer Sajja
- Nanoscale Science Program, Department of Chemistry
| | | | - Dmitry Fedorov
- ViQi Inc., Santa Barbara, California 93109, United States
| | | | - Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research Inc and
- RNA Biology Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ankit Shah
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dylan Dang
- Nanoscale Science Program, Department of Chemistry
| | - Jared Dahl
- Nanoscale Science Program, Department of Chemistry
| | | | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexey Krasnoslobodtsev
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department of Physics, University of Nebraska at Omaha, Omaha, Nebraska 68182, United States
| | - Bruce A. Shapiro
- RNA Biology Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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49
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Chandler M, Lyalina T, Halman J, Rackley L, Lee L, Dang D, Ke W, Sajja S, Woods S, Acharya S, Baumgarten E, Christopher J, Elshalia E, Hrebien G, Kublank K, Saleh S, Stallings B, Tafere M, Striplin C, Afonin KA. Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology. Molecules 2018; 23:E3178. [PMID: 30513826 PMCID: PMC6321606 DOI: 10.3390/molecules23123178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023] Open
Abstract
RNA aptamers selected to bind fluorophores and activate their fluorescence offer a simple and modular way to visualize native RNAs in cells. Split aptamers which are inactive until the halves are brought within close proximity can become useful for visualizing the dynamic actions of RNA assemblies and their interactions in real time with low background noise and eliminated necessity for covalently attached dyes. Here, we design and test several sets of F30 Broccoli aptamer splits, that we call fluorets, to compare their relative fluorescence and physicochemical stabilities. We show that the splits can be simply assembled either through one-pot thermal annealing or co-transcriptionally, thus allowing for direct tracking of transcription reactions via the fluorescent response. We suggest a set of rules that enable for the construction of responsive biomaterials that readily change their fluorescent behavior when various stimuli such as the presence of divalent ions, exposure to various nucleases, or changes in temperature are applied. We also show that the strand displacement approach can be used to program the controllable fluorescent responses in isothermal conditions. Overall, this work lays a foundation for the future development of dynamic systems for molecular computing which can be used to monitor real-time processes in cells and construct biocompatible logic gates.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Tatiana Lyalina
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, 191002 St. Petersburg, Russia.
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Rackley
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Lee
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Dylan Dang
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Sameer Sajja
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Steven Woods
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Shrija Acharya
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Elijah Baumgarten
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Jonathan Christopher
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Emman Elshalia
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Gabriel Hrebien
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kinzey Kublank
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Saja Saleh
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Bailey Stallings
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Michael Tafere
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Caryn Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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50
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Rackley L, Stewart JM, Salotti J, Krokhotin A, Shah A, Halman JR, Juneja R, Smollett J, Lee L, Roark K, Viard M, Tarannum M, Vivero-Escoto J, Johnson PF, Dobrovolskaia MA, Dokholyan NV, Franco E, Afonin KA. RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1805959. [PMID: 31258458 PMCID: PMC6599627 DOI: 10.1002/adfm.201805959] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 05/20/2023]
Abstract
RNA is a versatile biomaterial that can be used to engineer nanoassemblies for personalized treatment of various diseases. Despite promising advancements, the design of RNA nanoassemblies with minimal recognition by the immune system remains a major challenge. Here, an approach is reported to engineer RNA fibrous structures to operate as a customizable platform for efficient coordination of siRNAs and for maintaining low immunostimulation. Functional RNA fibers are studied in silico and their formation is confirmed by various experimental techniques and visualized by atomic force microscopy (AFM). It is demonstrated that the RNA fibers offer multiple advantages among which are: i) programmability and modular design that allow for simultaneous controlled delivery of multiple siRNAs and fluorophores, ii) reduced immunostimulation when compared to other programmable RNA nanoassemblies, and iii) simple production protocol for endotoxin-free fibers with the option of their cotranscriptional assembly. Furthermore, it is shown that functional RNA fibers can be efficiently delivered with various organic and inorganic carriers while retaining their structural integrity in cells. Specific gene silencing triggered by RNA fibers is assessed in human breast cancer and melanoma cell lines, with the confirmed ability of functional fibers to selectively target single nucleotide mutations.
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Affiliation(s)
- Lauren Rackley
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jaimie Marie Stewart
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Andrey Krokhotin
- Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27514, USA
| | - Ankit Shah
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Justin R Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Ridhima Juneja
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jaclyn Smollett
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lauren Lee
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kyle Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Mathias Viard
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mubin Tarannum
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Juan Vivero-Escoto
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27514, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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