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Stewart JM. RNA nanotechnology on the horizon: Self-assembly, chemical modifications, and functional applications. Curr Opin Chem Biol 2024; 81:102479. [PMID: 38889473 DOI: 10.1016/j.cbpa.2024.102479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024]
Abstract
RNA nanotechnology harnesses the unique chemical and structural properties of RNA to build nanoassemblies and supramolecular structures with dynamic and functional capabilities. This review focuses on design and assembly approaches to building RNA structures, the RNA chemical modifications used to enhance stability and functionality, and modern-day applications in therapeutics, biosensing, and bioimaging.
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2
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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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3
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Marie Haynes R, Myers J, López CS, Evans J, Davulcu O, Yoshioka C. A strategic approach for efficient cryo-EM grid optimization using design of experiments. J Struct Biol 2024:108068. [PMID: 38364988 DOI: 10.1016/j.jsb.2024.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become a practical and effective method of determining structures at previously unattainable resolutions due to advances in detection, automation, and data processing. However, sample preparation remains a major bottleneck in the cryo-EM workflow. Even after the arduous process of biochemical sample optimization, it often takes several iterations of grid vitrification and screening to determine the optimal grid freezing parameters that yield suitable ice thickness and particle distribution for data collection. Since a high-quality sample is imperative for high-resolution structure determination, grid optimization is a vital step. For researchers who rely on cryo-EM facilities for grid screening, each iteration of this optimization process may delay research progress by a matter of months. Therefore, a more strategic and efficient approach should be taken to ensure that the grid optimization process can be completed in as few iterations as possible. Here, we present an implementation of Design of Experiments (DOE) to expedite and strategize the grid optimization process. A Fractional Factorial Design (FFD) guides the determination of a limited set of experimental conditions which can model the full parameter space of interest. Grids are frozen with these conditions and screened for particle distribution and ice thickness. Quantitative scores are assigned to each of these grid characteristics based on a qualitative rubric. Input conditions and response scores are used to generate a least-squares regression model of the parameter space in JMP, which is used to determine the conditions which should, in theory, yield optimal grids. Upon testing this approach on apoferritin and L-glutamate dehydrogenase on both the Vitrobot Mark IV and the Leica GP2 plunge freezers, the resulting grid conditions reliably yielded grids with high-quality ice and particle distribution that were suitable for collecting large overnight datasets on a Krios. We conclude that a DOE-based approach is a cost-effective and time-saving tool for cryo-EM grid preparation.
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Affiliation(s)
- Rose Marie Haynes
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA; Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Janette Myers
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - Claudia S López
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - James Evans
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Omar Davulcu
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
| | - Craig Yoshioka
- Pacific Northwest Center for Cryo-Electron Microscopy, Oregon Health & Science University, Portland, OR 97201, USA
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4
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Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov EF. Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications. Biochemistry 2024; 63:312-325. [PMID: 38271599 DOI: 10.1021/acs.biochem.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We report a thorough investigation of the role of single-stranded thymidine (ssT) linkers in the stability and flexibility of minimal, multistranded DNA nanostructures. We systematically explore the impact of varying the number of ssTs in three-way junction motifs (3WJs) on their formation and properties. Through various UV melting experiments and molecular dynamics simulations, we demonstrate that while the number of ssTs minimally affects thermodynamic stability, the increasing ssT regions significantly enhance the structural flexibility of 3WJs. Utilizing this knowledge, we design triangular DNA nanoparticles with varying ssTs, all showing exceptional assembly efficiency except for the 0T triangle. All triangles demonstrate enhanced stability in blood serum and are nonimmunostimulatory and nontoxic in mammalian cell lines. The 4T 3WJ is chosen as the building block for constructing other polygons due to its enhanced flexibility and favorable physicochemical characteristics, making it a versatile choice for creating cost-effective, stable, and functional DNA nanostructures that can be stored in the dehydrated forms while retaining their structures. Our study provides valuable insights into the design and application of nucleic acid nanostructures, emphasizing the importance of understanding stability and flexibility in the realm of nucleic acid nanotechnology. Our findings suggest the intricate connection between these ssTs and the structural adaptability of DNA 3WJs, paving the way for more precise design and engineering of nucleic acid nanosystems suitable for broad biomedical applications.
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Affiliation(s)
- Ross Brumett
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Leyla Danai
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Abigail Coffman
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Yasmine Radwan
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Megan Teter
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Katelynn Pranger
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Sable Thornburgh
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Allison Dittmer
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tae Jin Kim
- Department of Physical Sciences, West Virginia University Institute of Technology, Beckley, West Virginia 25801, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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5
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Kim JE, Kang JH, Kwon WH, Lee I, Park SJ, Kim CH, Jeong WJ, Choi JS, Kim K. Self-assembling biomolecules for biosensor applications. Biomater Res 2023; 27:127. [PMID: 38053161 PMCID: PMC10696764 DOI: 10.1186/s40824-023-00466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Molecular self-assembly has received considerable attention in biomedical fields as a simple and effective method for developing biomolecular nanostructures. Self-assembled nanostructures can exhibit high binding affinity and selectivity by displaying multiple ligands/receptors on their surface. In addition, the use of supramolecular structure change upon binding is an intriguing approach to generate binding signal. Therefore, many self-assembled nanostructure-based biosensors have been developed over the past decades, using various biomolecules (e.g., peptides, DNA, RNA, lipids) and their combinations with non-biological substances. In this review, we provide an overview of recent developments in the design and fabrication of self-assembling biomolecules for biosensing. Furthermore, we discuss representative electrochemical biosensing platforms which convert the biochemical reactions of those biomolecules into electrical signals (e.g., voltage, ampere, potential difference, impedance) to contribute to detect targets. This paper also highlights the successful outcomes of self-assembling biomolecules in biosensor applications and discusses the challenges that this promising technology needs to overcome for more widespread use.
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Affiliation(s)
- Ji-Eun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Woo Hyun Kwon
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inseo Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Sang Jun Park
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Chun-Ho Kim
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
- Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Jun Shik Choi
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea.
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6
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Khalifah BA, Alghamdi SA, Alhasan AH. Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts. Front Bioeng Biotechnol 2023; 11:1244377. [PMID: 38047291 PMCID: PMC10690607 DOI: 10.3389/fbioe.2023.1244377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
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Affiliation(s)
- Bashayer A. Khalifah
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali H. Alhasan
- Institute for Bioengineering, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
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7
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Hınçer A, Ahan RE, Aras E, Şeker UÖŞ. Making the Next Generation of Therapeutics: mRNA Meets Synthetic Biology. ACS Synth Biol 2023; 12:2505-2515. [PMID: 37672348 PMCID: PMC10510722 DOI: 10.1021/acssynbio.3c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 09/08/2023]
Abstract
The development of mRNA-based therapeutics centers around the natural functioning of mRNA molecules to provide the genetic information required for protein translation. To improve the efficacy of these therapeutics and minimize side effects, researchers can focus on the features of mRNA itself or the properties of the delivery agent to achieve the desired response. The tools considered for mRNA manipulation can be improved in terms of targetability, tunability, and translatability to medicine. While ongoing studies are dedicated to improving conventional approaches, innovative approaches can also be considered to unleash the full potential of mRNA-based therapeutics. Here, we discuss the opportunities that emerged from introducing synthetic biology to mRNA therapeutics. It includes a discussion of modular self-assembled mRNA nanoparticles, logic gates on a single mRNA molecule, and other possibilities.
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Affiliation(s)
- Ahmet Hınçer
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Recep Erdem Ahan
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Ebru Aras
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center, Bilkent
University, Ankara 06800, Turkey
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8
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Yang L, Li Z, Binzel DW, Guo P, Williams TM. Targeting oncogenic KRAS in non-small cell lung cancer with EGFR aptamer-conjugated multifunctional RNA nanoparticles. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:559-571. [PMID: 37637206 PMCID: PMC10448464 DOI: 10.1016/j.omtn.2023.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
KRAS mutations are one of the most common oncogenic driver mutations in human cancers, including non-small cell lung cancer (NSCLC), and have established roles in cancer pathogenesis and therapeutic resistance. The development of effective inhibitors of mutant KRAS represents a significant challenge. Three-way junction (3WJ)-based multi-functional RNA nanoparticles have the potential to serve as an effective in vivo siRNA delivery platform with the ability to enhance tumor targeting specificity and visualize biodistribution through an imaging moiety. Herein, we assembled novel EGFRapt-3WJ-siKRASG12C mutation targeted nanoparticles to target EGFR-expressing human NSCLC harboring a KRASG12C mutation to silence KRASG12C expression in a tumor cell-specific fashion. We found that EGFRapt-3WJ-siKRASG12C nanoparticles potently depleted cellular KRASG12C expression, resulting in attenuation of downstream MAPK pathway signaling, cell proliferation, migration/invasion ability, and sensitized NSCLC cells to chemoradiotherapy. In vivo, these nanoparticles induced tumor growth inhibition in KRASG12C NSCLC tumor xenografts. Together, this study suggests that the 3WJ pRNA-based platform has the potential to suppress mutant KRAS activity for the treatment of KRAS-driven human cancers, and warrants further development for clinical translation.
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Affiliation(s)
- Linlin Yang
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Zhefeng Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, James Comprehensive Cancer Center, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel W. Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, James Comprehensive Cancer Center, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, James Comprehensive Cancer Center, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Terence M. Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
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9
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McRae EKS, Rasmussen HØ, Liu J, Bøggild A, Nguyen MTA, Sampedro Vallina N, Boesen T, Pedersen JS, Ren G, Geary C, Andersen ES. Structure, folding and flexibility of co-transcriptional RNA origami. NATURE NANOTECHNOLOGY 2023; 18:808-817. [PMID: 36849548 PMCID: PMC10566746 DOI: 10.1038/s41565-023-01321-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
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Affiliation(s)
- Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andreas Bøggild
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Michael T A Nguyen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Thomas Boesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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10
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:25300-25312. [PMID: 37204867 PMCID: PMC10331730 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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11
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Torelli E, Shirt-Ediss B, Navarro SA, Manzano M, Vizzini P, Krasnogor N. Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing. Int J Mol Sci 2023; 24:ijms24108483. [PMID: 37239830 DOI: 10.3390/ijms24108483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli-based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Silvia A Navarro
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Priya Vizzini
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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12
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Uddin N, Binzel DW, Shu D, Fu TM, Guo P. Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome. Acta Pharm Sin B 2023; 13:1383-1399. [PMID: 37139430 PMCID: PMC10149909 DOI: 10.1016/j.apsb.2022.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Exosome is an excellent vesicle for in vivo delivery of therapeutics, including RNAi and chemical drugs. The extremely high efficiency in cancer regression can partly be attributed to its fusion mechanism in delivering therapeutics to cytosol without endosome trapping. However, being composed of a lipid-bilayer membrane without specific recognition capacity for aimed-cells, the entry into nonspecific cells can lead to potential side-effects and toxicity. Applying engineering approaches for targeting-capacity to deliver therapeutics to specific cells is desirable. Techniques with chemical modification in vitro and genetic engineering in cells have been reported to decorate exosomes with targeting ligands. RNA nanoparticles have been used to harbor tumor-specific ligands displayed on exosome surface. The negative charge reduces nonspecific binding to vital cells with negatively charged lipid-membrane due to the electrostatic repulsion, thus lowering the side-effect and toxicity. In this review, we focus on the uniqueness of RNA nanoparticles for exosome surface display of chemical ligands, small peptides or RNA aptamers, for specific cancer targeting to deliver anticancer therapeutics, highlighting recent advances in targeted delivery of siRNA and miRNA that overcomes the previous RNAi delivery roadblocks. Proper understanding of exosome engineering with RNA nanotechnology promises efficient therapies for a wide range of cancer subtypes.
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Affiliation(s)
- Nasir Uddin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Daniel W. Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry & Pharmacology, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmacology, College of Pharmacy, the Ohio State University, Columbus, OH 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, the Ohio State University, Columbus, OH 43210, USA
- James Comprehensive Cancer Center, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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13
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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14
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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: 13] [Impact Index Per Article: 13.0] [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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15
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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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16
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Panigaj M, Skelly E, Beasock D, Marriott I, Johnson MB, Salotti J, Afonin KA. Therapeutic immunomodulation by rationally designed nucleic acids and nucleic acid nanoparticles. Front Immunol 2023; 14:1053550. [PMID: 36798121 PMCID: PMC9927404 DOI: 10.3389/fimmu.2023.1053550] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The immune system has evolved to defend organisms against exogenous threats such as viruses, bacteria, fungi, and parasites by distinguishing between "self" and "non-self". In addition, it guards us against other diseases, such as cancer, by detecting and responding to transformed and senescent cells. However, for survival and propagation, the altered cells and invading pathogens often employ a wide range of mechanisms to avoid, inhibit, or manipulate the immunorecognition. As such, the development of new modes of therapeutic intervention to augment protective and prevent harmful immune responses is desirable. Nucleic acids are biopolymers essential for all forms of life and, therefore, delineating the complex defensive mechanisms developed against non-self nucleic acids can offer an exciting avenue for future biomedicine. Nucleic acid technologies have already established numerous approaches in therapy and biotechnology; recently, rationally designed nucleic acids nanoparticles (NANPs) with regulated physiochemical properties and biological activities has expanded our repertoire of therapeutic options. When compared to conventional therapeutic nucleic acids (TNAs), NANP technologies can be rendered more beneficial for synchronized delivery of multiple TNAs with defined stabilities, immunological profiles, and therapeutic functions. This review highlights several recent advances and possible future directions of TNA and NANP technologies that are under development for controlled immunomodulation.
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Affiliation(s)
- Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States.,Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovakia
| | - Elizabeth Skelly
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, United States
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17
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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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18
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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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19
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Poppleton E, Urbanek N, Chakraborty T, Griffo A, Monari L, Göpfrich K. RNA origami: design, simulation and application. RNA Biol 2023; 20:510-524. [PMID: 37498217 PMCID: PMC10376919 DOI: 10.1080/15476286.2023.2237719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large 'origami' structures with thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures - the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox.
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Affiliation(s)
- Erik Poppleton
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Molecular Biomechanics, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Niklas Urbanek
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Taniya Chakraborty
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Luca Monari
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institut de Science Et D’ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg, France
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
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20
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Klotz K, Radwan Y, Chakrabarti K. Dissecting Functional Biological Interactions Using Modular RNA Nanoparticles. Molecules 2022; 28:molecules28010228. [PMID: 36615420 PMCID: PMC9821959 DOI: 10.3390/molecules28010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Nucleic acid nanoparticles (NANPs) are an exciting and innovative technology in the context of both basic and biomedical research. Made of DNA, RNA, or their chemical analogs, NANPs are programmed for carrying out specific functions within human cells. NANPs are at the forefront of preventing, detecting, and treating disease. Their nucleic acid composition lends them biocompatibility that provides their cargo with enhanced opportunity for coordinated delivery. Of course, the NANP system of targeting specific cells and tissues is not without its disadvantages. Accumulation of NANPs outside of the target tissue and the potential for off-target effects of NANP-mediated cargo delivery present challenges to research and medical professionals and these challenges must be effectively addressed to provide safe treatment to patients. Importantly, development of NANPs with regulated biological activities and immunorecognition becomes a promising route for developing versatile nucleic acid therapeutics. In a basic research context, NANPs can assist investigators in fine-tuning the structure-function relationship of final formulations and in this review, we explore the practical applications of NANPs in laboratory and clinical settings and discuss how we can use established nucleic acid research techniques to design effective NANPs.
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Affiliation(s)
- Kaitlin Klotz
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
| | - Yasmine Radwan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
- Correspondence:
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21
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Nucleic acid-based scaffold systems and application in enzyme cascade catalysis. Appl Microbiol Biotechnol 2022; 107:9-23. [DOI: 10.1007/s00253-022-12315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022]
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22
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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23
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Chandler M, Jain S, Halman J, Hong E, Dobrovolskaia MA, Zakharov AV, Afonin KA. Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204941. [PMID: 36216772 PMCID: PMC9671856 DOI: 10.1002/smll.202204941] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acid nanoparticles, or NANPs, rationally designed to communicate with the human immune system, can offer innovative therapeutic strategies to overcome the limitations of traditional nucleic acid therapies. Each set of NANPs is unique in their architectural parameters and physicochemical properties, which together with the type of delivery vehicles determine the kind and the magnitude of their immune response. Currently, there are no predictive tools that would reliably guide the design of NANPs to the desired immunological outcome, a step crucial for the success of personalized therapies. Through a systematic approach investigating physicochemical and immunological profiles of a comprehensive panel of various NANPs, the research team developes and experimentally validates a computational model based on the transformer architecture able to predict the immune activities of NANPs. It is anticipated that the freely accessible computational tool that is called an "artificial immune cell," or AI-cell, will aid in addressing the current critical public health challenges related to safety criteria of nucleic acid therapies in a timely manner and promote the development of novel biomedical tools.
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Affiliation(s)
- Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Justin Halman
- 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, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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24
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Elonen A, Natarajan AK, Kawamata I, Oesinghaus L, Mohammed A, Seitsonen J, Suzuki Y, Simmel FC, Kuzyk A, Orponen P. Algorithmic Design of 3D Wireframe RNA Polyhedra. ACS NANO 2022; 16:16608-16616. [PMID: 36178116 PMCID: PMC9620399 DOI: 10.1021/acsnano.2c06035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 06/01/2023]
Abstract
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.
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Affiliation(s)
- Antti Elonen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
| | | | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Natural
Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
| | - Lukas Oesinghaus
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Abdulmelik Mohammed
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
- Department
of Biomedical Engineering, San José
State University, San José, California 95192, United States
| | - Jani Seitsonen
- Department
of Applied Physics and Nanomicroscopy Center, Aalto University, 00076 Aalto, Finland
| | - Yuki Suzuki
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8577, Japan
- Division
of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Friedrich C. Simmel
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Pekka Orponen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
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25
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Chandler M, Rolband L, Johnson MB, Shi D, Avila YI, Cedrone E, Beasock D, Danai L, Stassenko E, Krueger JK, Jiang J, Lee JS, Dobrovolskaia MA, Afonin KA. Expanding Structural Space for Immunomodulatory Nucleic Acid Nanoparticles (Nanps) via Spatial Arrangement of Their Therapeutic Moieties. ADVANCED FUNCTIONAL MATERIALS 2022; 32:2205581. [PMID: 37008199 PMCID: PMC10065476 DOI: 10.1002/adfm.202205581] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 05/16/2023]
Abstract
Different therapeutic nucleic acids (TNAs) can be unified in a single structure by their elongation with short oligonucleotides designed to self-assemble into nucleic acid nanoparticles (NANPs). With this approach, therapeutic cocktails with precisely controlled composition and stoichiometry of active ingredients can be delivered to the same diseased cells for enhancing pharmaceutical action. In this work, an additional nanotechnology-based therapeutic option that enlists a biocompatible NANP-encoded platform for their controlled patient-specific immunorecognition is explored. For this, a set of representative functional NANPs is extensively characterized in vitro, ex vivo, and in vivo and then further analyzed for immunostimulation of human peripheral blood mononuclear cells freshly collected from healthy donor volunteers. The results of the study present the advancement of the current TNA approach toward personalized medicine and offer a new strategy to potentially address top public health challenges related to drug overdose and safety through the biodegradable nature of the functional platform with immunostimulatory regulation.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Lewis Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Da Shi
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yelixza I Avila
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Damian Beasock
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Leyla Danai
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Elizabeth Stassenko
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Joanna K Krueger
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jiancheng Jiang
- Department of Mathematics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jeoung Soo Lee
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC 29634, USA
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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26
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Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2022; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
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Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors.
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Corresponding authors.
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Corresponding authors.
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27
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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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28
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Li X, Bhullar AS, Binzel DW, Guo P. The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development. Adv Drug Deliv Rev 2022; 186:114316. [PMID: 35526663 DOI: 10.1016/j.addr.2022.114316] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Besides mRNA, rRNA, and tRNA, cells contain many other noncoding RNA that display critical roles in the regulation of cellular functions. Human genome sequencing revealed that the majority of non-protein-coding DNA actually codes for non-coding RNAs. The dynamic nature of RNA results in its motile and deformative behavior. These conformational transitions such as the change of base-pairing, breathing within complemented strands, and pseudoknot formation at the 2D level as well as the induced-fit and conformational capture at the 3D level are important for their biological functions including regulation, translation, and catalysis. The dynamic, motile and catalytic activity has led to a belief that RNA is the origin of life. We have recently reported that the deformative property of RNA nanoparticles enhances their penetration through the leaky blood vessel of cancers which leads to highly efficient tumor accumulation. This special deformative property also enables RNA nanoparticles to pass the glomerulus, overcoming the filtration size limit, resulting in fast renal excretion and rapid body clearance, thus low or no toxicity. The biodistribution of RNA nanoparticles can be further improved by the incorporation of ligands for cancer targeting. In addition to the favorable biodistribution profiles, RNA nanoparticles possess other properties including self-assembly, negative charge, programmability, and multivalency; making it a great material for pharmaceutical applications. The intrinsic negative charge of RNA nanoparticles decreases the toxicity of drugs by preventing nonspecific binding to the negative charged cell membrane and enhancing the solubility of hydrophobic drugs. The polyvalent property of RNA nanoparticles allows the multi-functionalization which can apply to overcome drug resistance. This review focuses on the summary of these unique properties of RNA nanoparticles, which describes the mechanism of RNA dynamic, motile and deformative properties, and elucidates and prepares to welcome the RNA therapeutics as the third milestone in pharmaceutical drug development.
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Affiliation(s)
- Xin Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Abhjeet S Bhullar
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, United States
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, United States; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States; College of Medicine, The Ohio State University, Columbus, OH 43210, United States.
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29
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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: 10] [Impact Index Per Article: 5.0] [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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30
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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31
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Liu X, Tong Y, Xia D, Peng E, Yang X, Liu H, Ye T, Wang X, He Y, Ye Z, Chen Z, Tang K. Circular RNAs in prostate cancer: Biogenesis,biological functions, and clinical significance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1130-1147. [PMID: 34820150 PMCID: PMC8585584 DOI: 10.1016/j.omtn.2021.10.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules that play important regulatory roles in various tumors. Prostate cancer (PCa) is one of the most common malignant tumors in the world, with high morbidity and mortality. In recent years, more and more circRNAs have been found to be abnormally expressed and involved in the occurrence and development of PCa, including cell proliferation, apoptosis, invasion, migration, metastasis, chemotherapy resistance, and radiotherapy resistance. Most of the circRNAs regulate biological behaviors of cancer through a competitive endogenous RNA (ceRNA) regulatory mechanism, and some can exert their functions by binding to proteins. circRNAs are also associated with many clinicopathological features of PCa, including tumor grade, lymph node metastasis, and distant metastasis. In addition, circRNAs are potential diagnostic and prognostic biomarkers for PCa. Considering their critical regulatory roles in the progression of PCa, circRNAs would be the potential therapeutic targets. In this paper, the current research status of circRNAs in PCa is briefly reviewed.
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Affiliation(s)
- Xiao Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yonghua Tong
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ding Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ejun Peng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoqi Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hailang Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tao Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xinguang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu He
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Tang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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32
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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33
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Domb AJ, Sharifzadeh G, Nahum V, Hosseinkhani H. Safety Evaluation of Nanotechnology Products. Pharmaceutics 2021; 13:pharmaceutics13101615. [PMID: 34683908 PMCID: PMC8539492 DOI: 10.3390/pharmaceutics13101615] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/11/2023] Open
Abstract
Nanomaterials are now being used in a wide variety of biomedical applications. Medical and health-related issues, however, have raised major concerns, in view of the potential risks of these materials against tissue, cells, and/or organs and these are still poorly understood. These particles are able to interact with the body in countless ways, and they can cause unexpected and hazardous toxicities, especially at cellular levels. Therefore, undertaking in vitro and in vivo experiments is vital to establish their toxicity with natural tissues. In this review, we discuss the underlying mechanisms of nanotoxicity and provide an overview on in vitro characterizations and cytotoxicity assays, as well as in vivo studies that emphasize blood circulation and the in vivo fate of nanomaterials. Our focus is on understanding the role that the physicochemical properties of nanomaterials play in determining their toxicity.
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Affiliation(s)
- Abraham J. Domb
- The Centers for Nanoscience and Nanotechnology, Alex Grass Center for Drug Design and Synthesis and Cannabinoids Research, School of Pharmacy, Faculty of Medicine, Institute of Drug Research, The Hebrew University of Jerusalem, Jerusalem 91120, Israel;
- Correspondence: (A.J.D.); (H.H.)
| | - Ghorbanali Sharifzadeh
- Department of Polymer Engineering, School of Chemical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia;
| | - Victoria Nahum
- The Centers for Nanoscience and Nanotechnology, Alex Grass Center for Drug Design and Synthesis and Cannabinoids Research, School of Pharmacy, Faculty of Medicine, Institute of Drug Research, The Hebrew University of Jerusalem, Jerusalem 91120, Israel;
| | - Hossein Hosseinkhani
- Innovation Center for Advanced Technology, Matrix, Inc., New York, NY 10029, USA
- Correspondence: (A.J.D.); (H.H.)
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34
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Blanco Carcache PJ, Guo S, Li H, Zhang K, Xu C, Chiu W, Guo P. Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes. RNA (NEW YORK, N.Y.) 2021; 27:971-980. [PMID: 34193550 PMCID: PMC8370748 DOI: 10.1261/rna.078718.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
In biological systems, conformational changes and allosteric modulation play pivotal roles in regulating biological functions, such as the dynamic change of protein molecules, in response to binding or interacting with other factors such as pH, voltage, salt, light, or ligand. RNA can be manipulated and tuned with a level of simplicity that is characteristic of DNA or polymers, while displaying versatility in structure, diversity in function, and adaptability in a configuration similar to proteins. In the past, the work on the investigation of conformational change mainly focused on protein. The induced-fit and conformational capture in RNA have also been explored, such as in the study of riboswitches. Herein, we report the engineering of three-dimensional RNA nanocubes and demonstrated the operation and regulation for its configuration. We demonstrate the operation of reconfigurable RNA nanocubes whose shapes change precisely and reversibly in response to a specific trigger strand. The shape, size, and conformation can be regulated precisely and reversibly in response to the specific triggering signals. The shape and conformational conversion were observed by cryo-EM and gel electrophoresis, respectively. Harnessing the size, shape, conformation, and self-assembly capabilities of the RNA nanocube can provide a new potential use of this technology as nanocarriers for the treatment of various diseases.
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Affiliation(s)
- Peter J Blanco Carcache
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kaiming Zhang
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, California 94305, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
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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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Wang H, Guo P. Radiolabeled RNA Nanoparticles for Highly Specific Targeting and Efficient Tumor Accumulation with Favorable In Vivo Biodistribution. Mol Pharm 2021; 18:2924-2934. [PMID: 34212728 DOI: 10.1021/acs.molpharmaceut.1c00035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Therapeutic efficiency and toxicity are two of the three critical factors in molecular therapy and pharmaceutical drug development. Specific tumor targeting and rapid renal excretion contribute to improving efficiency and reducing toxicity. We recently found that RNA nanoparticles display rubber-like properties, enabling them to deliver therapeutics to cancer with high efficiency. Off-target RNA nanoparticles were rapidly cleared by renal excretion, resulting in nontoxicity. However, previous biodistribution studies relied mainly on fluorescent markers, which can cause interference from fluorophore quenching and autofluorescence. Thus, the quantification of biodistribution requires further scrutiny. In this study, radionuclide [3H] markers were used for quantitative pharmacokinetic (PK) studies to elucidate the favorable PK profile of RNA nanoparticles. Approximately 5% of [3H]-RNA nanoparticles accumulated in tumors, in contrast to the 0.7% tumor accumulation reported in the literature for other kinds of nanoparticles. The amount of [3H]-RNA nanoparticles accumulated in tumors was higher than that in the liver, heart, lung, spleen, and brain throughout the entire process after IV injection. [3H]-RNA nanoparticles rapidly reached the tumor vasculature within 30 min and remained in tumors for more than 2 days. Nontargeting [3H]-RNA nanoparticles were found in the urine 30 min after IV injection without degradation and processing, and more than 55% of the IV-injected radiolabeled RNA nanoparticles were cleared from the body within 12 h, while the other 45% includes the radiative counts that cannot be recovered due to whole-body distribution and blood dilution after intravenous injection. The high specificity of tumor targeting, fast renal excretion, and low organ accumulation illustrate the high therapeutic potential of RNA nanoparticles in cancer treatment as efficient cancer-targeting carriers with low toxicity and side effects.
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Affiliation(s)
- Hongzhi Wang
- 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
| | - 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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37
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Johnson MB, Chandler M, Afonin KA. Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects. Adv Drug Deliv Rev 2021; 173:427-438. [PMID: 33857556 PMCID: PMC8178219 DOI: 10.1016/j.addr.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Nucleic acid nanoparticles (NANPs) represent a highly versatile molecular platform for the targeted delivery of various therapeutics. However, despite their promise, further clinical translation of this innovative technology can be hindered by immunological off-target effects. All human cells are equipped with an arsenal of receptors that recognize molecular patterns specific to foreign nucleic acids and understanding the rules that guide this recognition offer the key rationale for the development of therapeutic NANPs with tunable immune stimulation. Numerous recent studies have provided increasing evidence that in addition to NANPs' physicochemical properties and therapeutic effects, their interactions with cells of the immune system can be regulated through multiple independently programmable architectural parameters. The results further suggest that defined immunomodulation by NANPs can either support their immunoquiescent delivery or be used for conditional stimulation of beneficial immunological responses.
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Affiliation(s)
- M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - 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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38
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Gerasimova YV, Nedorezova DD, Kolpashchikov DM. Split light up aptamers as a probing tool for nucleic acids. Methods 2021; 197:82-88. [PMID: 33992774 DOI: 10.1016/j.ymeth.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Aptamers that bind non-fluorescent dyes and increase their fluorescence can be converted to fluorescent sensors. Here, we discuss and provide guidance for the design of split (binary) light up aptameric sensors (SLAS) for nucleic acid analysis. SLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. The two strands hybridize to the analyzed DNA or RNA sequence and form a dye-binding pocket, followed by dye binding, and increase in its fluorescence. SLAS can detect nucleic acids in a cost-efficient label-free format since it does not require conjugation of organic dyes with nucleic acids. SLAS design is preferable over monolith fluorescent sensors due to simpler assay optimization and improved selectivity. RNA-based SLAS can be expressed in cells and used for intracellular monitoring and imaging biological molecules.
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Affiliation(s)
- Yulia V Gerasimova
- University of Central Florida, Chemistry Department, 4111 Libra Drive, Physical Sciences 255, Orlando, FL 32816-2366, United States.
| | - Daria D Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, ChemBio Cluster, SCAMT Institute, ITMO University, 9 Lomonosova Str., Saint Petersburg 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- University of Central Florida, Chemistry Department, 4111 Libra Drive, Physical Sciences 255, Orlando, FL 32816-2366, United States; Laboratory of Molecular Robotics and Biosensor Materials, ChemBio Cluster, SCAMT Institute, ITMO University, 9 Lomonosova Str., Saint Petersburg 191002, Russian Federation.
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39
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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40
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Alam MM, Mahbub S, Hosen MM, Kumar D, Hoque MA. A conductivity and cloud point investigation of interaction of cationic and non-ionic surfactants with sodium carboxymethyl cellulose: effect of polyols and urea. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01568-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Shanaa OA, Rumyantsev A, Sambuk E, Padkina M. In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects. Molecules 2021; 26:molecules26051422. [PMID: 33800717 PMCID: PMC7961669 DOI: 10.3390/molecules26051422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.
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Affiliation(s)
- Ousama Al Shanaa
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Atomic Energy Commission of Syria, Damascus P.O.B 6091, Syria
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
| | - Andrey Rumyantsev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Elena Sambuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Marina Padkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
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42
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
| | - Alexander A. Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
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43
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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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44
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kewei Ren
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Puspam Keshri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Rigumula Wu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Zhining Sun
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qikun Yu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qian Tian
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Bin Zhao
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yousef Bagheri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yiwen Xie
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Mingxu You
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
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45
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020; 59:21986-21990. [PMID: 32797667 PMCID: PMC7747015 DOI: 10.1002/anie.202010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded RNA devices have emerged for various cellular applications in imaging and biosensing, but their functions as precise regulators in living systems are still limited. Inspired by protein photosensitizers, we propose here a genetically encoded RNA aptamer based photosensitizer (GRAP). Upon illumination, the RNA photosensitizer can controllably generate reactive oxygen species for targeted cell regulation. The GRAP system can be selectively activated by endogenous stimuli and light of different wavelengths. Compared with their protein analogues, GRAP is highly programmable and exhibits reduced off-target effects. These results indicate that GRAP enables efficient noninvasive target cell ablation with high temporal and spatial precision. This new RNA regulator system will be widely used for optogenetics, targeted cell ablation, subcellular manipulation, and imaging.
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Affiliation(s)
- Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yiwen Xie
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
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46
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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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47
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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: 21] [Impact Index Per Article: 5.3] [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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48
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Ghimire C, Wang H, Li H, Vieweger M, Xu C, Guo P. RNA Nanoparticles as Rubber for Compelling Vessel Extravasation to Enhance Tumor Targeting and for Fast Renal Excretion to Reduce Toxicity. ACS NANO 2020; 14:13180-13191. [PMID: 32902260 PMCID: PMC7799665 DOI: 10.1021/acsnano.0c04863] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rubber is a fascinating material in both industry and daily life. The development of elastomeric material in nanotechnology is imperative due to its economic and technological potential. By virtue of their distinctive physicochemical properties, nucleic acids have been extensively explored in material science. The Phi29 DNA packaging motor contains a 3WJ with three angles of 97°, 125°, and 138°. Here, the rubber-like property of RNA architectures was investigated using optical tweezers and in vivo imaging technologies. The 3WJ 97° interior angle was contracted or stretched to 60°, 90°, and 108° at will to build elegant RNA triangles, squares, pentagons, cubes, tetrahedrons, dendrimers, and prisms. RNA nanoarchitecture was stretchable and shrinkable by optical tweezer with multiple extension and relaxation repeats like a rubber. Comparing to gold and iron nanoparticles with the same size, RNA nanoparticles display stronger cancer-targeting outcomes, while less accumulation in healthy organs. Generally, the upper limit of renal excretion is 5.5 nm; however, the 5, 10, and 20 nm RNA nanoparticles passed the renal filtration and resumed their original structure identified in urine. These findings solve two previous mysteries: (1) Why RNA nanoparticles have an unusually high tumor targeting efficiency since their rubber or amoeba-like deformation property enables them to squeeze out of the leaky vasculature to improve the EPR effect; and (2) why RNA nanoparticles remain non-toxic since they can be rapidly cleared from the body via renal excretion into urine with little accumulation in the body. Considering its controllable shape and size plus its rubber-like property, RNA holds great promises for industrial and biomedical applications especially in cancer therapeutics delivery.
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Affiliation(s)
| | | | | | - Mario Vieweger
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020; 60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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Juneja R, Vadarevu H, Halman J, Tarannum M, Rackley L, Dobbs J, Marquez J, Chandler M, Afonin K, Vivero-Escoto JL. Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance In Vitro. ACS APPLIED MATERIALS & INTERFACES 2020; 12:38873-38886. [PMID: 32805923 PMCID: PMC7748385 DOI: 10.1021/acsami.0c07106] [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] [Indexed: 05/20/2023]
Abstract
Programmable nucleic acid nanoparticles (NANPs) with precisely controlled functional compositions can regulate the conditional activation of various biological pathways and responses in human cells. However, the intracellular delivery of NANPs alone is hindered by their susceptibility to nuclease activity and inefficient crossing of biological membranes. In this work, we optimized the internalization and therapeutic performance of several representative NANPs delivered with mesoporous silica nanoparticles (MSNPs) tailored for efficient electrostatic association with NANPs. We compared the immunostimulatory properties of different NA-MS-NP complexes formed with globular, planar, and fibrous NANPs and demonstrated the maximum immunostimulation for globular NANPs. As a proof of concept, we assessed the specific gene silencing by NA-MS-NP complexes functionalized with siRNA targeting green fluorescent protein expressed in triple-negative human breast cancer cells. We showed that the fibrous NANPs have the highest silencing efficiency when compared to globular or planar counterparts. Finally, we confirmed the multimodal ability of MSNPs to co-deliver a chemotherapy drug, doxorubicin, and NANPs targeting apoptosis regulator gene BCL2 in triple-negative breast cancer and melanoma cell lines. Overall, the combination of NANPs and MSNPs may become a new promising approach to efficiently treat cancer and other diseases via the simultaneous targeting of various pathways.
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Affiliation(s)
- Ridhima Juneja
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Hemapriyadarshini Vadarevu
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Justin Halman
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mubin Tarannum
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lauren Rackley
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jacob Dobbs
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jose Marquez
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill Afonin
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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