1
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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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2
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De Franceschi N, Hoogenberg B, Katan A, Dekker C. Engineering ssRNA tile filaments for (dis)assembly and membrane binding. NANOSCALE 2024; 16:4890-4899. [PMID: 38323489 DOI: 10.1039/d3nr06423a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Cytoskeletal protein filaments such as actin and microtubules confer mechanical support to cells and facilitate many cellular functions such as motility and division. Recent years have witnessed the development of a variety of molecular scaffolds that mimic such filaments. Indeed, filaments that are programmable and compatible with biological systems may prove useful in studying or substituting such proteins. Here, we explore the use of ssRNA tiles to build and modify filaments in vitro. We engineer a number of functionalities that are crucial to the function of natural proteins filaments into the ssRNA tiles, including the abilities to assemble or disassemble filaments, to tune the filament stiffness, to induce membrane binding, and to bind proteins. This work paves the way for building dynamic cytoskeleton-mimicking systems made out of rationally designed ssRNA tiles that can be transcribed in natural or synthetic cells.
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Affiliation(s)
- Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Baukje Hoogenberg
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Allard Katan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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3
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Ma X, Zhang Y, Huang K, Zhu L, Xu W. Multifunctional rolling circle transcription-based nanomaterials for advanced drug delivery. Biomaterials 2023; 301:122241. [PMID: 37451000 DOI: 10.1016/j.biomaterials.2023.122241] [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] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
As the up-and-comer in the development of RNA nanotechnology, RNA nanomaterials based on functionalized rolling circle transcription (RCT) have become promising carriers for drug production and delivery. This is due to RCT technology can self-produce polyvalent tandem nucleic acid prodrugs for intervention in intracellular gene expression and protein production. RNA component strands participating in de novo assembly enable RCT-based nanomaterials to exhibit good mechanical properties, biostability, and biocompatibility as delivery carriers. The biostability makes it to suitable for thermodynamically/kinetically favorable assembly, enzyme resistance and efficient expression in vivo. Controllable RCT system combined with polymers enables customizable and adjustable size, shape, structure, and stoichiometry of RNA building materials, which provide groundwork for the delivery of advanced drugs. Here, we review the assembly strategies and the dynamic regulation of RCT-based nanomaterials, summarize its functional properties referring to the bottom-up design philosophy, and describe its advancements in tumor gene therapy, synergistic chemotherapy, and immunotherapy. Last, we elaborate on the unique and practical value of RCT-based nanomaterials, namely "self-production and self-sale", and their potential challenges in nanotechnology, material science and biomedicine.
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Affiliation(s)
- Xuan Ma
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Kunlun Huang
- College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China.
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4
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Duan C, Chen Y, Hou Z, Li D, Jiao J, Sun W, Xiang Y. Heteromultivalent scaffolds fabricated by biomimetic co-assembly of DNA-RNA building blocks for the multi-analysis of miRNAs. J Mater Chem B 2023; 11:1478-1485. [PMID: 36723144 DOI: 10.1039/d2tb02663e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Heteromultivalent scaffolds with different repeated monomers have great potential in biomedicine, but convenient construction strategies for integrating various functional modules to achieve multiple biological functions are still lacking. Here, taking advantage of the heteromultivalent effect of dendritic nucleic acids and the specific biochemical properties of microRNAs (miRNAs), we assembled novel heteromultivalent nucleic acid scaffolds by biomimetic co-assembly of DNA-RNA building blocks. In our approach, two miRNAs were used to initiate and maintain dendritic structures in an interdependent manner; so, the heteromultivalent nanostructure can only form in the presence of both miRNAs. The proposed nanostructure can be used for one-step analysis of two miRNAs in an AND logic format. Taking miR-18b-5p and miR-342-3p which are associated with Alzheimer's disease as an example, a FRET sensing system was fabricated for the simultaneous analysis of two miRNAs within one hour at picomolar concentration. Further studies show that the designed device may have the potential to distinguish between AD patients and the healthy population by analysis of two miRNAs in CSF (cerebrospinal fluid) samples, suggesting its possible applicability in clinics.
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Affiliation(s)
- Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Yan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhiqiang Hou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Jin Jiao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P. R. China
| | - Weihao Sun
- Department of Geriatric Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China. .,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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5
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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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6
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Stewart JM, Subramanian HKK, Franco E. Assembly of RNA Nanostructures from Double-Crossover Tiles. Methods Mol Biol 2022; 2433:293-302. [PMID: 34985752 DOI: 10.1007/978-1-0716-1998-8_18] [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: 06/14/2023]
Abstract
Artificial self-assembling RNA scaffolds can be produced from many types of RNA motifs that are rationally designed. These scaffolds are of interest as nanoscale organizers, with applications in drug delivery and synthetic cells. Here we describe design strategies, production methods, and imaging of micrometer-sized RNA nanotubes and lattices that assemble from RNA tiles comprising multiple distinct strands.
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Affiliation(s)
- Jaimie Marie Stewart
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
| | | | - Elisa Franco
- Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA.
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7
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Chandrasekaran AR, Mathivanan J, Ebrahimi P, Vilcapoma J, Chen AA, Halvorsen K, Sheng J. Hybrid DNA/RNA nanostructures with 2'-5' linkages. NANOSCALE 2020; 12:21583-21590. [PMID: 33089274 PMCID: PMC7644649 DOI: 10.1039/d0nr05846g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nucleic acid nanostructures with different chemical compositions have shown utility in biological applications as they provide additional assembly parameters and enhanced stability. The naturally occurring 2'-5' linkage in RNA is thought to be a prebiotic analogue and has potential use in antisense therapeutics. Here, we report the first instance of DNA/RNA motifs containing 2'-5' linkages. We synthesized and incorporated RNA strands with 2'-5' linkages into different DNA motifs with varying number of branch points (a duplex, four arm junction, double crossover motif and tensegrity triangle motif). Using experimental characterization and molecular dynamics simulations, we show that hybrid DNA/RNA nanostructures can accommodate interspersed 2'-5' linkages with relatively minor effect on the formation of these structures. Further, the modified nanostructures showed improved resistance to ribonuclease cleavage, indicating their potential use in the construction of robust drug delivery vehicles with prolonged stability in physiological conditions.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
| | - Johnsi Mathivanan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Parisa Ebrahimi
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alan A. Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
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8
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Torelli E, Kozyra J, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami. ACS Synth Biol 2020; 9:1682-1692. [PMID: 32470289 DOI: 10.1021/acssynbio.0c00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in a high synthesis yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy, and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time. Our work suggests that the scaffolded origami technique is a viable, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Jerzy Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
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9
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Liu D, Geary CW, Chen G, Shao Y, Li M, Mao C, Andersen ES, Piccirilli JA, Rothemund PWK, Weizmann Y. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem 2020; 12:249-259. [PMID: 31959958 DOI: 10.1038/s41557-019-0406-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/06/2019] [Indexed: 01/31/2023]
Abstract
In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.
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Affiliation(s)
- Di Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cody W Geary
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA
| | - Gang Chen
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Ebbe S Andersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Paul W K Rothemund
- Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA.
| | - Yossi Weizmann
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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10
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Li G, Henry SA, Liu H, Kang TS, Nao SC, Zhao Y, Wu C, Jin J, Zhang JT, Leung CH, Wai Hong Chan P, Ma DL. A robust photoluminescence screening assay identifies uracil-DNA glycosylase inhibitors against prostate cancer. Chem Sci 2020; 11:1750-1760. [PMID: 34123270 PMCID: PMC8148385 DOI: 10.1039/c9sc05623h] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many cancers have developed resistance to 5-FU, due to removal by the enzyme uracil-DNA glycosylase (UDG), a type of base excision repair enzyme (BER) that can excise uracil and 5-fluorouracil (5-FU) from DNA. However, the development of UDG inhibitor screening methods, especially for the rapid and efficient screening of natural product/natural product-like compounds, is still limited so far. We developed herein a robust time-resolved photoluminescence method for screening UDG inhibitors, which could significantly improve sensitivity over the screening method based on the conventional steady-state spectroscopy, reducing the substantial fluorescence background interference. As a proof-of-concept, two potential UDG inhibitors were identified from a database of natural products and approved drugs. Co-treatment of these two compounds with 5-FU showed synergistic cytotoxicity, providing the basis for treating drug-resistant cancers. Overall, this method provides an avenue for the rapid screening of small molecule regulators of other BER enzyme activities that can avoid false negatives arising from the background fluorescence. The discovery of UDG inhibitors against prostate cancer by using a robust photoluminescence screening assay that can avoid false negatives arising from the background fluorescence.![]()
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Affiliation(s)
- Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | | | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Yichao Zhao
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Jianwen Jin
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Jia-Tong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Philip Wai Hong Chan
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK.,School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
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11
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Abstract
RNA is a functionally rich and diverse biomaterial responsible for regulating several cellular processes. This functionality has been harnessed to build predominately small nanoscale structures for drug delivery and the treatment of disease. The understanding of design principles to build large RNA structures will allow for further control of stoichiometry and spatial arrangement drugs and ligands. We present the design and characterization of RNA nanotubes that self-assemble from programmable monomers, or tiles, formed by five distinct RNA strands. Tiles include double crossover junctions and assemble via single-stranded sticky-end domains. We find that nanotube formation is dependent on the intertile crossover distance. The average length observed for the annealed RNA nanotubes is ≈1.5 μm, with many nanotubes exceeding 10 μm, enabling the characterization of RNA nanotubes length distribution via fluorescence microscopy. Assembled tubes were observed to be stable for more than 24 h, however post-annealing growth under isothermal conditions does not occur. Nanotubes assemble also from RNA tiles modified to include a single-stranded overhang (toehold), suggesting that it may be possible to decorate these large RNA scaffolds with nanoparticles or other nucleic acid molecules.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering , University of California at Riverside , Riverside , California 92521 , United States
| | - Cody Geary
- Department of Bioengineering , California Institute of Technology , Pasadena , California 91125 , United States
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus C 08000 , Denmark
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 92521 , United States
- Department of Mechanical and Aerospace Engineering , University of California , Los Angeles , California 90095 , United States
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12
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Kim J, Narayana A, Patel S, Sahay G. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides. Theranostics 2019; 9:3191-3212. [PMID: 31244949 PMCID: PMC6567962 DOI: 10.7150/thno.33921] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Cells utilize natural supramolecular assemblies to maintain homeostasis and biological functions. Naturally inspired modular assembly of biomaterials are now being exploited for understanding or manipulating cell biology for treatment, diagnosis, and detection of diseases. Supramolecular biomaterials, in particular peptides and oligonucleotides, can be precisely tuned to have diverse structural, mechanical, physicochemical and biological properties. These merits of oligonucleotides and peptides as building blocks have given rise to the evolution of numerous nucleic acid- and peptide-based self-assembling nanomaterials for various medical applications, including drug delivery, tissue engineering, regenerative medicine, and immunotherapy. In this review, we provide an extensive overview of the intracellular delivery approaches using supramolecular self-assembly of DNA, RNA, and peptides. Furthermore, we discuss the current challenges related to subcellular delivery and provide future perspectives of the application of supramolecular biomaterials for intracellular delivery in theranostics.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Ashwanikumar Narayana
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
- Department of Biomedical Engineering, Robertson Life Sciences Building, Oregon Health Science University, Portland, OR
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13
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Evolving methods for rational de novo design of functional RNA molecules. Methods 2019; 161:54-63. [PMID: 31059832 DOI: 10.1016/j.ymeth.2019.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022] Open
Abstract
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to experimental screening and selection pipelines. In this review, we describe methods common to many such computational approaches, thoroughly dissect these methods and highlight open questions for the individual steps. Initially, it is essential to investigate the biological target system, the regulatory mechanism that will be exploited, as well as the desired components in order to define design objectives. Subsequent computational design is needed to combine the selected components and to obtain novel functionality. This process can usually be split into constrained sequence sampling, the formulation of an optimization problem and an in silico analysis to narrow down the number of candidates with respect to secondary goals. Finally, experimental analysis is important to check whether the defined design objectives are indeed met in the target environment and detailed characterization experiments should be performed to improve the mechanistic models and detect missing design requirements.
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14
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Agarwal S, Franco E. Enzyme-Driven Assembly and Disassembly of Hybrid DNA-RNA Nanotubes. J Am Chem Soc 2019; 141:7831-7841. [PMID: 31042366 DOI: 10.1021/jacs.9b01550] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Living cells have the ability to control the dynamics of responsive assemblies such as the cytoskeleton by temporally activating and deactivating inert precursors. While DNA nanotechnology has demonstrated many synthetic supramolecular assemblies that rival biological ones in size and complexity, dynamic control of their formation is still challenging. Taking inspiration from nature, we developed a DNA-RNA nanotube system whose assembly and disassembly can be temporally controlled at physiological temperature using transcriptional programs. Nanotubes assemble when inert DNA monomers are directly and selectively activated by RNA molecules that become embedded in the structure, producing hybrid DNA-RNA assemblies. The reactions and molecular programs controlling nanotube formation are fueled by enzymes that produce or degrade RNA. We show that the speed of assembly and disassembly of the nanotubes can be controlled by tuning various reaction parameters in the transcriptional programs. We anticipate that these hybrid structures are a starting point to build integrated biological circuits and functional scaffolds inside natural and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid components on demand.
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Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
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15
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Abstract
In bacteria and archaea, small RNAs (sRNAs) regulate complex networks through antisense interactions with target mRNAs in trans, and riboswitches regulate gene expression in cis based on the ability to bind small-molecule ligands. Although our understanding and characterization of these two important regulatory RNA classes is far from complete, these RNA-based mechanisms have proven useful for a wide variety of synthetic biology applications. Besides classic and contemporary applications in the realm of metabolic engineering and orthogonal gene control, this review also covers newer applications of regulatory RNAs as biosensors, logic gates, and tools to determine RNA-RNA interactions. A separate section focuses on critical insights gained and challenges posed by fundamental studies of sRNAs and riboswitches that should aid future development of synthetic regulatory RNAs.
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16
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Ohno H, Akamine S, Saito H. RNA nanostructures and scaffolds for biotechnology applications. Curr Opin Biotechnol 2018; 58:53-61. [PMID: 30502620 DOI: 10.1016/j.copbio.2018.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/14/2018] [Indexed: 12/11/2022]
Abstract
RNA plays important roles in the regulation of gene expressions and other cellular functions. It functions as both as an informational carrier and a nanomachine due to its complementary base-pairing ability and complexed three-dimensional structure. Several nanostructures have been designed and constructed by exploiting these natural RNA properties. In this review, we will introduce the design principles of RNA nanostructures and their biotechnology applications as molecular scaffolds. RNA-based molecular scaffolds can control the accumulation and interaction of target proteins at nanometer-scale to regulate the function of bacterial and mammalian cells. Combining useful property of RNA as a nano-material and a molecular scaffold may provide us powerful tools in biological research, bioengineering, and future medicine.
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Affiliation(s)
- Hirohisa Ohno
- Center for iPS Cell Research and Application, Kyoto University, Kyoto City, Japan
| | - Sae Akamine
- Center for iPS Cell Research and Application, Kyoto University, Kyoto City, Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University, Kyoto City, Japan.
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17
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Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
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Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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18
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Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Sci Rep 2018; 8:6989. [PMID: 29725066 PMCID: PMC5934368 DOI: 10.1038/s41598-018-25270-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
| | - Jerzy Wieslaw Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom
| | - Jing-Ying Gu
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ulrich Stimming
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
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19
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Stewart JM, Viard M, Subramanian HKK, Roark BK, Afonin KA, Franco E. Correction: Programmable RNA microstructures for coordinated delivery of siRNAs. NANOSCALE 2017; 9:5019. [PMID: 28362443 DOI: 10.1039/c7nr90063e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Correction for 'Programmable RNA microstructures for coordinated delivery of siRNAs' by Jaimie Marie Stewart et al., Nanoscale, 2016, 8, 17542-17550.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
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