1
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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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2
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Graczyk A, Pawlowska R, Jedrzejczyk D, Chworos A. Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery. Molecules 2020; 25:E204. [PMID: 31947834 PMCID: PMC6982881 DOI: 10.3390/molecules25010204] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.
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Affiliation(s)
| | | | | | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (A.G.); (R.P.); (D.J.)
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3
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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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4
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Kim H, Lee E, Kang YY, Song J, Mok H, Lee JB. Enzymatically Produced miR34a Nanoparticles for Enhanced Antiproliferation Activity. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Eunju Lee
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Yoon Young Kang
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jihyun Song
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Hyejung Mok
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
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5
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Stewart JM, Subramanian HKK, Franco E. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res 2017; 45:5449-5457. [PMID: 28204562 PMCID: PMC5435959 DOI: 10.1093/nar/gkx063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/31/2017] [Indexed: 01/20/2023] Open
Abstract
Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
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6
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Stewart JM, Viard M, Subramanian HKK, Roark BK, Afonin KA, Franco E. Programmable RNA microstructures for coordinated delivery of siRNAs. NANOSCALE 2016; 8:17542-17550. [PMID: 27714127 PMCID: PMC5510167 DOI: 10.1039/c6nr05085a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
RNA is a natural multifunctional polymer, and is an essential component in both complex pathways and structures within the cellular environment. For this reason, artificial self-assembling RNA nanostructures are emerging as a powerful tool with broad applications in drug delivery and metabolic pathway regulation. To date, coordinated delivery of functional molecules via programmable RNA assemblies has been primarily done using nanosize RNA scaffolds. However, larger scaffolds could expand existing capabilities for spatial arrangement of ligands, and enable the controlled delivery of highly concentrated molecular loads. Here, we investigate whether micron-size RNA scaffolds can be assembled and further functionalized with different cargos (e.g. various siRNAs and fluorescent tags) for their synchronized delivery to diseased cells. Since known design approaches to build large RNA scaffolds are still underdeveloped, we apply a tiling method widely used in DNA nanotechnology. DNA tiles have been extensively used to build a variety of scalable and modular structures that are easily decorated with other ligands. Here, we adapt a double crossover (DX) DNA tile motif to design de novo DX RNA tiles that assemble and form lattices via programmed sticky end interactions. We optimize assembly protocols to guarantee high yield of RNA lattices. The resulting constructs are robust and modular with respect to the presence of distinct siRNAs and fluorophores. RNA tiles and lattices are successfully transfected in either human breast cancer or prostate cancer cells, where they efficiently knockdown the expression of target genes. Blood serum stability assays indicate that RNA lattices are more resilient to nuclease degradation when compared to individual tiles, thus making them better suited for therapeutic purposes. Overall, because of its design simplicity, we anticipate that this approach will be utilized for a wide range of applications in therapeutic RNA nanotechnology.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research, Inc., Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA 92521, USA.
| | - Brandon K Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA. and The Center for Biomedical Engineering and Science, 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. and The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Elisa Franco
- Department of Mechanical Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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7
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Jeong EH, Kim H, Jang B, Cho H, Ryu J, Kim B, Park Y, Kim J, Lee JB, Lee H. Technological development of structural DNA/RNA-based RNAi systems and their applications. Adv Drug Deliv Rev 2016; 104:29-43. [PMID: 26494399 DOI: 10.1016/j.addr.2015.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/04/2023]
Abstract
RNA interference (RNAi)-based gene therapy has drawn tremendous attention due to its highly specific gene regulation by selective degradation of any target mRNA. There have been multiple reports regarding the development of various cationic materials for efficient siRNA delivery, however, many studies still suffer from the conventional delivery problems such as suboptimal transfection performance, a lack of tissue specificity, and potential cytotoxicity. Despite the huge therapeutic potential of siRNAs, conventional gene carriers have failed to guarantee successful gene silencing in vivo, thus not warranting clinical trials. The relatively short double-stranded structure of siRNAs has resulted in uncompromising delivery formulations, as well as low transfection efficiency, compared with the conventional nucleic acid drugs such as plasmid DNAs. Recent developments in structural siRNA and RNAi nanotechnology have enabled more refined and reliable in vivo gene silencing with multiple advantages over naked siRNAs. This review focuses on recent progress in the development of structural DNA/RNA-based RNAi systems and their potential therapeutic applications. In addition, an extensive list of prior reports on various RNAi systems is provided and categorized by their distinctive molecular characters.
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8
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Qian GS, Kang B, Zhang ZL, Li XL, Zhao W, Xu JJ, Chen HY. Plasmonic nanohalo optical probes for highly sensitive imaging of survivin mRNA in living cells. Chem Commun (Camb) 2016; 52:11052-5. [DOI: 10.1039/c6cc02831d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strategy for sensitive detection of survivin mRNA based on Rayleigh light scattering spectroscopy of AuNP nanohalo probes.
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Affiliation(s)
- Guang-Sheng Qian
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Zhuo-Lei Zhang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Xiang-Ling Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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9
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Afonin K, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO, Shapiro BA. Multifunctional RNA nanoparticles. NANO LETTERS 2014; 14:5662-71. [PMID: 25267559 PMCID: PMC4189619 DOI: 10.1021/nl502385k] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/27/2014] [Indexed: 05/06/2023]
Abstract
Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA-DNA hybrids aimed to conditionally activate multiple split functionalities inside cells.
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Affiliation(s)
- Kirill
A. Afonin
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexey Y. Koyfman
- National
Center for Macromolecular Imaging, Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Angelica N. Martins
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland 21702, United
States
| | - Wojciech K. Kasprzak
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Martin Panigaj
- Food
and Drug Administration, Center for Biologics Evaluation and Research,
Office of Cellular, Tissue and Gene Therapies, Silver Spring, Maryland 20993, United States
| | - Ravi Desai
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Arti Santhanam
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wade W. Grabow
- Department
of Chemistry, Seattle Pacific University, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Biomolecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Eliahu Heldman
- Basic
Science Program, Leidos Biomedical Research,
Inc., NCI Center for Cancer Research, Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Jakob Reiser
- Food
and Drug Administration, Center for Biologics Evaluation and Research,
Office of Cellular, Tissue and Gene Therapies, Silver Spring, Maryland 20993, United States
| | - Wah Chiu
- National
Center for Macromolecular Imaging, Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Eric O. Freed
- HIV
Drug Resistance Program, National Cancer
Institute, Frederick, Maryland 21702, United
States
| | - Bruce A. Shapiro
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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10
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Braun GB, Friman T, Pang HB, Pallaoro A, de Mendoza TH, Willmore AMA, Kotamraju VR, Mann AP, She ZG, Sugahara KN, Reich NO, Teesalu T, Ruoslahti E. Etchable plasmonic nanoparticle probes to image and quantify cellular internalization. NATURE MATERIALS 2014; 13:904-11. [PMID: 24907927 PMCID: PMC4141013 DOI: 10.1038/nmat3982] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 04/14/2014] [Indexed: 04/14/2023]
Abstract
There is considerable interest in using nanoparticles as labels or to deliver drugs and other bioactive compounds to cells in vitro and in vivo. Fluorescent imaging, commonly used to study internalization and subcellular localization of nanoparticles, does not allow unequivocal distinction between cell surface-bound and internalized particles, as there is no methodology to turn particles 'off'. We have developed a simple technique to rapidly remove silver nanoparticles outside living cells, leaving only the internalized pool for imaging or quantification. The silver nanoparticle (AgNP) etching is based on the sensitivity of Ag to a hexacyanoferrate-thiosulphate redox-based destain solution. In demonstration of the technique we present a class of multicoloured plasmonic nanoprobes comprising dye-labelled AgNPs that are exceptionally bright and photostable, carry peptides as model targeting ligands, can be etched rapidly and with minimal toxicity in mice, and that show tumour uptake in vivo.
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Affiliation(s)
- Gary B. Braun
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106, USA
- Corresponding Authors: Correspondence should be addressed to: or
| | - Tomas Friman
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106, USA
| | - Hong-Bo Pang
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Alessia Pallaoro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | | - Anne-Mari A. Willmore
- Laboratory of Cancer Biology, Institute of Biomedicine, Centre of Excellence for Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Venkata Ramana Kotamraju
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106, USA
| | - Aman P. Mann
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Zhi-Gang She
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Kazuki N. Sugahara
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Norbert O. Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | - Tambet Teesalu
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106, USA
- Laboratory of Cancer Biology, Institute of Biomedicine, Centre of Excellence for Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Erkki Ruoslahti
- Cancer Research Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
- Center for Nanomedicine, Sanford-Burnham Medical Research Institute at University of California, Santa Barbara, CA 93106, USA
- Corresponding Authors: Correspondence should be addressed to: or
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11
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Abstract
CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such as the ribosome, large ribozymes, and riboswitches. Thus, the next step in synthetic RNA design will involve new ways to implement these same types of dynamic and responsive architectures into nanostructures functioning as real nanomachines in and outside the cell. RNA nanotechnology will likely garner broader utility and influence with a greater focus on the interplay between thermodynamic and kinetic influences on RNA self-assembly and using natural RNAs as guiding principles.
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Affiliation(s)
- Wade W. Grabow
- Department
of Chemistry and Biochemistry, Seattle Pacific University, 3307 Third
Avenue West, Seattle, Washington 98119, United States
| | - Luc Jaeger
- Department
of Chemistry and Biochemistry, Bio-Molecular Science and Engineering
Program, University of California, Santa Barbara, California 93106-9510, United States
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12
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Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat Commun 2014; 5:3890. [DOI: 10.1038/ncomms4890] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/15/2014] [Indexed: 02/08/2023] Open
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13
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Dey P, Blakey I, Thurecht KJ, Fredericks PM. Hyperbranched polymer-gold nanoparticle assemblies: role of polymer architecture in hybrid assembly formation and SERS activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:2249-2258. [PMID: 24548062 DOI: 10.1021/la4047462] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plasmonic gold nanoassemblies that self-assemble with the aid of linking molecules or polymers have the potential to yield controlled hierarchies of morphologies and consequently result in materials with tailored optical (e.g., localized surface plasmon resonances (LSPR)) and spectroscopic properties (e.g., surface-enhanced Raman scattering (SERS)). Molecular linkers that are structurally well-defined are promising for forming hybrid nanoassemblies which are stable in aqueous solution and are increasingly finding application in nanomedicine. Despite much ongoing research in this field, the precise role of molecular linkers in governing the morphology and properties of the hybrid nanoassemblies remains unclear. Previously we have demonstrated that branched linkers, such as hyperbranched polymers, with specific anchoring end groups can be successfully employed to form assemblies of gold NPs demonstrating near-infrared SPRs and intense SERS scattering. We herein introduce a tailored polymer as a versatile molecular linker, capable of manipulating nanoassembly morphologies and hot-spot density. In addition, this report explores the role of the polymeric linker architecture, specifically the degree of branching of the tailored polymer in determining the formation, morphology, and properties of the hybrid nanoassemblies. The degree of branching of the linker polymer, in addition to the concentration and number of anchoring groups, is observed to strongly influence the self-assembly process. The assembly morphology shifts primarily from 1D-like chains to 2D plates and finally to 3D-like globular structures, with increase in degree of branching of the macromolecular linker. Insights have been gained into how the morphology influences the SERS performance of these nanoassemblies with respect to hot-spot density. These findings supplement the understanding of the morphology determining nanoassembly formation and pave the way for the possible application of these nanoassemblies as SERS biosensors for medical diagnostics.
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Affiliation(s)
- Priyanka Dey
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology , Brisbane, Queensland 4001, Australia
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14
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Dey P, Zhu S, Thurecht KJ, Fredericks PM, Blakey I. Self assembly of plasmonic core–satellite nano-assemblies mediated by hyperbranched polymer linkers. J Mater Chem B 2014; 2:2827-2837. [DOI: 10.1039/c4tb00263f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The morphology of plasmonic nano-assemblies has a direct influence on optical properties, such as localised surface plasmon resonance (LSPR) and surface enhanced Raman scattering (SERS) intensity.
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Affiliation(s)
- Priyanka Dey
- School of Chemistry
- Physics and Mechanical Engineering
- Queensland University of Technology
- Brisbane, Australia
- Institute of Future Environments
| | - Shaoli Zhu
- Australian Institute of Bioengineering and Nanotechnology
- University of Queensland
- St. Lucia, Australia
| | - Kristofer J. Thurecht
- Australian Institute of Bioengineering and Nanotechnology
- University of Queensland
- St. Lucia, Australia
- Centre for Advanced Imaging
- University of Queensland
| | - Peter M. Fredericks
- School of Chemistry
- Physics and Mechanical Engineering
- Queensland University of Technology
- Brisbane, Australia
- Institute of Future Environments
| | - Idriss Blakey
- Australian Institute of Bioengineering and Nanotechnology
- University of Queensland
- St. Lucia, Australia
- Centre for Advanced Imaging
- University of Queensland
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15
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Grabow WW, Zhuang Z, Swank ZN, Shea JE, Jaeger L. The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns. J Mol Biol 2012; 424:54-67. [PMID: 22999957 DOI: 10.1016/j.jmb.2012.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 12/16/2022]
Abstract
The right angle (RA) motif, previously identified in the ribosome and used as a structural module for nano-construction, is a recurrent structural motif of 13 nucleotides that establishes a 90° bend between two adjacent helices. Comparative sequence analysis was used to explore the sequence space of the RA motif within ribosomal RNAs in order to define its canonical sequence space signature. We investigated the sequence constraints associated with the RA signature using several artificial self-assembly systems. Thermodynamic and topological investigations of sequence variants associated with the RA motif in both minimal and expanded structural contexts reveal that the presence of a helix at the 3' end of the RA motif increases the thermodynamic stability and rigidity of the resulting three-helix junction domain. A search for the RA in naturally occurring RNAs as well as its experimental characterization led to the identification of the RA in groups IC1 and ID intron ribozymes, where it is suggested to play an integral role in stabilizing peripheral structural domains. The present study exemplifies the need of empirical analysis of RNA structural motifs for facilitating the rational design and structure prediction of RNAs.
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Affiliation(s)
- Wade W Grabow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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16
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Kim T, Shapiro BA. The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures. J Biomol Struct Dyn 2012; 31:495-510. [PMID: 22881341 DOI: 10.1080/07391102.2012.706072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The subtype-B monomers of the human immunodeficiency virus type-1 (HIV-1) have experimentally been shown to dimerize at high salt concentration or in the presence of magnesium, while the dimerization of the subtype-A monomers requires magnesium binding at the G273 or G274 phosphate groups regardless of salt concentration. We used explicit solvent molecular dynamics (MD) simulations to investigate the conformational changes in subtype-A and -B monomers in different salt concentrations, and we found that our MD simulation results are consistent with those of experiments. At low salt concentration, hairpin loop structures of both subtypes were deformed and bases in the hairpin loop were turned inside. At high salt concentrations, the subtype-B monomer maintained the hairpin loop shape and most bases in the hairpin loop pointed out, while the subtype-A monomer showed a severe deformation. We also found that the flanking bases in the subtype-B stabilize the hairpin loop, while the flanking base G273 in the subtype-A caused a significant deformation. However, a bound magnesium ion at the G273 or G274 phosphate groups controlled the behavior of the G273 base and prevented the subtype-A monomer from deformation. We also applied restraints to both subtypes to examine the role of high salt concentration or magnesium binding. While restraints were applied, both subtypes at 0 M salt concentration maintained their shapes. However, when restraints were removed, they deformed significantly. Therefore, we suggest that the dimerization of both subtypes requires the proper conformation of the monomers which is induced by the appropriate salt strength and magnesium ion binding.
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Affiliation(s)
- Taejin Kim
- Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick , MD 20872, USA
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17
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Bida JP, Das R. Squaring theory with practice in RNA design. Curr Opin Struct Biol 2012; 22:457-66. [PMID: 22832174 DOI: 10.1016/j.sbi.2012.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/20/2012] [Indexed: 11/26/2022]
Abstract
Ribonucleic acid (RNA) design offers unique opportunities for engineering genetic networks and nanostructures that self-assemble within living cells. Recent years have seen the creation of increasingly complex RNA devices, including proof-of-concept applications for in vivo three-dimensional scaffolding, imaging, computing, and control of biological behaviors. Expert intuition and simple design rules--the stability of double helices, the modularity of noncanonical RNA motifs, and geometric closure--have enabled these successful applications. Going beyond heuristics, emerging algorithms may enable automated design of RNAs with nucleotide-level accuracy but, as illustrated on a recent RNA square design, are not yet fully predictive. Looking ahead, technological advances in RNA synthesis and interrogation are poised to radically accelerate the discovery and stringent testing of design methods.
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Affiliation(s)
- J P Bida
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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18
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Li H, LaBean TH, Leong KW. Nucleic acid-based nanoengineering: novel structures for biomedical applications. Interface Focus 2011; 1:702-24. [PMID: 23050076 PMCID: PMC3262286 DOI: 10.1098/rsfs.2011.0040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 01/21/2023] Open
Abstract
Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.
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Affiliation(s)
| | | | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall, PO Box 90281, Durham, NC 27708, USA
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19
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Saha K, Bajaj A, Duncan B, Rotello VM. Beauty is skin deep: a surface monolayer perspective on nanoparticle interactions with cells and bio-macromolecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1903-18. [PMID: 21671432 PMCID: PMC3516997 DOI: 10.1002/smll.201100478] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Indexed: 05/24/2023]
Abstract
Surface recognition of biosystems is a critical component in the development of novel biosensors and delivery vehicles, and for the therapeutic regulation of biological processes. Monolayer-protected nanoparticles present a highly versatile scaffold for selective interaction with bio-macromolecules and cells. Through the engineering of the monolayer surface, nanoparticles can be tailored for surface recognition of biomolecules and cells. This review highlights recent progress in nanoparticle-bio-macromolecule/cellular interactions, emphasizing the effect of the surface monolayer structure on the interactions with proteins, DNA, and cell surfaces. The extension of these tailored interactions to hybrid nanomaterials, biosensing platforms, and delivery vehicles is also discussed.
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Affiliation(s)
- Krishnendu Saha
- Department of Chemistry, University of Massachusetts Amherst 710 North Pleasant Street, Amherst, MA 01003
| | - Avinash Bajaj
- Department of Chemistry, University of Massachusetts Amherst 710 North Pleasant Street, Amherst, MA 01003
- Regional Centre for Biotechnology, 180 Udyog Vihar Phase 1, Gurgaon-122016, Haryana, India
| | - Bradley Duncan
- Department of Chemistry, University of Massachusetts Amherst 710 North Pleasant Street, Amherst, MA 01003
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst 710 North Pleasant Street, Amherst, MA 01003
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20
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Kasprzak W, Bindewald E, Kim TJ, Jaeger L, Shapiro BA. Use of RNA structure flexibility data in nanostructure modeling. Methods 2011; 54:239-50. [PMID: 21163354 PMCID: PMC3107926 DOI: 10.1016/j.ymeth.2010.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 01/15/2023] Open
Abstract
In the emerging field of RNA-based nanotechnology there is a need for automation of the structure design process. Our goal is to develop computer methods for aiding in this process. Towards that end, we created the RNA junction database, which is a repository of RNA junctions, i.e. internal, multi-branch and kissing loops with emanating stem stubs, extracted from the larger RNA structures stored in the PDB database. These junctions can be used as building blocks for nanostructures. Two programs developed in our laboratory, NanoTiler and RNA2D3D, can combine such building blocks with idealized fragments of A-form helices to produce desired 3D nanostructures. Initially, the building blocks are treated as rigid objects and the resulting geometry is tested against the design objectives. Experimental data, however, shows that RNA accommodates its shape to the constraints of larger structural contexts. Therefore we are adding analysis of the flexibility of our building blocks to the full design process. Here we present an example of RNA-based nanostructure design, putting emphasis on the need to characterize the structural flexibility of the building blocks to induce ring closure in the automated exploration. We focus on the use of kissing loops (KL) in nanostructure design, since they have been shown to play an important role in RNA self-assembly. By using an experimentally proven system, the RNA tectosquare, we show that considering the flexibility of the KLs as well as distortions of helical regions may be necessary to achieve a realistic design.
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Affiliation(s)
- Wojciech Kasprzak
- Basic Science Program, SAIC-Frederick, Inc., NCI at Frederick, Frederick, MD 21702, United States
| | - Eckart Bindewald
- Basic Science Program, SAIC-Frederick, Inc., NCI at Frederick, Frederick, MD 21702, United States
| | - Tae-Jin Kim
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Luc Jaeger
- Chemistry and Biochemistry Department, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, MD 21702, United States
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21
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Gu X, Schroeder SJ. Different sequences show similar quaternary interaction stabilities in prohead viral RNA self-assembly. J Biol Chem 2011; 286:14419-26. [PMID: 21349846 DOI: 10.1074/jbc.m110.191064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prohead RNA (pRNA) is an essential component of the self-assembling ϕ29 bacteriophage DNA packaging motor. Different related species of bacteriophage share only 12% similarity in pRNA sequences. The secondary structure for pRNA is conserved, however. In this study, we present evidence for self-assembly in different pRNA sequences and new measurements of the energetics for the quaternary interactions in pRNA dimers and trimers. The energetics for self-assembly in different pRNA sequences are similar despite very different sequences in the loop-loop interactions. The architecture surrounding the interlocking loops contributes to the stability of the pRNA quaternary interactions, and sequence variation outside the interlocking loops may counterbalance the changes in the loop sequences. Thus, the evolutionary divergence of pRNA sequences maintains not only conservation of function and secondary structure but also stabilities of quaternary interactions. The self-assembly of pRNA can be fine-tuned with variations in magnesium chloride, sodium chloride, temperature, and concentration. The ability to control pRNA self-assembly holds promise for the development of nanoparticle therapeutic applications for this biological molecule. The pRNA system is well suited for future studies to further understand the energetics of RNA tertiary and quaternary interactions, which can provide insight into larger biological assemblies such as viruses and biomolecular motors.
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Affiliation(s)
- Xiaobo Gu
- Department of Chemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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22
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Abstract
Like DNA, RNA can be designed and manipulated to produce a variety of different nanostructures. Moreover, RNA has a flexible structure and possesses catalytic functions that are similar to proteins. Although RNA nanotechnology resembles DNA nanotechnology in many ways, the base-pairing rules for constructing nanoparticles are different. The large variety of loops and motifs found in RNA allows it to fold into numerous complicated structures, and this diversity provides a platform for identifying viable building blocks for various applications. The thermal stability of RNA also allows the production of multivalent nanostructures with defined stoichiometry. Here we review techniques for constructing RNA nanoparticles from different building blocks, we describe the distinct attributes of RNA inside the body, and discuss potential applications of RNA nanostructures in medicine. We also offer some perspectives on the yield and cost of RNA production.
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Affiliation(s)
- Peixuan Guo
- Nanobiomedical Center, College of Engineering and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45221, USA.
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23
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Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, Shapiro BA, Jaeger L. In vitro assembly of cubic RNA-based scaffolds designed in silico. NATURE NANOTECHNOLOGY 2010; 5:676-82. [PMID: 20802494 PMCID: PMC2934861 DOI: 10.1038/nnano.2010.160] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 07/09/2010] [Indexed: 05/19/2023]
Abstract
The organization of biological materials into versatile three-dimensional assemblies could be used to build multifunctional therapeutic scaffolds for use in nanomedicine. Here, we report a strategy to design three-dimensional nanoscale scaffolds that can be self-assembled from RNA with precise control over their shape, size and composition. These cubic nanoscaffolds are only approximately 13 nm in diameter and are composed of short oligonucleotides, making them amenable to chemical synthesis, point modifications and further functionalization. Nanocube assembly is verified by gel assays, dynamic light scattering and cryogenic electron microscopy. Formation of functional RNA nanocubes is also demonstrated by incorporation of a light-up fluorescent RNA aptamer that is optimally active only upon full RNA assembly. Moreover, we show that the RNA nanoscaffolds can self-assemble in isothermal conditions (37 degrees C) during in vitro transcription, which opens a route towards the construction of sensors, programmable packaging and cargo delivery systems for biomedical applications.
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Affiliation(s)
- Kirill A Afonin
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Eckart Bindewald
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Alan J. Yaghoubian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Neil Voss
- Automated Molecular Imaging Group, Dept. of Cell Biology, The Scripps Research Institute, MC CB129, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Erica Jacovetty
- Automated Molecular Imaging Group, Dept. of Cell Biology, The Scripps Research Institute, MC CB129, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | | | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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24
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Abstract
Supra-molecular assembly is a powerful strategy used by nature for building nano-scale architectures with predefined sizes and shapes. Numerous challenges remain however to be solved in order to demonstrate precise control over the synthesis, folding and assembly of rationally designed three-dimensional (3D) nano-objects made of RNA. Using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular 3D particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs to build thermostable 3D nano-architectures that do not rely on helix bundles or tensegrity. RNA 3D particles can potentially be used as carriers or scaffolds in nano-medicine and synthetic biology.
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25
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Abstract
Stable RNAs are modular and hierarchical three-dimensional (3D) architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions (1, 2). Using comparative sequence and structural analysis of known X-ray structures of RNAs, folding and assembly principles of RNA can presently be gathered to generate the syntax of a proto-language for rational design and prediction of RNA 3D shapes. RNA architectonics refers to the deciphering of this proto-language and to its use to build new functional RNA shapes with self-assembly properties (3-5). This approach can therefore contribute to the prediction and rational design of RNA tertiary structures for potential applications in nanotechnology, synthetic biology and medicine.
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Affiliation(s)
- Luc Jaeger
- Chemistry and Biochemistry Department, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
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26
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Abstract
Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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27
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Koyfman AY, Braun GB, Reich NO. Cell-targeted self-assembled DNA nanostructures. J Am Chem Soc 2009; 131:14237-9. [PMID: 19754205 DOI: 10.1021/ja9015638] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present two strategies for attaching self-assembled DNA arrays to the surfaces of cells. Our first approach uses biotin-streptavidin interactions to bind DNA architectures to biotinylated cells. The second approach takes advantage of specific antibody-cell surface interactions, conjugated arrays and the subsequent binding to native epidermal growth factor receptors expressed on cancer cells. DNA array-cell surface interactions were visualized by fluorescence, confocal microscopy, and scanning electron microscopy. This novel application of DNA nanoarrays provides strategies to specifically label cell surfaces with micrometer-sized patches, bind cells onto a designed functionalized DNA scaffold, engineer cell/cell networks into microtissues, and deliver materials to cell surfaces.
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Affiliation(s)
- Alexey Y Koyfman
- Biomolecular Science and Engineering Program, University of California-Santa Barbara, Santa Barbara, California 93106-9510, USA
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28
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Severcan I, Geary C, Verzemnieks E, Chworos A, Jaeger L. Square-shaped RNA particles from different RNA folds. NANO LETTERS 2009; 9:1270-7. [PMID: 19239258 PMCID: PMC2664548 DOI: 10.1021/nl900261h] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The structural information encoding specific conformations of natural RNAs can be implemented within artificial RNA sequences to control both three-dimensional (3D) shape and self-assembling interfaces for nanotechnology and synthetic biology applications. We have identified three natural RNA motifs known to direct helical topology into approximately 90 degrees bends: a five-way tRNA junction, a three-way junction, and a two-helix bend. These three motifs, embedded within rationally designed RNAs (tectoRNA), were chosen for generating square-shaped tetrameric RNA nanoparticles. The ability of each motif to direct the formation of supramolecular assemblies was compared by both native gel assays and atomic force microscopy. While there are multiple structural solutions for building square-shaped RNA particles, differences in the thermodynamics and molecular dynamics of the 90 degrees motif can lead to different biophysical behaviors for the resulting supramolecular complexes. We demonstrate via structural assembly programming how the different 90 degrees motifs can preferentially direct the formation of either 2D or 3D assemblies.
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Affiliation(s)
- Isil Severcan
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Cody Geary
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Erik Verzemnieks
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Arkadiusz Chworos
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
- To whom correspondence should be addressed: Phone: 805-893-3628; Fax: 805-893-4120; Email;
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29
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Shindel MM, Mohraz A, Mumm DR, Wang SW. Modulating colloidal adsorption on a two-dimensional protein crystal. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1038-1046. [PMID: 19099535 DOI: 10.1021/la802911p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The geometric and physicochemical properties of the protein streptavidin make it a useful building block in the construction and manipulation of nanoscale structures and devices. However, one requirement in exploiting streptavidin for "bottom-up" assembly is the capability to modulate protein-nanoparticle interactions. This work examines the effects of pH and the biotin-streptavidin interaction on the adsorption of colloidal gold onto a two-dimensional streptavidin crystal. Particle deposition was carried out below (pH 6), at (pH 7), and above (pH 8) the protein's isoelectric point with both biotinylated and nonbiotinylated nanoparticles. Particle surface coverage depends on deposition time and pH, and increases by 1.4-10 times when biotin is incorporated onto the particle surface. This coverage is highest for both particle types at pH 6 and decreases monotonically with increasing pH. Calculations of interparticle potentials based on Derjaguin-Landau-Verwey-Overbeek (DLVO) theory demonstrate that this trend in surface coverage is most likely due to alterations in particle-surface electrostatic interactions and not a result of changes in interparticle electrostatic repulsion. Furthermore, post-adsorption alterations in pH demonstrate that electrostatically adsorbed particles can be selectively desorbed from the surface. Evaluation of the nonspecifically adsorbed fraction of biotinylated particles indicates that the receptor-ligand adsorption mechanism gives a higher rate of attachment to the substrate than nonspecific, electrostatic adsorption. This results in faster adsorption kinetics and higher coverages for biotinylated particles relative to the nonbiotinylated case.
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Affiliation(s)
- Matthew M Shindel
- Department of Chemical Engineering and Materials Science, University of California, Irvine, California 92697-2575, USA
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30
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Koyfman AY, Magonov SN, Reich NO. Self-assembly of DNA arrays into multilayer stacks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1091-1096. [PMID: 19177652 DOI: 10.1021/la801306j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We describe the self-assembly of multilayer hexagonal DNA arrays through highly regular interlayer packing. Slow cooling of a mixture of three single-stranded DNA sequences with various Mg2+ concentrations leads to the self-assembly of diverse multilayer architectures. The self-assembled aggregates were deposited onto mica surfaces and examined with atomic force microscopy. The size of the two-dimensional arrays and subsequent stacking to form multilayer structures are highly dependent on Mg2+ concentration. DNA bilayers and multilayers of defined shape are favored in 2-5 mM Mg2+ with an average lateral size of 700 nm. Arrays are much larger (up to 20 microm across) in 10-15 mM Mg2+, although multiple layers still make up 20-60% of the observed structures. Domains within single layer architectures were identified using Moiré pattern analysis. Distinct structural phases within the multilayer assemblies include two layers translated by 17.5 nm and interlayer rotations of 20 degrees and 30 degrees. Three layer assemblies have cubic close packing and taller multilayer architectures of 2D DNA sheets were also identified.
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Affiliation(s)
- Alexey Y Koyfman
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California - Santa Barbara, Santa Barbara, California 93106-9510, USA
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31
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Fischler M, Homberger M, Simon U. DNA-Mediated Assembly of Metal Nanoparticles: Fabrication, Structural Features, and Electrical Properties. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-0-387-09459-5_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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32
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Ray PC, Yu H, Fu PP. Toxicity and environmental risks of nanomaterials: challenges and future needs. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2009; 27:1-35. [PMID: 19204862 PMCID: PMC2844666 DOI: 10.1080/10590500802708267] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nanotechnology has gained a great deal of public interest because of the needs and applications of nanomaterials in many areas of human endeavors including industry, agriculture, business, medicine, and public health. Environmental exposure to nanomaterials is inevitable as nanomaterials become part of our daily life, and, as a result, nanotoxicity research is gaining attention. This review presents a summary of recent research efforts on fate, behavior, and toxicity of different classes of nanomaterials in the environment. A critical evaluation of challenges and future needs for the safe environmental nanotechnology are discussed.
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Affiliation(s)
- Paresh Chandra Ray
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA.
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33
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Jaeger L, Verzemnieks EJ, Geary C. The UA_handle: a versatile submotif in stable RNA architectures. Nucleic Acids Res 2008; 37:215-30. [PMID: 19036788 PMCID: PMC2615604 DOI: 10.1093/nar/gkn911] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5'XU/AN(n)X3'). It consists of a U:A Watson-Crick: Hoogsteen trans base pair stacked over a classic Watson-Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.
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Affiliation(s)
- Luc Jaeger
- Chemistry and Biochemistry Department, University of California, Santa Barbara, CA 93106-9510, USA.
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34
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Shapiro BA, Bindewald E, Kasprzak W, Yingling Y. Protocols for the in silico design of RNA nanostructures. Methods Mol Biol 2008; 474:93-115. [PMID: 19031063 DOI: 10.1007/978-1-59745-480-3_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Recent developments in the field of nanobiology have significantly expanded the possibilities for new modalities in the treatment of many diseases, including cancer. Ribonucleic acid (RNA) represents a relatively new molecular material for the development of these biologically oriented nanodevices. In addition, RNA nanobiology presents a relatively new approach for the development of RNA-based nanoparticles that can be used as crystallization substrates and scaffolds for RNA-based nanoarrays. Presented in this chapter are some methodological shaped-based protocols for the design of such RNA nanostructures. Included are descriptions and background materials describing protocols that use a database of three-dimensional RNA structure motifs; designed RNA secondary structure motifs; and a combination of the two approaches. An example is also given illustrating one of the protocols.
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Affiliation(s)
- Bruce A Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD, USA
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Shen Z, Yamada M, Miyake M. Control of Stripelike and Hexagonal Self-Assembly of Gold Nanoparticles by the Tuning of Interactions between Triphenylene Ligands. J Am Chem Soc 2007; 129:14271-80. [DOI: 10.1021/ja073518c] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhongrong Shen
- Contribution from the School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1, Asahidai, Nomi-shi, Ishikawa, 923-1292, Japan, and PRESTO/Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Mami Yamada
- Contribution from the School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1, Asahidai, Nomi-shi, Ishikawa, 923-1292, Japan, and PRESTO/Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Mikio Miyake
- Contribution from the School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1, Asahidai, Nomi-shi, Ishikawa, 923-1292, Japan, and PRESTO/Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
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Yingling YG, Shapiro BA. Computational design of an RNA hexagonal nanoring and an RNA nanotube. NANO LETTERS 2007; 7:2328-34. [PMID: 17616164 DOI: 10.1021/nl070984r] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The combination of computer modeling, RNA structure versatility, and siRNA function can be efficiently used to design an all-RNA nanoparticle capable of siRNA delivery. Here, we present a computational design of an RNA nanoring and a nanotube. An RNA nanoring consists of six simple linear building blocks that are assembled together via known noncovalent loop-loop contacts based on RNAI/RNAII inverse sequences. The helical sequences of the building blocks can include siRNAs for drug delivery.
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Affiliation(s)
- Yaroslava G Yingling
- Center for Cancer Research Nanobiology Program, National Cancer Institute, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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Affiliation(s)
- Jennifer A Dahl
- Department of Chemistry and Materials Science Institute, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403, USA
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Liu HG, Xiao F, Wang CW, Xue Q, Chen X, Lee YI, Hao J, Jiang J. Synthesis of one-dimensional silver oxide nanoparticle arrays and silver nanorods templated by Langmuir monolayers. J Colloid Interface Sci 2007; 314:297-303. [PMID: 17570381 DOI: 10.1016/j.jcis.2007.05.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 05/02/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
One-dimensional (1D) silver oxide nanoparticle arrays were synthesized by illuminating the composite Langmuir-Blodgett monolayers of porphyrin derivatives/Ag(+) and n-hexadecyl dihydrogen phosphate (n-HDP)/Ag(+) deposited on carbon-coated copper grids with daylight and then exposing them to air. Transmission electron microscopy (TEM) observation shows that the nanoparticle size is around 3 nm, with the separation of about 2-3 nm. High-resolution TEM (HRTEM) investigation indicates that the particles are made up of Ag(2)O. Ag nanorods with the width of 15-35 nm and the length of several hundreds of nanometers were synthesized by irradiating the composite Langmuir monolayers of porphyrin derivatives/Ag(+) and n-HDP/Ag(+) by UV-light directly at the air/water interface at room temperature. HRTEM image and selected-area electron diffraction (SAED) pattern indicate that the nanorods are single crystals with the (110) face of the face-centered cubic (fcc) silver parallel to the air/water interface. The formation of the 1D arrays and the nanorods should be attributed to the templating effect of the linear supramolecules formed by porphyrin derivative or n-HDP molecules in Langmuir monolayers through non-covalent interactions.
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Affiliation(s)
- Hong-Guo Liu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, Jinan 250100, China.
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van Herrikhuyzen J, George SJ, Vos MRJ, Sommerdijk NAJM, Ajayaghosh A, Meskers SCJ, Schenning APHJ. Self-Assembled Hybrid Oligo(p-phenylenevinylene)–Gold Nanoparticle Tapes. Angew Chem Int Ed Engl 2007; 46:1825-8. [PMID: 17450609 DOI: 10.1002/anie.200604225] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jeroen van Herrikhuyzen
- Laboratory for Macromolecular and Organic Chemistry, Eindhoven University of Technology, PO Box 513, 5600MB Eindhoven, The Netherlands
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van Herrikhuyzen J, George S, Vos M, Sommerdijk N, Ajayaghosh A, Meskers S, Schenning A. Self-Assembled Hybrid Oligo(p-phenylenevinylene)–Gold Nanoparticle Tapes. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604225] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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He Y, Tian Y, Ribbe AE, Mao C. Highly connected two-dimensional crystals of DNA six-point-stars. J Am Chem Soc 2007; 128:15978-9. [PMID: 17165718 DOI: 10.1021/ja0665141] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper reports a novel DNA six-point-star motif assembled from only three different DNA single-strands. This motif readily assembles into hexagonal two-dimensional arrays with high connectivity. Such a high connectivity could potentially improve the array stability.
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Affiliation(s)
- Yu He
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Abstract
Beyond its biological importance, short DNA sequences are of increasing interest as excellent and versatile building blocks, in material science and nanotechnology. DNA nanotechnology has been rapidly developed and has branched into several significantly different directions. Controlling DNA nanostructures is one of the most important branches, in which well-defined static nanostructures are constructed from rationally designed DNA motifs. The diversity and complexity of such DNA nanostructures also endow them with promising applications in nanofabrications, nanoelectronics, biodiagnostics, and DNA computations. In this review, we will summarize our recent efforts in this direction.
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Affiliation(s)
- Yu He
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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Patterning Metallic Nanoparticles by DNA Scaffolds. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 620:107-16. [DOI: 10.1007/978-0-387-76713-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Jaeger L, Chworos A. The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol 2006; 16:531-43. [PMID: 16843653 DOI: 10.1016/j.sbi.2006.07.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 06/14/2006] [Accepted: 07/04/2006] [Indexed: 11/30/2022]
Abstract
The past several years have witnessed the emergence of a new world of nucleic-acid-based architectures with highly predictable and programmable self-assembly properties. For almost two decades, DNA has been the primary material for nucleic acid nanoconstruction. More recently, the dramatic increase in RNA structural information led to the development of RNA architectonics, the scientific study of the principles of RNA architecture with the aim of constructing RNA nanostructures of any arbitrary size and shape. The remarkable modularity and the distinct but complementary nature of RNA and DNA nanomaterials are revealed by the various self-assembly strategies that aim to achieve control of the arrangement of matter at a nanoscale level.
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Affiliation(s)
- Luc Jaeger
- Department of Chemistry and Biochemistry, Material Research Laboratory, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
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Zhan C, Léger JM, Huc I. Cross-Hybridization of Pyridinedicarboxamide Helical Strands and TheirN-Oxides. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600785] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhan C, Léger JM, Huc I. Cross-Hybridization of Pyridinedicarboxamide Helical Strands and TheirN-Oxides. Angew Chem Int Ed Engl 2006; 45:4625-8. [PMID: 16789035 DOI: 10.1002/anie.200600785] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chuanlang Zhan
- Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
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Abstract
DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.
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Affiliation(s)
- Udo Feldkamp
- Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Universität Dortmund, Germany.
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Abstract
Fundamental control over supra-molecular self-assembly for organization of matter on the nano-scale is a major objective of nanoscience and nanotechnology. 'RNA tectonics' is the design of modular RNA units, called tectoRNAs, that can be programmed to self-assemble into novel nano- and meso-scopic architectures of desired size and shape. We report the three-dimensional design of tectoRNAs incorporating modular 4-way junction (4WJ) motifs, hairpin loops and their cognate loop-receptors to create extended, programmable interaction interfaces. Specific and directional RNA-RNA interactions at these interfaces enable conformational, topological and orientational control of tectoRNA self-assembly. The interacting motifs are precisely positioned within the helical arms of the 4WJ to program assembly from only one helical stacking conformation of the 4WJ. TectoRNAs programmed to assemble with orientational compensation produce micrometer-scale RNA filaments through supra-molecular equilibrium polymerization. As visualized by transmission electron microscopy, these RNA filaments resemble actin filaments from the protein world. This work emphasizes the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins.
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Affiliation(s)
- Lorena Nasalean
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Stéphanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State UniversityOH 43402, USA
- Center for Biomolecular Sciences, Bowling Green State UniversityOH 43402, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, Material Research Laboratory, University of CaliforniaSanta Barbara, CA 93106-9510, USA
- To whom correspondence should be addressed. Tel: +1 805 893 3628; Fax: +1 805 893 4210;
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You CC, Verma A, Rotello VM. Engineering the nanoparticle-biomacromolecule interface. SOFT MATTER 2006; 2:190-204. [PMID: 32646145 DOI: 10.1039/b517354j] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Monolayer-protected nanoparticles feature tunable size, surface functionality and core material, providing scaffolds for targeting biomacromolecules. This review highlights recent advances in nanoparticle-biomacromolecule interactions, focusing on two key areas: (1) The modulation of structure and function of biomacromolecules through engineered interactions with nanoparticle surfaces; (2) The use of biomacromolecules as building blocks for nanostructured materials.
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Affiliation(s)
- Chang-Cheng You
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA.
| | - Ayush Verma
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA.
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA.
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