1
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Schaffter SW, Kengmana E, Fern J, Byrne SR, Schulman R. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synth Biol 2024. [PMID: 38885464 DOI: 10.1021/acssynbio.3c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Bacteriophage RNA polymerases, in particular T7 RNA polymerase (RNAP), are well-characterized and popular enzymes for many RNA applications in biotechnology both in vitro and in cellular settings. These monomeric polymerases are relatively inexpensive and have high transcription rates and processivity to quickly produce large quantities of RNA. T7 RNAP also has high promoter-specificity on double-stranded DNA (dsDNA) such that it only initiates transcription downstream of its 17-base promoter site on dsDNA templates. However, there are many promoter-independent T7 RNAP transcription reactions involving transcription initiation in regions of single-stranded DNA (ssDNA) that have been reported and characterized. These promoter-independent transcription reactions are important to consider when using T7 RNAP transcriptional systems for DNA nanotechnology and DNA computing applications, in which ssDNA domains often stabilize, organize, and functionalize DNA nanostructures and facilitate strand displacement reactions. Here we review the existing literature on promoter-independent transcription by bacteriophage RNA polymerases with a specific focus on T7 RNAP, and provide examples of how promoter-independent reactions can disrupt the functionality of DNA strand displacement circuit components and alter the stability and functionality of DNA-based materials. We then highlight design strategies for DNA nanotechnology applications that can mitigate the effects of promoter-independent T7 RNAP transcription. The design strategies we present should have an immediate impact by increasing the rate of success of using T7 RNAP for applications in DNA nanotechnology and DNA computing.
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Affiliation(s)
- Samuel W Schaffter
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eli Kengmana
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joshua Fern
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shane R Byrne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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2
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Zhang S, Zhou N, Chen J, Li Q, Wang Y, Sun W, Lv C. DNA Polymerase-Endonuclease Efficiently Synthesizes DNA to Prepare DNA Materials and Develop Novel Signal Amplification System. Anal Chem 2024; 96:9285-9293. [PMID: 38768388 DOI: 10.1021/acs.analchem.4c01964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
DNA biosynthesis, a focus of fundamental and applied research, typically involves DNA polymerases by using templates, primers, and dNTPs. Some polymerases can polymerize dNTPs for DNA de novo synthesis, although this is generally to occur randomly. This novel synthesis method has garnered our attention and practical use. Herein, we observed that the addition of endonuclease significantly enhances the efficiency of the de novo synthesis reaction catalyzed by the DNA polymerase. We further investigated the reaction conditions that influence this efficiency. Building on the optimal reaction conditions, we developed a rapid and efficient strategy for preparing DNA hydrogel. Further, coupled with the CRISPR-Cas system, we developed a nucleic acid signal amplification system characterized by versatility, sensitivity, specificity, and no risk of aerosol contamination. We successfully detected viral nucleic acids in clinical samples. In summary, our study demonstrates the significant potential of DNA polymerase- and endonuclease-catalyzed DNA de novo synthesis in diverse applications.
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Affiliation(s)
- Shun Zhang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Ning Zhou
- Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong 524045, P. R. China
| | - Jiao Chen
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Quan Li
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Yang Wang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610000, P. R. China
| | - ChuanZhu Lv
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
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3
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Dubrovin EV. Atomic force microscopy-based approaches for single-molecule investigation of nucleic acid- protein complexes. Biophys Rev 2023; 15:1015-1033. [PMID: 37974971 PMCID: PMC10643717 DOI: 10.1007/s12551-023-01111-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023] Open
Abstract
The interaction of nucleic acids with proteins plays an important role in many fundamental biological processes in living cells, including replication, transcription, and translation. Therefore, understanding nucleic acid-protein interaction is of high relevance in many areas of biology, medicine and technology. During almost four decades of its existence atomic force microscopy (AFM) accumulated a significant experience in investigation of biological molecules at a single-molecule level. AFM has become a powerful tool of molecular biology and biophysics providing unique information about properties, structure, and functioning of biomolecules. Despite a great variety of nucleic acid-protein systems under AFM investigations, there are a number of typical approaches for such studies. This review is devoted to the analysis of the typical AFM-based approaches of investigation of DNA (RNA)-protein complexes with a major focus on transcription studies. The basic strategies of AFM analysis of nucleic acid-protein complexes including investigation of the products of DNA-protein reactions and real-time dynamics of DNA-protein interaction are categorized and described by the example of the most relevant research studies. The described approaches and protocols have many universal features and, therefore, are applicable for future AFM studies of various nucleic acid-protein systems.
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Affiliation(s)
- Evgeniy V. Dubrovin
- Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny, 141700 Russian Federation
- Sirius University of Science and Technology, Olimpiyskiy Ave 1, Township Sirius, Krasnodar Region, 354349 Russia
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4
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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5
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Ding J. High-Resolution Atomic Force Microscopy Imaging of RNA Molecules in Solution. Methods Mol Biol 2023; 2568:133-145. [PMID: 36227566 DOI: 10.1007/978-1-0716-2687-0_9] [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: 06/16/2023]
Abstract
Atomic force microscopy (AFM) is an important and versatile technique to investigate the structures and dynamics of biomolecules under physiologically relevant conditions at the single-molecule level. Recent progresses in high-resolution AFM imaging of nucleic acids have expanded this technique from simple characterization of double-stranded DNA or RNA to detailed analyses of the structure and dynamics of large functional RNAs with complex folds. Several technical developments, such as sharper probes and more stable instruments with novel imaging modes, AFM is capable of directly visualizing RNA conformational heterogeneity in solution in real time. Here, we introduce a comprehensive method for recording high-resolution images of RNA molecules, including sample preparation, instrument setup, data acquisition, and image processing.
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Affiliation(s)
- Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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6
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Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALB. Atomic force microscopy-A tool for structural and translational DNA research. APL Bioeng 2021; 5:031504. [PMID: 34286171 PMCID: PMC8272649 DOI: 10.1063/5.0054294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.
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Affiliation(s)
| | - James I. Provan
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - John A. Hartley
- UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
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7
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Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription. Nat Commun 2021; 12:1491. [PMID: 33674598 PMCID: PMC7935978 DOI: 10.1038/s41467-021-21690-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Abnormally formed FUS/EWS/TAF15 (FET) fusion oncoproteins are essential oncogenic drivers in many human cancers. Interestingly, at the molecular level, they also form biomolecular condensates at specific loci. However, how these condensates lead to gene transcription and how features encoded in the DNA element regulate condensate formation remain unclear. Here, we develop an in vitro single-molecule assay to visualize phase separation on DNA. Using this technique, we observe that FET fusion proteins undergo phase separation at target binding loci and the phase separated condensates recruit RNA polymerase II and enhance gene transcription. Furthermore, we determine a threshold number of fusion-binding DNA elements that can enhance the formation of FET fusion protein condensates. These findings suggest that FET fusion oncoprotein promotes aberrant gene transcription through loci-specific phase separation, which may contribute to their oncogenic transformation ability in relevant cancers, such as sarcomas and leukemia.
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9
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Li F, Li J, Dong B, Wang F, Fan C, Zuo X. DNA nanotechnology-empowered nanoscopic imaging of biomolecules. Chem Soc Rev 2021; 50:5650-5667. [DOI: 10.1039/d0cs01281e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.
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Affiliation(s)
- Fan Li
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Jiang Li
- Bioimaging Center
- Shanghai Synchrotron Radiation Facility
- Zhangjiang Laboratory
- Shanghai Advanced Research Institute
- Chinese Academy of Sciences
| | - Baijun Dong
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- China
| | - Chunhai Fan
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Xiaolei Zuo
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
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10
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Hahn J, Chou LYT, Sørensen RS, Guerra RM, Shih WM. Extrusion of RNA from a DNA-Origami-Based Nanofactory. ACS NANO 2020; 14:1550-1559. [PMID: 31922721 DOI: 10.1021/acsnano.9b06466] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cells often spatially organize biomolecules to regulate biological interactions. Synthetic mimicry of complex spatial organization may provide a route to similar levels of control for artificial systems. As a proof-of-principle, we constructed an RNA-extruding nanofactory using a DNA-origami barrel with an outer diameter of 60 nm as a chassis for integrated rolling-circle transcription and processing of RNA through spatial organization of DNA templates, RNA polymerases, and RNA endonucleases. The incorporation efficiency of molecular components was quantified to be roughly 50% on designed sites within the DNA-origami chassis. Each integrated nanofactory with RNA-producing units, composed of DNA templates and RNA polymerases, produced 100 copies of target RNA in 30 min on average. Further integration of RNA endonucleases that cleave rolling-circle transcripts from concatemers into monomers resulted in 30% processing efficiency. Disabling spatial organization of molecular components on DNA origami resulted in suppression of RNA production as well as processing.
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Affiliation(s)
- Jaeseung Hahn
- Division of Health Sciences and Technology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Cancer Biology , Dana Farber Cancer Institute , Boston , Massachusetts 02115 , United States
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Leo Y T Chou
- Department of Cancer Biology , Dana Farber Cancer Institute , Boston , Massachusetts 02115 , United States
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Rasmus S Sørensen
- Department of Cancer Biology , Dana Farber Cancer Institute , Boston , Massachusetts 02115 , United States
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Richard M Guerra
- Department of Cancer Biology , Dana Farber Cancer Institute , Boston , Massachusetts 02115 , United States
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - William M Shih
- Department of Cancer Biology , Dana Farber Cancer Institute , Boston , Massachusetts 02115 , United States
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
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11
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Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
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Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
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12
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Dubrovin EV, Schächtele M, Klinov DV, Schäffer TE. Time-Lapse Single-Biomolecule Atomic Force Microscopy Investigation on Modified Graphite in Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10027-10034. [PMID: 28850785 DOI: 10.1021/acs.langmuir.7b02220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Atomic force microscopy (AFM) of biomolecular processes at the single-molecule level can provide unique information for understanding molecular function. In AFM studies of biomolecular processes in solution, mica surfaces are predominantly used as substrates. However, owing to its high surface charge, mica may induce high local ionic strength in the vicinity of its surface, which may shift the equilibrium of studied biomolecular processes such as biopolymer adsorption or protein-DNA interaction. In the search for alternative substrates, we have investigated the behavior of adsorbed biomolecules, such as plasmid DNA and E. coli RNA polymerase σ70 subunit holoenzyme (RNAP), on highly oriented pyrolytic graphite (HOPG) surfaces modified with stearylamine and oligoglycine-hydrocarbon derivative (GM) monolayers using AFM in solution. We have demonstrated ionic-strength-dependent DNA mobility on GM HOPG and nativelike dimensions of RNAP molecules adsorbed on modified HOPG surfaces. We propose an approach to the real-time AFM investigation of transcription on stearylamine monolayers on graphite. We conclude that modified graphite allows us to study biomolecules and biomolecular processes on its surface at controlled ionic strength and may be used as a complement to mica in AFM investigations.
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Affiliation(s)
- Evgeniy V Dubrovin
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Federal Research and Clinical Center of Physical-Chemical Medicine , Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation
- Lomonosov Moscow State University , Leninskie gory 1-2, Moscow 119991, Russian Federation
| | - Marc Schächtele
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine , Malaya Pirogovskaya 1a, Moscow 119435, Russian Federation
| | - Tilman E Schäffer
- University of Tübingen , Institute of Applied Physics, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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13
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Schön P. Atomic force microscopy of RNA: State of the art and recent advancements. Semin Cell Dev Biol 2017; 73:209-219. [PMID: 28843977 DOI: 10.1016/j.semcdb.2017.08.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering.
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Affiliation(s)
- Peter Schön
- NanoBioInterface Research Group, Research Center Design and Technology, Saxion University of Applied Sciences, 7500 KB Enschede, The Netherlands; Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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14
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Kasas S, Dietler G. DNA-protein interactions explored by atomic force microscopy. Semin Cell Dev Biol 2017; 73:231-239. [PMID: 28716606 DOI: 10.1016/j.semcdb.2017.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022]
Abstract
DNA-protein interactions play an important role in all living organisms on Earth. The advent of atomic force microscopy permitted for the first time to follow and to characterize interaction forces between these two molecular species. After a short description of the AFM and its imaging modes we review, in a chronological order some of the studies that we think importantly contributed to the field.
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Affiliation(s)
- S Kasas
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Plateforme de Morphologie, Faculté de Médecine, Université de Lausanne, Bugnion 9, 1005 Lausanne, Switzerland.
| | - G Dietler
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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15
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Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem 2017; 85:349-73. [PMID: 27294440 DOI: 10.1146/annurev-biochem-060815-014244] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.
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Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Aneesh T Veetil
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York 10065;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , , .,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637
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16
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Marchetti M, Malinowska A, Heller I, Wuite GJL. How to switch the motor on: RNA polymerase initiation steps at the single-molecule level. Protein Sci 2017; 26:1303-1313. [PMID: 28470684 DOI: 10.1002/pro.3183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 11/06/2022]
Abstract
RNA polymerase (RNAP) is the central motor of gene expression since it governs the process of transcription. In prokaryotes, this holoenzyme is formed by the RNAP core and a sigma factor. After approaching and binding the specific promoter site on the DNA, the holoenzyme-promoter complex undergoes several conformational transitions that allow unwinding and opening of the DNA duplex. Once the first DNA basepairs (∼10 bp) are transcribed in an initial transcription process, the enzyme unbinds from the promoter and proceeds downstream along the DNA while continuously opening the helix and polymerizing the ribonucleotides in correspondence with the template DNA sequence. When the gene is transcribed into RNA, the process generally is terminated and RNAP unbinds from the DNA. The first step of transcription-initiation, is considered the rate-limiting step of the entire process. This review focuses on the single-molecule studies that try to reveal the key steps in the initiation phase of bacterial transcription. Such single-molecule studies have, for example, allowed real-time observations of the RNAP target search mechanism, a mechanism still under debate. Moreover, single-molecule studies using Förster Resonance Energy Transfer (FRET) revealed the conformational changes that the enzyme undergoes during initiation. Force-based techniques such as scanning force microscopy and magnetic tweezers allowed quantification of the energy that drives the RNAP translocation along DNA and its dynamics. In addition to these in vitro experiments, single particle tracking in vivo has provided a direct quantification of the relative populations in each phase of transcription and their locations within the cell.
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Affiliation(s)
- M Marchetti
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - I Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - G J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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18
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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20
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Chao J, Zhang P, Wang Q, Wu N, Zhang F, Hu J, Fan CH, Li B. Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy. NANOSCALE 2016; 8:5842-5846. [PMID: 26932823 DOI: 10.1039/c5nr06544e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA.
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Affiliation(s)
- J Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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21
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Kalay Z. Kinetics of self-assembly via facilitated diffusion: Formation of the transcription complex. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042716. [PMID: 26565281 DOI: 10.1103/physreve.92.042716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 06/05/2023]
Abstract
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in three dimensions and one dimension. Our study is motivated by single-molecule-level observations revealing the dynamics of transcription factors that bind to the deoxyribonucleic acid at early stages of transcription. We calculate the probability that a complex made up of a given number of molecules is completely formed, as well as the distribution of completion times, upon the binding of a seed molecule at a target site on the filament (without explicitly modeling the three-dimensional diffusion that precedes binding). We compare two different mechanisms of assembly where molecules bind in sequential and random order. Our results indicate that while the probability of completion is greater for random binding, the completion time scales exponentially with the size of the complex; in contrast, it scales as a power law or slower for sequential binding, asymptotically. Furthermore, we provide model predictions for the dissociation and residence times of the seed molecule, which are observables accessible in single-molecule tracking experiments.
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Affiliation(s)
- Ziya Kalay
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, 606-8501, Kyoto, Japan
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22
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Studying RNAP–promoter interactions using atomic force microscopy. Methods 2015; 86:4-9. [DOI: 10.1016/j.ymeth.2015.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 01/02/2023] Open
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23
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Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy. Molecules 2014; 19:13803-23. [PMID: 25191873 PMCID: PMC6271098 DOI: 10.3390/molecules190913803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/21/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022] Open
Abstract
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
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24
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Zhang F, Nangreave J, Liu Y, Yan H. Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 2014; 136:11198-211. [PMID: 25029570 PMCID: PMC4140475 DOI: 10.1021/ja505101a] [Citation(s) in RCA: 393] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 12/12/2022]
Abstract
Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson-Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming.
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Affiliation(s)
- Fei Zhang
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Jeanette Nangreave
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Yan Liu
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
| | - Hao Yan
- Center
for Molecular Design and Biomimicry, Biodesign Institute, and Department of
Chemistry and Biochemistry, Arizona State
University, Tempe, Arizona 85287, United
States
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25
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Endo M, Sugiyama H. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc Chem Res 2014; 47:1645-53. [PMID: 24601497 DOI: 10.1021/ar400299m] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONSPECTUS: Direct imaging of molecular motions is one of the most fundamental issues for elucidating the physical properties of individual molecules and their reaction mechanisms. Atomic force microscopy (AFM) enables direct molecular imaging, especially for biomolecules in the physiological environment. Because AFM can visualize the molecules at nanometer-scale spatial resolution, a versatile observation scaffold is needed for the precise imaging of molecule interactions in the reactions. The emergence of DNA origami technology allows the precise placement of desired molecules in the designed nanostructures and enables molecules to be detected at the single-molecule level. In our study, the DNA origami system was applied to visualize the detailed motions of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic motions of biomolecules in a subsecond time resolution. In this system, biochemical properties such as the placement of various double-stranded DNAs (dsDNAs) containing unrestricted DNA sequences, modified nucleosides, and chemical functions can be incorporated. From a physical point of view, the tension and rotation of dsDNAs can be controlled by placement into the DNA nanostructures. From a topological point of view, the orientations of dsDNAs and various shapes of dsDNAs including Holliday junctions can be incorporated for studies on reaction mechanisms. In this Account, we describe the combination of the DNA origami system and HS-AFM for imaging various biochemical reactions including enzymatic reactions and DNA structural changes. To observe the behaviors and reactions of DNA methyltransferase and DNA repair enzymes, the substrate dsDNAs were incorporated into the cavity of the DNA frame, and the enzymes that bound to the target dsDNA were observed using HS-AFM. DNA recombination was also observed using the recombination substrates and Holliday junction intermediates placed in the DNA frame, and the direction of the reactions was controlled by introducing structural stress to the substrates. In addition, the movement of RNA polymerase and its reaction were visualized using a template dsDNA attached to the origami structure. To observe DNA structural changes, G-quadruplex formation and disruption, the switching behaviors of photoresponsive oligonucleotides, and B-Z transition were visualized using the DNA frame observation system. For the formation and disruption of G-quadruplex and double-helix DNA, the two dsDNA chains incorporated into the DNA frame could amplify the small structural change to the global structural change, which enabled the visualization of their association and dissociation by HS-AFM. The dynamic motion of the helical rotation induced by the B-Z transition was also directly imaged in the DNA frame. Furthermore, the stepwise motions of mobile DNA along the DNA track were visualized on the DNA origami surface. These target-orientated observation systems should contribute to the detailed analysis of biomolecule motions in real time and at molecular resolution.
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Affiliation(s)
- Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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26
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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27
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Rajendran A, Endo M, Sugiyama H. State-of-the-Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins. Chem Rev 2013; 114:1493-520. [DOI: 10.1021/cr300253x] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Arivazhagan Rajendran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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Sørensen RS, Okholm AH, Schaffert D, Kodal ALB, Gothelf KV, Kjems J. Enzymatic ligation of large biomolecules to DNA. ACS NANO 2013; 7:8098-104. [PMID: 23927463 DOI: 10.1021/nn403386f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to synthesize, characterize, and manipulate DNA forms the foundation of a range of advanced disciplines including genomics, molecular biology, and biomolecular engineering. In particular for the latter field, DNA has proven useful as a structural or functional component in nanoscale self-assembled structures, antisense therapeutics, microarray diagnostics, and biosensors. Such applications frequently require DNA to be modified and conjugated to other macromolecules, including proteins, polymers, or fatty acids, in order to equip the system with properties required for a particular application. However, conjugation of DNA to large molecular components using classical chemistries often suffers from suboptimal yields. Here, we report the use of terminal deoxynucleotidyl transferase (TdT) for direct enzymatic ligation of native DNA to nucleotide triphosphates coupled to proteins and other large macromolecules. We demonstrate facile synthesis routes for a range of NTP-activated macromolecules and subsequent ligation to the 3' hydroxyl group of oligodeoxynucleotides using TdT. The reaction is highly specific and proceeds rapidly and essentially to completion at micromolar concentrations. As a proof of principle, parallelly labeled oligonucleotides were used to produce nanopatterned DNA origami structures, demonstrating rapid and versatile incorporation of non-DNA components into DNA nanoarchitectures.
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Affiliation(s)
- Rasmus Schøler Sørensen
- Interdisciplinary Nanoscience Center, ‡Department of Molecular Biology, §Department of Chemistry, and ⊥Centre for DNA Nanotechnology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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29
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Modern biophysical approaches probe transcription-factor-induced DNA bending and looping. Biochem Soc Trans 2013; 41:368-73. [PMID: 23356313 DOI: 10.1042/bst20120301] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The genetic information of every living organism is stored in its genomic DNA that is perceived as a chemically stable and robust macromolecule. But at the same time, to fulfil its functions properly, it also needs to be highly dynamic and flexible. This includes partial melting of the double helix or compaction and bending of the DNA often brought about by protein factors that are able to interact with DNA stretches in a specific and non-specific manner. The conformational changes in the DNA need to be understood in order to describe biological systems in detail. As these events play out on the nanometre scale, new biophysical approaches have been employed to monitor conformational changes in this regime at the single-molecule level. Focusing on transcription factor action on promoter DNA, we discuss how current biophysical techniques are able to quantitatively describe this molecular process.
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30
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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31
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-molecule visualization of the hybridization and dissociation of photoresponsive oligonucleotides and their reversible switching behavior in a DNA nanostructure. Angew Chem Int Ed Engl 2012; 51:10518-22. [PMID: 22965475 DOI: 10.1002/anie.201205247] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 12/20/2022]
Abstract
A framed photo of DNA: A pair of photoresponsive oligonucleotides containing azobenzene moieties was introduced into double-stranded DNA within the cavity of a DNA nanostructure (see scheme). The two dsDNAs, in contact at the center, were dissociated using UV irradiation and hybridized with visible light; this was directly observed using high-speed atomic force microscopy.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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