1
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Kang Y, An S, Min D, Lee JY. Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair. Front Bioeng Biotechnol 2022; 10:973314. [PMID: 36185427 PMCID: PMC9520083 DOI: 10.3389/fbioe.2022.973314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.
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Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Soyeong An
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Center for Genomic Integrity, Institute of Basic Sciences, Ulsan, South Korea
- *Correspondence: Ja Yil Lee,
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2
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Mahmoud R, Dhakal S. Single-Molecule Analysis of DNA Branch Migration under Biomimetic Environments. J Phys Chem B 2022; 126:7252-7261. [DOI: 10.1021/acs.jpcb.2c03153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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3
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The Role of the Rad55-Rad57 Complex in DNA Repair. Genes (Basel) 2021; 12:genes12091390. [PMID: 34573372 PMCID: PMC8472222 DOI: 10.3390/genes12091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/29/2022] Open
Abstract
Homologous recombination (HR) is a mechanism conserved from bacteria to humans essential for the accurate repair of DNA double-stranded breaks, and maintenance of genome integrity. In eukaryotes, the key DNA transactions in HR are catalyzed by the Rad51 recombinase, assisted by a host of regulatory factors including mediators such as Rad52 and Rad51 paralogs. Rad51 paralogs play a crucial role in regulating proper levels of HR, and mutations in the human counterparts have been associated with diseases such as cancer and Fanconi Anemia. In this review, we focus on the Saccharomyces cerevisiae Rad51 paralog complex Rad55–Rad57, which has served as a model for understanding the conserved role of Rad51 paralogs in higher eukaryotes. Here, we discuss the results from early genetic studies, biochemical assays, and new single-molecule observations that have together contributed to our current understanding of the molecular role of Rad55–Rad57 in HR.
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4
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Probing DNA-protein interactions using single-molecule diffusivity contrast. BIOPHYSICAL REPORTS 2021; 1:100009. [PMID: 36425309 PMCID: PMC9680706 DOI: 10.1016/j.bpr.2021.100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Single-molecule fluorescence investigations of protein-nucleic acid interactions require robust means to identify the binding state of individual substrate molecules in real time. Here, we show that diffusivity contrast, widely used in fluorescence correlation spectroscopy at the ensemble level and in single-particle tracking on individual (but slowly diffusing) species, can be used as a general readout to determine the binding state of single DNA molecules with unlabeled proteins in solution. We first describe the technical basis of drift-free single-molecule diffusivity measurements in an anti-Brownian electrokinetic trap. We then cross-validate our method with protein-induced fluorescence enhancement, a popular technique to detect protein binding on nucleic acid substrates with single-molecule sensitivity. We extend an existing hydrodynamic modeling framework to link measured diffusivity to particular DNA-protein structures and obtain good agreement between the measured and predicted diffusivity values. Finally, we show that combining diffusivity contrast with protein-induced fluorescence enhancement allows simultaneous mapping of binding stoichiometry and location on individual DNA-protein complexes, potentially enhancing single-molecule views of relevant biophysical processes.
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5
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Elucidating Recombination Mediator Function Using Biophysical Tools. BIOLOGY 2021; 10:biology10040288. [PMID: 33916151 PMCID: PMC8066028 DOI: 10.3390/biology10040288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary This review recapitulates the initial knowledge acquired with genetics and biochemical experiments on Recombination mediator proteins in different domains of life. We further address how recent in vivo and in vitro biophysical tools were critical to deepen the understanding of RMPs molecular mechanisms in DNA and replication repair, and unveiled unexpected features. For instance, in bacteria, genetic and biochemical studies suggest a close proximity and coordination of action of the RecF, RecR and RecO proteins in order to ensure their RMP function, which is to overcome the single-strand binding protein (SSB) and facilitate the loading of the recombinase RecA onto ssDNA. In contrary to this expectation, using single-molecule fluorescent imaging in living cells, we showed recently that RecO and RecF do not colocalize and moreover harbor different spatiotemporal behavior relative to the replication machinery, suggesting distinct functions. Finally, we address how new biophysics tools could be used to answer outstanding questions about RMP function. Abstract The recombination mediator proteins (RMPs) are ubiquitous and play a crucial role in genome stability. RMPs facilitate the loading of recombinases like RecA onto single-stranded (ss) DNA coated by single-strand binding proteins like SSB. Despite sharing a common function, RMPs are the products of a convergent evolution and differ in (1) structure, (2) interaction partners and (3) molecular mechanisms. The RMP function is usually realized by a single protein in bacteriophages and eukaryotes, respectively UvsY or Orf, and RAD52 or BRCA2, while in bacteria three proteins RecF, RecO and RecR act cooperatively to displace SSB and load RecA onto a ssDNA region. Proteins working alongside to the RMPs in homologous recombination and DNA repair notably belongs to the RAD52 epistasis group in eukaryote and the RecF epistasis group in bacteria. Although RMPs have been studied for several decades, molecular mechanisms at the single-cell level are still not fully understood. Here, we summarize the current knowledge acquired on RMPs and review the crucial role of biophysical tools to investigate molecular mechanisms at the single-cell level in the physiological context.
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6
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Kim R, Kanamaru S, Mikawa T, Prévost C, Ishii K, Ito K, Uchiyama S, Oda M, Iwasaki H, Kim SK, Takahashi M. RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro. Nucleic Acids Res 2019; 46:2548-2559. [PMID: 29390145 PMCID: PMC5861410 DOI: 10.1093/nar/gky048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/23/2018] [Indexed: 11/15/2022] Open
Abstract
Mg2+ ion stimulates the DNA strand exchange reaction catalyzed by RecA, a key step in homologous recombination. To elucidate the molecular mechanisms underlying the role of Mg2+ and the strand exchange reaction itself, we investigated the interaction of RecA with Mg2+ and sought to determine which step of the reaction is affected. Thermal stability, intrinsic fluorescence, and native mass spectrometric analyses of RecA revealed that RecA binds at least two Mg2+ ions with KD ≈ 2 mM and 5 mM. Deletion of the C-terminal acidic tail of RecA made its thermal stability and fluorescence characteristics insensitive to Mg2+ and similar to those of full-length RecA in the presence of saturating Mg2+. These observations, together with the results of a molecular dynamics simulation, support the idea that the acidic tail hampers the strand exchange reaction by interacting with other parts of RecA, and that binding of Mg2+ to the tail prevents these interactions and releases RecA from inhibition. We observed that binding of the first Mg2+ stimulated joint molecule formation, whereas binding of the second stimulated progression of the reaction. Thus, RecA is actively involved in the strand exchange step as well as bringing the two DNAs close to each other.
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Affiliation(s)
- Raeyeong Kim
- Department of Chemistry, Yeungnam University, Gyeonsan-city 38541, Republic of Korea
| | - Shuji Kanamaru
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Tsutomu Mikawa
- RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, UPR9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Kentaro Ito
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Seog K Kim
- Department of Chemistry, Yeungnam University, Gyeonsan-city 38541, Republic of Korea
| | - Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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7
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He Z, Han Z, Kizer M, Linhardt RJ, Wang X, Sinyukov AM, Wang J, Deckert V, Sokolov AV, Hu J, Scully MO. Tip-Enhanced Raman Imaging of Single-Stranded DNA with Single Base Resolution. J Am Chem Soc 2018; 141:753-757. [DOI: 10.1021/jacs.8b11506] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Zhe He
- Texas A&M University, College Station, Texas 77843, United States
| | - Zehua Han
- Texas A&M University, College Station, Texas 77843, United States
| | - Megan Kizer
- Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | | | - Xing Wang
- Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | | | - Jizhou Wang
- Texas A&M University, College Station, Texas 77843, United States
| | - Volker Deckert
- Friedrich-Schiller-Universitaet Jena, Lessingstraße 10, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einsteinstraße 9, 07745 Jena, Germany
| | - Alexei V. Sokolov
- Texas A&M University, College Station, Texas 77843, United States
- Baylor University, Waco, Texas 76798, United States
| | - Jonathan Hu
- Baylor University, Waco, Texas 76798, United States
| | - Marlan O. Scully
- Texas A&M University, College Station, Texas 77843, United States
- Baylor University, Waco, Texas 76798, United States
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8
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van der Zon NL, Kanaar R, Wyman C. Variation in RAD51 details a hub of functions: opportunities to advance cancer diagnosis and therapy. F1000Res 2018; 7. [PMID: 30271574 PMCID: PMC6137408 DOI: 10.12688/f1000research.15650.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2018] [Indexed: 11/30/2022] Open
Abstract
Loss of genome stability is one of the hallmarks of the enabling characteristics of cancer development. Homologous recombination is a DNA repair process that often breaks down as a prelude to developing cancer. Conversely, homologous recombination can be the Achilles’ heel in common anti-cancer therapies, which are effective by inducing irreparable DNA damage. Here, we review recent structural and functional studies of RAD51, the protein that catalyzes the defining step of homologous recombination: homology recognition and DNA strand exchange. Specific mutations can be linked to structural changes and known essential functions. Additional RAD51 interactions and functions may be revealed. The identification of viable mutations in this essential protein may help define the range of activity and interactions needed. All of this information provides opportunities to fine-tune existing therapies based on homologous recombination status, guide diagnosis, and hopefully develop new clinical tools.
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Affiliation(s)
- Nick Ll van der Zon
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands.,Oncode Institute, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
| | - Claire Wyman
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands.,Department of Radiation Oncology, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
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9
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van der Zon NLL, Kanaar R, Wyman C. Variation in RAD51 details a hub of functions: opportunities to advance cancer diagnosis and therapy. F1000Res 2018; 7:F1000 Faculty Rev-1453. [PMID: 30271574 PMCID: PMC6137408 DOI: 10.12688/f1000research.15650.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2018] [Indexed: 11/06/2023] Open
Abstract
Loss of genome stability is one of the hallmarks of the enabling characteristics of cancer development. Homologous recombination is a DNA repair process that often breaks down as a prelude to developing cancer. Conversely, homologous recombination can be the Achilles' heel in common anti-cancer therapies, which are effective by inducing irreparable DNA damage. Here, we review recent structural and functional studies of RAD51, the protein that catalyzes the defining step of homologous recombination: homology recognition and DNA strand exchange. Specific mutations can be linked to structural changes and known essential functions. Additional RAD51 interactions and functions may be revealed. The identification of viable mutations in this essential protein may help define the range of activity and interactions needed. All of this information provides opportunities to fine-tune existing therapies based on homologous recombination status, guide diagnosis, and hopefully develop new clinical tools.
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Affiliation(s)
- Nick LL van der Zon
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
| | - Claire Wyman
- Department of Molecular Genetics, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
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10
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Abstract
Human RAD51 promotes accurate DNA repair by homologous recombination and is involved in protection and repair of damaged DNA replication forks. The active species of RAD51 and related recombinases in all organisms is a nucleoprotein filament assembled on single-stranded DNA (ssDNA). The formation of a nucleoprotein filament competent for the recombination reaction, or for DNA replication support, is a delicate and strictly regulated process, which occurs through filament nucleation followed by filament extension. The rates of these two phases of filament formation define the capacity of RAD51 to compete with the ssDNA-binding protein RPA, as well as the lengths of the resulting filament segments. Single-molecule approaches can provide a wealth of quantitative information on the kinetics of RAD51 nucleoprotein filament assembly, internal dynamics, and disassembly. In this chapter, we describe how to set up a single-molecule total internal reflection fluorescence microscopy experiment to monitor the initial steps of RAD51 nucleoprotein filament formation in real-time and at single-monomer resolution. This approach is based on the unique, stretched-ssDNA conformation within the recombinase nucleoprotein filament and follows the efficiency of Förster resonance energy transfer (EFRET) between two DNA-conjugated fluorophores. We will discuss the practical aspects of the experimental setup, extraction of the FRET trajectories, and how to analyze and interpret the data to obtain information on RAD51 nucleation kinetics, the mechanism of nucleation, and the oligomeric species involved in filament formation.
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11
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Abstract
Genetic recombination occurs in all organisms and is vital for genome stability. Indeed, in humans, aberrant recombination can lead to diseases such as cancer. Our understanding of homologous recombination is built upon more than a century of scientific inquiry, but achieving a more complete picture using ensemble biochemical and genetic approaches is hampered by population heterogeneity and transient recombination intermediates. Recent advances in single-molecule and super-resolution microscopy methods help to overcome these limitations and have led to new and refined insights into recombination mechanisms, including a detailed understanding of DNA helicase function and synaptonemal complex structure. The ability to view cellular processes at single-molecule resolution promises to transform our understanding of recombination and related processes.
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12
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Ma CJ, Gibb B, Kwon Y, Sung P, Greene EC. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 2016; 45:749-761. [PMID: 27903895 PMCID: PMC5314761 DOI: 10.1093/nar/gkw1125] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly.
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Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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13
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Greene EC. On the influence of protein-DNA register during homologous recombination. Cell Cycle 2016; 15:172-5. [PMID: 26652653 DOI: 10.1080/15384101.2015.1121352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Homologous recombination enables the exchange of genetic information between related DNA molecules and is a driving force in evolution. Using single-molecule optical microscopy we have recently shown that members of the Rad51/RecA family of recombinases stabilize paired homologous strand of DNA in precise 3-nt increments. Here we discuss an interesting conceptual implication of these results, which is that the recombinases may actively sense and reorganize their alignment register relative to the bound DNA sequences to ensure optimal base triplet pairing interactions during the early stages of recombination.
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Affiliation(s)
- Eric C Greene
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
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14
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Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
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15
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Visualizing recombination intermediates with single-stranded DNA curtains. Methods 2016; 105:62-74. [PMID: 27038747 DOI: 10.1016/j.ymeth.2016.03.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 01/23/2023] Open
Abstract
Homologous recombination (HR) is a critical cellular process for repairing double-stranded DNA breaks (DSBs) - a toxic type of DNA lesion that can result in chromosomal rearrangements and cancer. During the early stages of HR, members from the Rad51/RecA family of recombinases assemble into long filaments on the single-stranded DNA overhangs that are present at processed DSBs. These nucleoprotein filaments are referred to as presynaptic complexes, and these presynaptic complexes must align and pair homologous DNA sequences during HR. Traditional ensemble methods cannot easily access the transient and often heterogeneous intermediates that are typical of DNA recombination reactions, and as a consequence, there remain many open questions with respect to the molecular details of this pathway. Novel single-molecule approaches that are capable of directly visualizing reaction intermediates in solution and in real time offer the potential for new insights into the mechanism of homologous DNA recombination. Here we highlight recently developed single stranded DNA curtain methods for studying the properties of individual Rad51 presynaptic complexes and other related recombination intermediates at the single-molecule level.
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16
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Machado RA, Moreira HSB, de Aquino SN, Martelli-Junior H, de Almeida Reis SR, Persuhn DC, Wu T, Yuan Y, Coletta RD. Interactions between RAD51 rs1801321 and maternal cigarette smoking as risk factor for nonsyndromic cleft lip with or without cleft palate. Am J Med Genet A 2015; 170A:536-539. [PMID: 26507587 DOI: 10.1002/ajmg.a.37281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/05/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Helenara Salvati Bertolossi Moreira
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil.,Department of Physiotherapy, State University of Western Paraná, Paraná, Brazil
| | - Sibele Nascimento de Aquino
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil.,Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | - Hercilio Martelli-Junior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosário Vellano, Minas Gerais, Brazil
| | | | - Darlene Camati Persuhn
- Molecular Biology Department, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Tao Wu
- Peking University School of Public Health, Beijing, China
| | - Yuan Yuan
- Peking University School of Public Health, Beijing, China
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
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17
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Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution. Proc Natl Acad Sci U S A 2014; 111:15090-5. [PMID: 25288749 DOI: 10.1073/pnas.1307824111] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
During recombinational repair of double-stranded DNA breaks, RAD51 recombinase assembles as a nucleoprotein filament around single-stranded DNA to form a catalytically proficient structure able to promote homology recognition and strand exchange. Mediators and accessory factors guide the action and control the dynamics of RAD51 filaments. Elucidation of these control mechanisms necessitates development of approaches to quantitatively probe transient aspects of RAD51 filament dynamics. Here, we combine fluorescence microscopy, optical tweezers, and microfluidics to visualize the assembly of RAD51 filaments on bare single-stranded DNA and quantify the process with single-monomer sensitivity. We show that filaments are seeded from RAD51 nuclei that are heterogeneous in size. This heterogeneity appears to arise from the energetic balance between RAD51 self-assembly in solution and the size-dependent interaction time of the nuclei with DNA. We show that nucleation intrinsically is substrate selective, strongly favoring filament formation on bare single-stranded DNA. Furthermore, we devised a single-molecule fluorescence recovery after photobleaching assay to independently observe filament nucleation and growth, permitting direct measurement of their contributions to filament formation. Our findings yield a comprehensive, quantitative understanding of RAD51 filament formation on bare single-stranded DNA that will serve as a basis to elucidate how mediators help RAD51 filament assembly and accessory factors control filament dynamics.
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18
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Renkawitz J, Lademann CA, Jentsch S. Mechanisms and principles of homology search during recombination. Nat Rev Mol Cell Biol 2014; 15:369-83. [PMID: 24824069 DOI: 10.1038/nrm3805] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.
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Affiliation(s)
- Jörg Renkawitz
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2] Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria. [3]
| | - Claudio A Lademann
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2]
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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Sanchez H, Reuter M, Yokokawa M, Takeyasu K, Wyman C. Taking it one step at a time in homologous recombination repair. DNA Repair (Amst) 2014; 20:110-118. [PMID: 24636751 DOI: 10.1016/j.dnarep.2014.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/10/2023]
Abstract
The individual steps in the process of homologous recombination are particularly amenable to analysis by single-molecule imaging and manipulation experiments. Over the past 20 years these have provided a wealth of new information on the DNA transactions that make up this vital process. Exciting progress in developing new tools and techniques to analyze more complex components, dynamic reaction steps and molecular coordination continues at a rapid pace. Here we highlight recent results and indicate some emerging techniques likely to produce the next stage of advanced insight into homologous recombination. In this and related fields the future is bright.
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Affiliation(s)
- Humberto Sanchez
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Reuter
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Masatoshi Yokokawa
- Graduate School of Pure and Applied Science, University of Tsukuba, Japan
| | | | - Claire Wyman
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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