1
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Sabei A, Prentiss M, Prévost C. Modeling the Homologous Recombination Process: Methods, Successes and Challenges. Int J Mol Sci 2023; 24:14896. [PMID: 37834348 PMCID: PMC10573387 DOI: 10.3390/ijms241914896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information.
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Affiliation(s)
- Afra Sabei
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA02138, USA;
| | - Chantal Prévost
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 Rue Pierre et Marie Curie, F-75005 Paris, France;
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, F-75005 Paris, France
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2
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Yu F, Zhang D, Zhao C, Zhao Q, Jiang G, Wang H. Flanking strand separation activity of RecA nucleoprotein filaments in DNA strand exchange reactions. Nucleic Acids Res 2023; 51:2270-2283. [PMID: 36807462 PMCID: PMC10018334 DOI: 10.1093/nar/gkad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/22/2023] Open
Abstract
The recombinase RecA/Rad51 ATPase family proteins catalyze paramount DNA strand exchange reactions that are critically involved in maintaining genome integrity. However, it remains unclear how DNA strand exchange proceeds when encountering RecA-free defects in recombinase nucleoprotein filaments. Herein, by designing a series of unique substrates (e.g. truncated or conjugated incoming single-stranded DNA, and extended donor double-stranded DNA) and developing a two-color alternating excitation-modified single-molecule real-time fluorescence imaging assay, we resolve the two key steps (donor strand separation and new base-pair formation) that are usually inseparable during the reaction, revealing a novel long-range flanking strand separation activity of synaptic RecA nucleoprotein filaments. We further evaluate the kinetics and free energetics of strand exchange reactions mediated by various substrates, and elucidate the mechanism of flanking strand separation. Based on these findings, we propose a potential fundamental molecular model involved in flanking strand separation, which provides new insights into strand exchange mechanism and homologous recombination.
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Affiliation(s)
- Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chubin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- School of Environment and Health, Jianghan University, Wuhan 430056, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Front Mol Biosci 2022; 9:826136. [PMID: 35480882 PMCID: PMC9035671 DOI: 10.3389/fmolb.2022.826136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.
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Affiliation(s)
- Anne-Elisabeth Molza
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Yvonne Westermaier
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | - Pierre Ducrot
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, United States
| | - Charles H. Robert
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Chantal Prévost
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
- *Correspondence: Chantal Prévost ,
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4
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Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW. Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination. Nucleic Acids Res 2021; 49:13135-13149. [PMID: 34871438 PMCID: PMC8682777 DOI: 10.1093/nar/gkab1141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/01/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022] Open
Abstract
Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51-DNA and Dmc1-DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
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Affiliation(s)
- Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Sijia Peng
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Rui Liang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Tian
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60615, USA
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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5
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Maman N, Kumar P, Yadav A, Feingold M. Single Molecule Study of the Polymerization of RecA on dsDNA: The Dynamics of Individual Domains. Front Mol Biosci 2021; 8:609076. [PMID: 33842536 PMCID: PMC8025788 DOI: 10.3389/fmolb.2021.609076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
In the Escherichia coli, RecA plays a central role in the recombination and repair of the DNA. For homologous recombination, RecA binds to ssDNA forming a nucleoprotein filament. The RecA-ssDNA filament searches for a homologous sequence on a dsDNA and, subsequently, RecA mediates strand exchange between the ssDNA and the dsDNA. In vitro, RecA binds to both ssDNA and dsDNA. Despite a wide range of studies of the polymerization of RecA on dsDNA, both at the single molecule level and by means of biochemical methods, important aspects of this process are still awaiting a better understanding. Specifically, a detailed, quantitative description of the nucleation and growth dynamics of the RecA-dsDNA filaments is still lacking. Here, we use Optical Tweezers together with a single molecule analysis approach to measure the dynamics of the individual RecA domains on dsDNA and the corresponding growth rates for each of their fronts. We focus on the regime where the nucleation and growth rate constants, kn and kg, are comparable, leading to a coverage of the dsDNA molecule that consists of a small number of RecA domains. For the case of essentially irreversible binding (using ATPγS instead of ATP), we find that domain growth is highly asymmetric with a ratio of about 10:1 between the fast and slow fronts growth rates.
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Affiliation(s)
- Nitzan Maman
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Pramod Kumar
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Amarjeet Yadav
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Mario Feingold
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
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6
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Mismatch sensing by nucleofilament deciphers mechanism of RecA-mediated homologous recombination. Proc Natl Acad Sci U S A 2020; 117:20549-20554. [PMID: 32788357 DOI: 10.1073/pnas.1920265117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recombinases polymerize along single-stranded DNA (ssDNA) at the end of a broken DNA to form a helical nucleofilament with a periodicity of ∼18 bases. The filament catalyzes the search and checking for homologous sequences and promotes strand exchange with a donor duplex during homologous recombination (HR), the mechanism of which has remained mysterious since its discovery. Here, by inserting mismatched segments into donor duplexes and using single-molecule techniques to catch transient intermediates in HR, we found that, even though 3 base pairs (bp) is still the basic unit, both the homology checking and the strand exchange may proceed in multiple steps at a time, resulting in ∼9-bp large steps on average. More interestingly, the strand exchange is blocked remotely by the mismatched segment, terminating at positions ∼9 bp before the match-mismatch joint. The homology checking and the strand exchange are thus separated in space, with the strand exchange lagging behind. Our data suggest that the strand exchange progresses like a traveling wave in which the donor DNA is incorporated successively into the ssDNA-RecA filament to check homology in ∼9-bp steps in the frontier, followed by a hypothetical transitional segment and then the post-strand-exchanged duplex.
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7
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Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51. Nat Commun 2020; 11:2950. [PMID: 32528002 PMCID: PMC7289862 DOI: 10.1038/s41467-020-16750-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/19/2020] [Indexed: 02/03/2023] Open
Abstract
During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1–C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases. Rad51 drives DNA strand exchange, the central reaction in recombinational DNA repair. Two sites of Rad51 are responsible for DNA binding, but the function of these sites has proven elusive. Here, the authors employ real-time assays to reveal catalytic roles for the two DNA binding sites of Rad51.
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8
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Boyer B, Danilowicz C, Prentiss M, Prévost C. Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res 2019; 47:7798-7808. [PMID: 31372639 PMCID: PMC6735932 DOI: 10.1093/nar/gkz667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
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Affiliation(s)
- Benjamin Boyer
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Presently in Laboratoire Génomique Bioinformatique et Applications, EA4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chantal Prévost
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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9
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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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10
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Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW. Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange. Nat Struct Mol Biol 2016; 24:40-46. [PMID: 27941862 DOI: 10.1038/nsmb.3336] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/07/2016] [Indexed: 01/16/2023]
Abstract
The central step in eukaryotic homologous recombination (HR) is ATP-dependent DNA-strand exchange mediated by the Rad51 recombinase. In this process, Rad51 assembles on single-stranded DNA (ssDNA) and generates a helical filament that is able to search for and invade homologous double-stranded DNA (dsDNA), thus leading to strand separation and formation of new base pairs between the initiating ssDNA and the complementary strand within the duplex. Here, we used cryo-EM to solve the structures of human RAD51 in complex with DNA molecules, in presynaptic and postsynaptic states, at near-atomic resolution. Our structures reveal both conserved and distinct structural features of the human RAD51-DNA complexes compared with their prokaryotic counterpart. Notably, we also captured the structure of an arrested synaptic complex. Our results provide new insight into the molecular mechanisms of the DNA homology search and strand-exchange processes.
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Affiliation(s)
- Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Xu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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11
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Lee JY, Qi Z, Greene EC. ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex. J Biol Chem 2016; 291:22218-22230. [PMID: 27587394 DOI: 10.1074/jbc.m116.740563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 01/13/2023] Open
Abstract
Homologous recombination is an important DNA repair pathway that plays key roles in maintaining genome stability. Escherichia coli RecA is an ATP-dependent DNA-binding protein that catalyzes the DNA strand exchange reactions in homologous recombination. RecA assembles into long helical filaments on single-stranded DNA, and these presynaptic complexes are responsible for locating and pairing with a homologous duplex DNA. Recent single molecule studies have provided new insights into RecA behavior, but the potential influence of ATP in the reactions remains poorly understood. Here we examine how ATP influences the ability of the RecA presynaptic complex to interact with homologous dsDNA. We demonstrate that over short time regimes, RecA presynaptic complexes sample heterologous dsDNA similarly in the presence of either ATP or ATPγS, suggesting that initial interactions do not depend on ATP hydrolysis. In addition, RecA stabilizes pairing intermediates in three-base steps, and stepping energetics is seemingly unaltered in the presence of ATP. However, the overall dissociation rate of these paired intermediates with ATP is ∼4-fold higher than with ATPγS. These experiments suggest that ATP plays an unanticipated role in promoting the turnover of captured duplex DNA intermediates as RecA attempts to align homologous sequences during the early stages of recombination.
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Affiliation(s)
- Ja Yil Lee
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Zhi Qi
- the Center of Quantitative Biology & Center of Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
| | - Eric C Greene
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
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12
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Liu C, Danilowicz C, Kleckner N, Prentiss M. Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA. Nucleic Acids Res 2016; 45:894-901. [PMID: 27580717 PMCID: PMC5314784 DOI: 10.1093/nar/gkw758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/02/2016] [Accepted: 08/20/2016] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro. Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA. We propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes.
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Affiliation(s)
- Chenli Liu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.,Center for Synthetic Biology Engineering Research, Shenzhen Institute Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | | | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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13
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León SC, Prentiss M, Fyta M. Binding energies of nucleobase complexes: Relevance to homology recognition of DNA. Phys Rev E 2016; 93:062410. [PMID: 27415301 DOI: 10.1103/physreve.93.062410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 06/06/2023]
Abstract
The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into the Watson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.
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Affiliation(s)
- Sergio Cruz León
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
- Departamento de Ciencias Naturales, Escuela Colombiana de Ingeniería Julio Garavito, AK 45 205-59, Bogotá, Colombia
| | - Mara Prentiss
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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14
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Abstract
Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination.
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Affiliation(s)
- Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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15
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Lee JY, Terakawa T, Qi Z, Steinfeld JB, Redding S, Kwon Y, Gaines WA, Zhao W, Sung P, Greene EC. DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases. Science 2016; 349:977-81. [PMID: 26315438 DOI: 10.1126/science.aab2666] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA strand exchange plays a central role in genetic recombination across all kingdoms of life, but the physical basis for these reactions remains poorly defined. Using single-molecule imaging, we found that bacterial RecA and eukaryotic Rad51 and Dmc1 all stabilize strand exchange intermediates in precise three-nucleotide steps. Each step coincides with an energetic signature (0.3 kBT) that is conserved from bacteria to humans. Triplet recognition is strictly dependent on correct Watson-Crick pairing. Rad51, RecA, and Dmc1 can all step over mismatches, but only Dmc1 can stabilize mismatched triplets. This finding provides insight into why eukaryotes have evolved a meiosis-specific recombinase. We propose that canonical Watson-Crick base triplets serve as the fundamental unit of pairing interactions during DNA recombination.
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Affiliation(s)
- Ja Yil Lee
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Department of Biophysics, Kyoto University, Sakyo, Kyoto, Japan
| | - Zhi Qi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sy Redding
- Department of Chemistry, Columbia University, New York, NY, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - William A Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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16
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Prentiss M, Prévost C, Danilowicz C. Structure/function relationships in RecA protein-mediated homology recognition and strand exchange. Crit Rev Biochem Mol Biol 2015; 50:453-76. [DOI: 10.3109/10409238.2015.1092943] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Yang D, Boyer B, Prévost C, Danilowicz C, Prentiss M. Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res 2015; 43:10251-63. [PMID: 26384422 PMCID: PMC4666392 DOI: 10.1093/nar/gkv883] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022] Open
Abstract
RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.
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Affiliation(s)
- Darren Yang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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18
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Abstract
Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.
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Affiliation(s)
- M Scott Brown
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
| | - Douglas K Bishop
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
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19
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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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Zhang L, Wang Y, Chen M, Luo Y, Deng K, Chen D, Fu W. A new system for the amplification of biological signals: RecA and complimentary single strand DNA probes on a leaky surface acoustic wave biosensor. Biosens Bioelectron 2014; 60:259-64. [PMID: 24813916 DOI: 10.1016/j.bios.2014.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/10/2014] [Accepted: 04/21/2014] [Indexed: 01/05/2023]
Abstract
This research describes a new amplification signals system of the leaky surface acoustic wave (LSAW) bis-peptide nucleic acid (bis-PNA) biosensor for the simple, sensitive and rapid detection of the target double-stranded DNA (dsDNA). The system consists of a RecA protein-coated complementary single-stranded DNA (cssDNA) probe complex that amplifies the biological signal to improve the sensitivity of the biosensor. The bis-PNA probe for detecting HPV was first immobilized on a gold surface membrane of the detection channel. After the probe was completely hybridized with the corresponding target DNA, different concentrations of the "RecA protein-complementary single strand DNA probe" were added to react with the bis-PNA/dsDNA complex. The phase shift of the LSAW biosensors, which was measured and found to be most significant when the RecA protein was 45 μg/mL and the ATPγS was 2.5 mmol/L. Compared with other concentrations (P<0.01) of RecA and ATPγS, the value of the phase shift was (11.74 ± 1.03) degrees and the ratio of the phase shift and hybridization time clearly outperformed that of the other concentrations. Compared to the direct hybridization of the bis-PNA probe and the target DNA sequence, the sensitivity was effectively improved and the detection time was significantly shortened. PNA binding adjacent to the area of the target sequence homologous to the probe significantly increased the yield of the hybridization reaction between the PNA/dsDNA complex and the RecA protein-coated cssDNA probe. In this condition, the phase shift was significantly obvious and the detection time was significantly shortened. In conclusion, the combination of the RecA protein-coated cssDNA probe and the LSAW bis-PNA biosensor provides sensitivity and simple and rapid detection of clinical trace pathogenic microorganisms.
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Affiliation(s)
- Liqun Zhang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China.
| | - Yunxia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Ming Chen
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, PR China
| | - Yang Luo
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Kun Deng
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Weiling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China.
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Danilowicz C, Peacock-Villada A, Vlassakis J, Facon A, Feinstein E, Kleckner N, Prentiss M. The differential extension in dsDNA bound to Rad51 filaments may play important roles in homology recognition and strand exchange. Nucleic Acids Res 2013; 42:526-33. [PMID: 24084082 PMCID: PMC3874182 DOI: 10.1093/nar/gkt867] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
RecA and Rad51 proteins play an important role in DNA repair and homologous recombination. For RecA, X-ray structure information and single molecule force experiments have indicated that the differential extension between the complementary strand and its Watson–Crick pairing partners promotes the rapid unbinding of non-homologous dsDNA and drives strand exchange forward for homologous dsDNA. In this work we find that both effects are also present in Rad51 protein. In particular, pulling on the opposite termini (3′ and 5′) of one of the two DNA strands in a dsDNA molecule allows dsDNA to extend along non-homologous Rad51-ssDNA filaments and remain stably bound in the extended state, but pulling on the 3′5′ ends of the complementary strand reduces the strand-exchange rate for homologous filaments. Thus, the results suggest that differential extension is also present in dsDNA bound to Rad51. The differential extension promotes rapid recognition by driving the swift unbinding of dsDNA from non-homologous Rad51-ssDNA filaments, while at the same time, reducing base pair tension due to the transfer of the Watson–Crick pairing of the complementary strand bases from the highly extended outgoing strand to the slightly less extended incoming strand, which drives strand exchange forward.
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Affiliation(s)
- Claudia Danilowicz
- Department of Physics and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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22
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Vlassakis J, Feinstein E, Yang D, Tilloy A, Weiller D, Kates-Harbeck J, Coljee V, Prentiss M. Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:032702. [PMID: 27499708 PMCID: PMC4973255 DOI: 10.1103/physreve.87.032702] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that calculates the distribution of tension in the extended dsDNA during strand exchange. The model suggests that the binding of additional dsDNA base pairs to the DNA/RecA filament alters the tension in dsDNA that was already bound to the filament, resulting in a non-linear increase in the mechanical energy as a function of the number of bound base pairs. This collective mechanical response may promote homology stringency and underlie unexplained experimental results.
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Affiliation(s)
- Julea Vlassakis
- Harvard University, Department of Physics, Cambridge, MA, 02138
| | | | - Darren Yang
- Harvard University, Department of Physics, Cambridge, MA, 02138
| | - Antoine Tilloy
- Harvard University, Department of Physics, Cambridge, MA, 02138
| | - Dominic Weiller
- Harvard University, Department of Physics, Cambridge, MA, 02138
| | | | - Vincent Coljee
- Harvard University, Department of Physics, Cambridge, MA, 02138
| | - Mara Prentiss
- Harvard University, Department of Physics, Cambridge, MA, 02138
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Ragunathan K, Liu C, Ha T. RecA filament sliding on DNA facilitates homology search. eLife 2012; 1:e00067. [PMID: 23240082 PMCID: PMC3510455 DOI: 10.7554/elife.00067] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/04/2012] [Indexed: 01/07/2023] Open
Abstract
During homologous recombination, RecA forms a helical filament on a single stranded (ss) DNA that searches for a homologous double stranded (ds) DNA and catalyzes the exchange of complementary base pairs to form a new heteroduplex. Using single molecule fluorescence imaging tools with high spatiotemporal resolution we characterized the encounter complex between the RecA filament and dsDNA. We present evidence in support of the 'sliding model' wherein a RecA filament diffuses along a dsDNA track. We further show that homology can be detected during sliding. Sliding occurs with a diffusion coefficient of approximately 8000 bp(2)/s allowing the filament to sample several hundred base pairs before dissociation. Modeling suggests that sliding can accelerate homology search by as much as 200 fold. Homology recognition can occur for as few as 6 nt of complementary basepairs with the recognition efficiency increasing for higher complementarity. Our data represents the first example of a DNA bound multi-protein complex which can slide along another DNA to facilitate target search.DOI:http://dx.doi.org/10.7554/eLife.00067.001.
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Affiliation(s)
- Kaushik Ragunathan
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States [corrected]
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Peacock-Villada A, Yang D, Danilowicz C, Feinstein E, Pollock N, McShan S, Coljee V, Prentiss M. Complementary strand relocation may play vital roles in RecA-based homology recognition. Nucleic Acids Res 2012; 40:10441-51. [PMID: 22941658 PMCID: PMC3488227 DOI: 10.1093/nar/gks769] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RecA-family proteins mediate homologous recombination and recombinational DNA repair through homology search and strand exchange. Initially, the protein forms a filament with the incoming single-stranded DNA (ssDNA) bound in site I. The RecA–ssDNA filament then binds double-stranded DNA (dsDNA) in site II. Non-homologous dsDNA rapidly unbinds, whereas homologous dsDNA undergoes strand exchange yielding heteroduplex dsDNA in site I and the leftover outgoing strand in site II. We show that applying force to the ends of the complementary strand significantly retards strand exchange, whereas applying the same force to the outgoing strand does not. We also show that crystallographically determined binding site locations require an intermediate structure in addition to the initial and final structures. Furthermore, we demonstrate that the characteristic dsDNA extension rates due to strand exchange and free RecA binding are the same, suggesting that relocation of the complementary strand from its position in the intermediate structure to its position in the final structure limits both rates. Finally, we propose that homology recognition is governed by transitions to and from the intermediate structure, where the transitions depend on differential extension in the dsDNA. This differential extension drives strand exchange forward for homologs and increases the free energy penalty for strand exchange of non-homologs.
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Mechanism of homology recognition in DNA recombination from dual-molecule experiments. Mol Cell 2012; 46:616-24. [PMID: 22560720 DOI: 10.1016/j.molcel.2012.03.029] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 02/21/2012] [Accepted: 03/30/2012] [Indexed: 11/24/2022]
Abstract
In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule manipulation, combining magnetic and optical tweezers. We find that the filament's secondary DNA-binding site interacts with a single strand of the incoming double-stranded DNA during homology sampling. Recognition requires opening of the helix and is strongly promoted by unwinding torsional stress. Recognition is achieved upon binding of both strands of the incoming dsDNA to each of two ssDNA-binding sites in the filament. The data indicate a physical picture for homology recognition in which the fidelity of the search process is governed by the distance between the DNA-binding sites.
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