1
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Muhammad AA, Basto C, Peterlini T, Guirouilh-Barbat J, Thomas M, Veaute X, Busso D, Lopez B, Mazon G, Le Cam E, Masson JY, Dupaigne P. Human RAD52 stimulates the RAD51-mediated homology search. Life Sci Alliance 2024; 7:e202201751. [PMID: 38081641 PMCID: PMC10713436 DOI: 10.26508/lsa.202201751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Homologous recombination (HR) is a DNA repair mechanism of double-strand breaks and blocked replication forks, involving a process of homology search leading to the formation of synaptic intermediates that are regulated to ensure genome integrity. RAD51 recombinase plays a central role in this mechanism, supported by its RAD52 and BRCA2 partners. If the mediator function of BRCA2 to load RAD51 on RPA-ssDNA is well established, the role of RAD52 in HR is still far from understood. We used transmission electron microscopy combined with biochemistry to characterize the sequential participation of RPA, RAD52, and BRCA2 in the assembly of the RAD51 filament and its activity. Although our results confirm that RAD52 lacks a mediator activity, RAD52 can tightly bind to RPA-coated ssDNA, inhibit the mediator activity of BRCA2, and form shorter RAD51-RAD52 mixed filaments that are more efficient in the formation of synaptic complexes and D-loops, resulting in more frequent multi-invasions as well. We confirm the in situ interaction between RAD51 and RAD52 after double-strand break induction in vivo. This study provides new molecular insights into the formation and regulation of presynaptic and synaptic intermediates by BRCA2 and RAD52 during human HR.
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Affiliation(s)
- Ali Akbar Muhammad
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Clara Basto
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Thibaut Peterlini
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Josée Guirouilh-Barbat
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Melissa Thomas
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Xavier Veaute
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Didier Busso
- https://ror.org/02vjkv261 CIGEx Platform, INSERM, IRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Université de Paris and Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Bernard Lopez
- https://ror.org/02vjkv261 INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, Université de Paris, Paris, France
| | - Gerard Mazon
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Eric Le Cam
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Quebec City, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Canada
| | - Pauline Dupaigne
- Genome Integrity and Cancers UMR 9019 CNRS, Université Paris- Saclay, Gustave Roussy, Villejuif Cedex, France
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2
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Ziesel A, Weng Q, Ahuja JS, Bhattacharya A, Dutta R, Cheng E, Börner GV, Lichten M, Hollingsworth NM. Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase. PLoS Genet 2022; 18:e1010407. [PMID: 36508468 PMCID: PMC9779700 DOI: 10.1371/journal.pgen.1010407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5' end resection of the DSBs creates 3' single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to involve a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5'-3' helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, and (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates.
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Affiliation(s)
- Andrew Ziesel
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Qixuan Weng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Jasvinder S. Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Abhishek Bhattacharya
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Raunak Dutta
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Evan Cheng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nancy M. Hollingsworth
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
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3
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Benureau Y, Moreira Tavares E, Muhammad AA, Baconnais S, Le Cam E, Dupaigne P. Method combining BAC film and positive staining for the characterization of DNA intermediates by dark-field electron microscopy. Biol Methods Protoc 2020; 5:bpaa012. [PMID: 32913896 PMCID: PMC7474861 DOI: 10.1093/biomethods/bpaa012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/15/2022] Open
Abstract
DNA intermediate structures are formed in all major pathways of DNA metabolism. Transmission electron microscopy (TEM) is a tool of choice to study their choreography and has led to major advances in the understanding of these mechanisms, particularly those of homologous recombination (HR) and replication. In this article, we describe specific TEM procedures dedicated to the structural characterization of DNA intermediates formed during these processes. These particular DNA species contain single-stranded DNA regions and/or branched structures, which require controlling both the DNA molecules spreading and their staining for subsequent visualization using dark-field imaging mode. Combining BAC (benzyl dimethyl alkyl ammonium chloride) film hyperphase with positive staining and dark-field TEM allows characterizing synthetic DNA substrates, joint molecules formed during not only in vitro assays mimicking HR, but also in vivo DNA intermediates.
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Affiliation(s)
- Yann Benureau
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
- UMR9019-CNRS, Genome Integrity and Cancer, Equipe labellisée Ligue contre le Cancer, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Eliana Moreira Tavares
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Ali-Akbar Muhammad
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Sonia Baconnais
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Eric Le Cam
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
- Correspondence address. DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France. Tel: 00 33 1 42 11 48 76 and 00 33 1 42 11 48 74; E-mail:
| | - Pauline Dupaigne
- DSB Repair, Replication Stress and Genome Integrity, UMR9019-CNRS ‘Genome Integrity and Cancer’, CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
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4
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Tavares EM, Wright WD, Heyer WD, Le Cam E, Dupaigne P. In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation. Nat Commun 2019; 10:4058. [PMID: 31492866 PMCID: PMC6731316 DOI: 10.1038/s41467-019-12082-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/12/2019] [Indexed: 11/28/2022] Open
Abstract
Homologous recombination (HR) uses a homologous template to accurately repair DNA double-strand breaks and stalled replication forks to maintain genome stability. During homology search, Rad51 nucleoprotein filaments probe and interact with dsDNA, forming the synaptic complex that is stabilized on a homologous sequence. Strand intertwining leads to the formation of a displacement-loop (D-loop). In yeast, Rad54 is essential for HR in vivo and required for D-loop formation in vitro, but its exact role remains to be fully elucidated. Using electron microscopy to visualize the DNA-protein complexes, here we find that Rad54 is crucial for Rad51-mediated synaptic complex formation and homology search. The Rad54−K341R ATPase-deficient mutant protein promotes formation of synaptic complexes but not D-loops and leads to the accumulation of stable heterologous associations, suggesting that the Rad54 ATPase is involved in preventing non-productive intermediates. We propose that Rad51/Rad54 form a functional unit operating in homology search, synaptic complex and D-loop formation. Homologous recombination uses a template to accurately repair DNA double-strand breaks and stalled replication forks to maintain genome stability. Here authors use electron microscopy to investigate the role of Rad54 in homology search and synaptic complex formation.
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Affiliation(s)
- Eliana Moreira Tavares
- Genome Maintenance and Molecular Microscopy UMR8126 CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - William Douglass Wright
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR8126 CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR8126 CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France.
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5
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Wright WD, Shah SS, Heyer WD. Homologous recombination and the repair of DNA double-strand breaks. J Biol Chem 2018; 293:10524-10535. [PMID: 29599286 DOI: 10.1074/jbc.tm118.000372] [Citation(s) in RCA: 404] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination enables the cell to access and copy intact DNA sequence information in trans, particularly to repair DNA damage affecting both strands of the double helix. Here, we discuss the DNA transactions and enzymatic activities required for this elegantly orchestrated process in the context of the repair of DNA double-strand breaks in somatic cells. This includes homology search, DNA strand invasion, repair DNA synthesis, and restoration of intact chromosomes. Aspects of DNA topology affecting individual steps are highlighted. Overall, recombination is a dynamic pathway with multiple metastable and reversible intermediates designed to achieve DNA repair with high fidelity.
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Affiliation(s)
| | | | - Wolf-Dietrich Heyer
- From the Departments of Microbiology and Molecular Genetics and .,Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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6
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Lu CH, Li HW. DNA with Different Local Torsional States Affects RecA-Mediated Recombination Progression. Chemphyschem 2017; 18:584-590. [PMID: 28054431 DOI: 10.1002/cphc.201601281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/04/2017] [Indexed: 11/10/2022]
Abstract
DNA topology is thought to affect DNA enzyme activity. The helical structure of duplex DNA dictates the change of topological states during strand separation when DNA is constrained. During the repair of DNA double-stranded breaks, the RecA nucleoprotein filament invades DNA and carries out consecutive strand exchange reactions coupled with duplex DNA strand separation. It has been suggested that torsional strain could be generated and its accumulation could inhibit strand exchange. We used hairpin and nicked DNA substrates to test how torsional strain alters the RecA-mediated strand exchange efficiency. Single-molecule tethered particle motion (TPM) experiments showed that torsionally constrained hairpin DNA substrates returned nearly no successful strand exchange events catalyzed by RecA. Surprisingly, the strand exchange efficiencies increase in the presence of DNA nicks or loop disruption. The dwell time of transient RecA events in hairpin is shorter compared to those found in nicked or fork DNA substrates, which suggests a limited strand exchange progression in hairpin substrates. Our observation shows that RecA generates local torsional strain during strand exchange, and the inability to dissipate this torsional strain inhibits homologous recombination progression. DNA topological states are thus important regulation measures of DNA recombination.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan) (R.O.C
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan) (R.O.C
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7
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Mehta A, Beach A, Haber JE. Homology Requirements and Competition between Gene Conversion and Break-Induced Replication during Double-Strand Break Repair. Mol Cell 2017; 65:515-526.e3. [PMID: 28065599 DOI: 10.1016/j.molcel.2016.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/27/2016] [Accepted: 12/01/2016] [Indexed: 11/27/2022]
Abstract
Saccharomyces cerevisiae mating-type switching is initiated by a double-strand break (DSB) at MATa, leaving one cut end perfectly homologous to the HMLα donor, while the second end must be processed to remove a non-homologous tail before completing repair by gene conversion (GC). When homology at the matched end is ≤150 bp, efficient repair depends on the recombination enhancer, which tethers HMLα near the DSB. Thus, homology shorter than an apparent minimum efficient processing segment can be rescued by tethering the donor near the break. When homology at the second end is ≤150 bp, second-end capture becomes inefficient and repair shifts from GC to break-induced replication (BIR). But when pol32 or pif1 mutants block BIR, GC increases 3-fold, indicating that the steps blocked by these mutations are reversible. With short second-end homology, absence of the RecQ helicase Sgs1 promotes gene conversion, whereas deletion of the FANCM-related Mph1 helicase promotes BIR.
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Affiliation(s)
- Anuja Mehta
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Annette Beach
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA.
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8
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Mismatch repair and homeologous recombination. DNA Repair (Amst) 2015; 38:75-83. [PMID: 26739221 DOI: 10.1016/j.dnarep.2015.11.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 10/26/2015] [Accepted: 11/30/2015] [Indexed: 12/27/2022]
Abstract
DNA mismatch repair influences the outcome of recombination events between diverging DNA sequences. Here we discuss how mismatch repair proteins are active in different homologous recombination subpathways and specific reaction steps, resulting in differential modulation of these recombination events, with a focus on the mechanism of heteroduplex rejection during the inhibition of recombination between slightly diverged (homeologous) DNA sequences.
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9
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Abstract
In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.
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Affiliation(s)
- Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
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10
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Real-time analysis of double-strand DNA break repair by homologous recombination. Proc Natl Acad Sci U S A 2011; 108:3108-15. [PMID: 21292986 DOI: 10.1073/pnas.1019660108] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability to induce synchronously a single site-specific double-strand break (DSB) in a budding yeast chromosome has made it possible to monitor the kinetics and genetic requirements of many molecular steps during DSB repair. Special attention has been paid to the switching of mating-type genes in Saccharomyces cerevisiae, a process initiated by the HO endonuclease by cleaving the MAT locus. A DSB in MATa is repaired by homologous recombination--specifically, by gene conversion--using a heterochromatic donor, HMLα. Repair results in the replacement of the a-specific sequences (Ya) by Yα and switching from MATa to MATα. We report that MAT switching requires the DNA replication factor Dpb11, although it does not require the Cdc7-Dbf4 kinase or the Mcm and Cdc45 helicase components. Using Southern blot, PCR, and ChIP analysis of samples collected every 10 min, we extend previous studies of this process to identify the times for the loading of Rad51 recombinase protein onto the DSB ends at MAT, the subsequent strand invasion by the Rad51 nucleoprotein filament into the donor sequences, the initiation of new DNA synthesis, and the removal of the nonhomologous Y sequences. In addition we report evidence for the transient displacement of well-positioned nucleosomes in the HML donor locus during strand invasion.
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11
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12
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Sinha M, Peterson CL. A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand break. Mol Cell 2008; 30:803-10. [PMID: 18570881 DOI: 10.1016/j.molcel.2008.04.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 03/05/2008] [Accepted: 04/24/2008] [Indexed: 01/17/2023]
Abstract
Repair of chromosomal DNA double-strand breaks by homologous recombination is essential for cell survival and genome stability. Within eukaryotic cells, this repair pathway requires a search for a homologous donor sequence and a subsequent strand invasion event on chromatin fibers. We employ a biotin-streptavidin minichromosome capture assay to show that yRad51 or hRad51 presynaptic filaments are sufficient to locate a homologous sequence and form initial joints, even on the surface of a nucleosome. Furthermore, we present evidence that the Rad54 chromatin-remodeling enzyme functions to convert these initial metastable products of the homology search to a stable joint molecule that is competent for subsequent steps of the repair process. Thus, contrary to popular belief, nucleosomes do not pose a potent barrier for successful recognition and capture of homology by an invading presynaptic filament.
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Affiliation(s)
- Manisha Sinha
- Program in Molecular Medicine, Interdisciplinary Graduate Program, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
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13
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Hülter N, Wackernagel W. Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi. Mol Microbiol 2008; 67:984-95. [PMID: 18194157 DOI: 10.1111/j.1365-2958.2007.06096.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acquisition of foreign DNA by horizontal gene transfer is seen as a major source of genetic diversity in prokaryotes. However, strongly divergent DNA is not genomically integrated by homologous recombination and would depend on illegitimate recombination (IR) events which are rare. We show that, by two mechanisms, during natural transformation of Acinetobacter baylyi two IR events can integrate DNA segments. One mechanism is double illegitimate recombination (DIR) acting in the absence of any homology (frequency: 7 x 10(-13) per cell). It occurs about 10(10)-fold less frequent than homologous transformation. The other mechanism is homology-facilitated double illegitimate recombination (HFDIR) being about 440-fold more frequent (3 x 10(-10) per cell) than DIR. HFDIR depends on a homologous sequence located between the IR sites and on recA(+). In HFDIR two IR events act on the same donor DNA molecule as shown by the joint inheritance of molecular DNA tags. While the IR events in HFDIR occurred at microhomologies, in DIR microhomologies were not used. The HFDIR phenomenon indicates that a temporal recA-dependent association of donor DNA at a homology in recipient DNA may facilitate two IR events on the 5' and 3' heterologous parts of the transforming DNA molecule.
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Affiliation(s)
- Nils Hülter
- Genetics, Department of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, D-26111 Oldenburg, Germany
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14
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Selmane T, Wittung-Stafshede P, Maraboeuf F, Voloshin ON, Nordén B, Camerini-Otero DR, Takahashi M. The L2 loop peptide of RecA stiffens and restricts base motions of single-stranded DNA similar to the intact protein. FEBS Lett 1999; 446:30-4. [PMID: 10100609 DOI: 10.1016/s0014-5793(99)00181-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The L2 loop in the RecA protein is the catalytic center for DNA strand exchange. Here we investigate the DNA binding properties of the L2 loop peptide using optical spectroscopy with polarized light. Both fluorescence intensity and anisotropy of an etheno-modified poly(dA) increase upon peptide binding, indicate that the base motions of single-stranded DNA are restricted in the complex. In agreement with this conclusion, the peptide-poly(dT) complex exhibits a significant linear dichroism signal. The peptide is also found to modify the structure of double-stranded DNA, but does not denature it. It is inferred that strand separation may not be required for the formation of a joint molecule.
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Affiliation(s)
- T Selmane
- Unité Mixte de Recherche 216, Institut Curie and CNRS, Orsay, France
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15
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Wong BC, Chiu SK, Chow SA. The role of negative superhelicity and length of homology in the formation of paranemic joints promoted by RecA protein. J Biol Chem 1998; 273:12120-7. [PMID: 9575157 DOI: 10.1074/jbc.273.20.12120] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli RecA protein pairs homologous DNA molecules to form paranemic joints when there is an absence of a free end in the region of homologous contact. Paranemic joints are a key intermediate in homologous recombination and are important in understanding the mechanism for a search of homology. The efficiency of paranemic joint formation depended on the length of homology and the topological forms of the duplex DNA. The presence of negative superhelicity increased the pairing efficiency and reduced the minimal length of homology required for paranemic joint formation. Negative superhelicity stimulated joint formation by favoring the initial unwinding of duplex DNA that occurred during the homology search and was not essential in the maintenance of the paired structure. Regardless of length of homology, formation of paranemic joints using circular duplex DNA required the presence of more than six negative supercoils. Above six negative turns, an increasing degree of negative superhelicity resulted in a linear increase in the pairing efficiency. These results support a model of two distinct kinds of DNA unwinding occurring in paranemic joint formation: an initial unwinding caused by heterologous contacts during synapsis and a later one during pairing of the homologous molecules.
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Affiliation(s)
- B C Wong
- Department of Biochemistry, University of Hong Kong, Hong Kong
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16
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Kowalczykowski SC, Dixon DA, Eggleston AK, Lauder SD, Rehrauer WM. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 1994; 58:401-65. [PMID: 7968921 PMCID: PMC372975 DOI: 10.1128/mr.58.3.401-465.1994] [Citation(s) in RCA: 778] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
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Affiliation(s)
- S C Kowalczykowski
- Division of Biological Sciences, University of California, Davis 95616-8665
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17
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Chen J, Kanaar R, Cozzarelli NR. The Sep1 strand exchange protein from Saccharomyces cerevisiae promotes a paranemic joint between homologous DNA molecules. Genes Dev 1994; 8:1356-66. [PMID: 7926736 DOI: 10.1101/gad.8.11.1356] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Strand exchange protein 1 (Sep1) from the yeast Saccharomyces cerevisiae promotes the transfer of one strand of a linear duplex DNA to a homologous single-stranded DNA circle. Using a nitrocellulose filter binding assay and electron microscopy, we find that Sep1 promotes the pairing of homologous DNA molecules via a paranemic joint. In this joint there is no net intertwining of the parental DNA molecules, as in the standard plectonemic double helix. The paranemic joints form with as little as 41 bp of homology between the parental DNA molecules. The substrates used were a circular molecule (either single-stranded DNA or duplex supercoiled DNA) and a linear duplex with heterologous regions at both ends to bar duplex plectonemic intertwining. We excluded the possibility that the exonuclease activity of Sep1 exposes complementary single-stranded regions that constitute the joint. The paranemic joint is the key intermediate in the search for homologous DNA by the RecA protein of Escherichia coli. Our results imply that the search process in a eukaryote such as yeast can be mechanistically similar.
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Affiliation(s)
- J Chen
- Department of Molecular and Cell Biology, University of California, Berkeley 94720
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18
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Le Cam E, Théveny B, Mignotte B, Révet B, Delain E. Quantitative electron microscopic analysis of DNA-protein interactions. JOURNAL OF ELECTRON MICROSCOPY TECHNIQUE 1991; 18:375-86. [PMID: 1656003 DOI: 10.1002/jemt.1060180406] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Electron microscopy offers a unique potentiality to visualize individual molecules. For the last 30 years it has been used to study the structure and the interactions of various biological macromolecules. The contribution of electron microscopy is important because of its capacity to demonstrate the existence of conformational structures such as kinks, bents, loops, etc., either on naked DNA, or on DNA associated with various proteins or ligands. Increasing interest was given to such observations when it was found that they provide a direct visualization of interacting molecules involved in DNA metabolism and gene regulation. Technical advances in the preparation of the specimens, their observation in the electron microscope, and the image processing by computers have allowed the shifting from qualitative to quantitative analysis, as illustrated by a few examples from our laboratory.
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Affiliation(s)
- E Le Cam
- Laboratoire de Microscopie Cellulaire et Moléculaire, URA 147 and SDI6268 du CNRS, Institut Gustave-Roussy, Villejuif, France
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19
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Abstract
A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.
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MESH Headings
- Animals
- Base Sequence
- Chromosomes/ultrastructure
- DNA/drug effects
- DNA/metabolism
- DNA/ultrastructure
- DNA Helicases/metabolism
- DNA Replication
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/metabolism
- DNA, Single-Stranded/ultrastructure
- DNA, Superhelical/drug effects
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/metabolism
- Endonucleases/metabolism
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation/drug effects
- Nucleic Acid Denaturation
- Plasmids
- Transcription, Genetic
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Affiliation(s)
- G Yagil
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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20
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Abstract
The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.
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Affiliation(s)
- R R Meyer
- Department of Biological Sciences, University of Cincinnati, Ohio 45221
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Kubista M, Takahashi M, Nordén B. Stoichiometry, base orientation, and nuclease accessibility of RecA.DNA complexes seen by polarized light in flow-oriented solution. Implications for the mechanism of genetic recombination. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)30599-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Affiliation(s)
- A I Roca
- Department of Biochemistry, University of Wisconsin-Madison 53706
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24
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Takahashi M, Kubista M, Nordén B. Binding of RecA Protein to Z-form DNA Studied with Circular and Linear Dichroism Spectroscopy. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81829-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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25
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Blaho JA, Wells RD. Left-handed Z-DNA and genetic recombination. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:107-26. [PMID: 2672108 DOI: 10.1016/s0079-6603(08)60696-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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26
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Direct visualization of RecA protein binding to and unwinding duplex DNA following the D-loop cycle. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37911-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Schutte BC, Cox MM. Homology-dependent changes in adenosine 5'-triphosphate hydrolysis during recA protein promoted DNA strand exchange: evidence for long paranemic complexes. Biochemistry 1987; 26:5616-25. [PMID: 3314992 DOI: 10.1021/bi00392a006] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As a first step in DNA strand exchange, recA protein forms a filamentous complex on single-stranded DNA (ssDNA), which contains stoichiometric (one recA monomer per four nucleotides) amounts of recA protein. recA protein monomers within this complex hydrolyze ATP with a turnover number of 25 min-1. Upon introduction of linear homologous duplex DNA to initiate strand exchange, this rate of ATP hydrolysis drops by 33%. The decrease in rate is complete in less than 2 min, and the rate of ATP hydrolysis then remains constant during and subsequent to the strand exchange reaction. This drop is completely dependent upon homology in the duplex DNA. In addition, the magnitude of the drop is linearly dependent upon the length of the homologous region in the linear duplex DNA. Linear DNA substrates in which pairing is topologically restricted to a paranemic joint also follow this relationship. Taken together, these properties imply that all of the available homology in the incoming duplex DNA is detected very early in the DNA strand exchange reaction, with the linear duplex DNA paired paranemically with the homologous ssDNA in the complex throughout its length. The results indicate that paranemic joints can extend over thousands of base pairs. We note elsewhere [Pugh, B. F., & Cox, M. M. (1987b) J. Biol. Chem. 262, 1337-1343] that this duplex acquires resistance to digestion by DNase with a much slower time course (30 min), which parallels the progress of strand exchange. Together these results imply that the duplex DNA is paired with the ssDNA but remains outside the nucleoprotein filament. Finally, the results also support the notion that ATP hydrolysis occurs throughout the recA nucleoprotein filament.
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Affiliation(s)
- B C Schutte
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin--Madison 53706
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29
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Electron microscopic visualization of the RecA protein-mediated pairing and branch migration phases of DNA strand exchange. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45279-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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30
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Shaner SL, Radding CM. Translocation of Escherichia coli recA protein from a single-stranded tail to contiguous duplex DNA. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)48069-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Harris LD, Griffith J. Visualization of the homologous pairing of DNA catalyzed by the bacteriophage T4 UvsX protein. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)48078-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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