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Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res 2010; 38:6313-23. [PMID: 20507912 PMCID: PMC2965220 DOI: 10.1093/nar/gkq459] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
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Affiliation(s)
- Adrien Saladin
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005 Paris, MTI, France
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2
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Xiao J, Lee AM, Singleton SF. Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination. Chembiochem 2006; 7:1265-78. [PMID: 16847846 DOI: 10.1002/cbic.200600038] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Escherichia coli RecA protein is the prototype of a class of proteins that play central roles in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding homologous recombination. We explored the mechanism of RecA-mediated DNA-strand exchange using oligonucleotide substrates with the intrinsic fluorophore 6-methylisoxanthopterin. Pre-steady-state spectrofluorometric analysis elucidated the earliest transient intermediates formed during recombination and delineated the mechanistic strategy by which RecA facilitates this process. The structural features of the first detectable intermediate and the energetic characteristics of its formation were consistent with interactions between a few bases of the single-stranded DNA and the minor groove of a locally melted or stretched duplex DNA. Further analysis revealed RecA to be an unusual enzyme in that entropic rather than enthalpic contributions dominate its catalytic function, and no unambiguously active role for the protein was detected in the earliest molecular events of recombination. The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics.
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Affiliation(s)
- Jie Xiao
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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3
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Voloshin ON, Camerini-Otero RD. Synaptic complex revisited; a homologous recombinase flips and switches bases. Mol Cell 2004; 15:846-7. [PMID: 15383274 DOI: 10.1016/j.molcel.2004.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While it is still unclear how RecA and its eukaryotic homologs conduct genome-wide homology searches, Radding and colleagues report in this issue of Molecular Cell (Folta-Stogniew et al., 2004) that the latter stages of homologous recognition or alignment involve base flipping (localized melting) and switching (annealing) at A:T rich regions.
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Affiliation(s)
- Oleg N Voloshin
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Abstract
The p53 tumor suppressor gene plays an important role in preventing cancer development, by arresting or killing potential tumor cells. Mutations within the p53 gene, leading to the loss of p53 activity, are found in about half of all human cancers, while many of the tumors that retain wild type p53 carry mutations in the pathways that allow full activation of p53. In either case, the result is a defect in the ability to induce a p53 response in cells undergoing oncogenic stress. Significant advances have been made recently in our understanding of the molecular pathways through which p53 activity is regulated, bringing with them fresh possibilities for the design of cancer therapies based on reactivation of the p53 response.
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Affiliation(s)
- Karen H Vousden
- Regulation of Cell Growth Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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5
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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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6
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Cheng RZ, Shammas MA, Li J, Shmookler Reis RJ. Expression of SV40 large T antigen stimulates reversion of a chromosomal gene duplication in human cells. Exp Cell Res 1997; 234:300-12. [PMID: 9260898 DOI: 10.1006/excr.1997.3649] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transformation of human cells is characterized by altered cell morphology, frequent karyotypic abnormalities, reduced dependence on growth factors and substrate, and rare "immortalization"-clonal acquisition of unlimited proliferative potential. We previously reported a marked increase in DNA rearrangements, arising between two duplicated segments in a transfected plasmid substrate, for five immortal human cell lines relative to three normal fibroblast strains [Finn et al. (1989) Mol. Cell. Biol. 9, 4009-4017]. We have now assessed reversion of a 14-kilobase-pair duplication within the hypoxanthine phosphoribosyl transferase (HPRT) gene locus, in a fibroblast strain during its normal replicative lifespan and after stable transformation with SV40 large-T antigen. Revertants, selected under HPRT-dependent growth conditions immediately after purging preexisting HPRT+ cells, were confirmed as HPRT+ by hypoxanthine incorporation and 6-thioguanine sensitivity. Southern blot analyses indicate loss from most revertant clones of a restriction fragment representing the duplicated HPRT region, as predicted for homologous recombination between the 14-kilobase-pair repeats. Amplification of a subregion of HPRT mRNA implicated deletion of duplicated exons in 93% of revertant colonies. Reversion to HPRT+ was unaltered during the normal in vitro lifespan of these cells, but increased in 9 clones stably transformed with large-T antigen (mean = 3.8-fold; each P < 10(-5)). Stimulation of HPRT-reversion is abrogated in a variety of T-antigen mutants, and depends on continued induction of T antigen by glucocorticoid in two clones tested 10-30 doublings before replicative senescence. Since no immortal subclones arose from these clones, elevated reversion must precede immortalization. Increased DNA rearrangements, in cells expressing T-antigen, could facilitate the rare concurrence of multiple mutations necessary for immortalization.
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Affiliation(s)
- R Z Cheng
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock 72205, USA
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7
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Zhou X, Adzuma K. DNA strand exchange mediated by the Escherichia coli RecA protein initiates in the minor groove of double-stranded DNA. Biochemistry 1997; 36:4650-61. [PMID: 9109676 DOI: 10.1021/bi9630063] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Escherichia coli RecA protein can recognize sequence homology between a single-stranded DNA (ssDNA) and homologous double-stranded DNA (dsDNA). One model for the homology recognition invokes a DNA triplex intermediate in which specific hydrogen bonds connect the ssDNA with groups in the major groove of dsDNA. Using photo-cross-linking methods, we have analyzed the arrangement of DNA strands after the local strand exchange. The results showed that the displaced strand sits in the major groove of the hybrid duplex product. This arrangement indicates that the ssDNA invades the minor groove of dsDNA and hence argues against the involvement of triplex intermediates. The results support an alternative model for the homology recognition that invokes melting of the dsDNA and annealing of the one strand to the invading ssDNA.
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Affiliation(s)
- X Zhou
- Rockefeller University, New York 10021, USA
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8
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Acharya S, Choudhury NR, Rao MR. Characterisation of a DNA pairing activity copurifying with DNA ligase in a partially purified extract from rat testis. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1309:131-46. [PMID: 8950188 DOI: 10.1016/s0167-4781(96)00120-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rat testicular nuclear extracts were fractionated sequentially on phosphocellulose, heparin-agarose and ssDNA-cellulose columns, in order to isolate and characterise a strand-transfer activity from a mammalian meiotic tissue. A partially purified fraction, eluting at 0.6 M KCl from ssDNA-cellulose column, catalyzed the formation of two classes of products migrating slowly on an agarose gel. The formation of one of these classes of products-the aggregates-was dependent on the presence of both the substrates (M13mp19 RF III and M13mp19 ssDNA) and on homology. The presence of ATP was essential for the formation of aggregates, though its hydrolysis was not required. EM analysis of the products indicated the presence of structures which resembled paired DNA molecules: duplex-duplex paired (Y-shaped and ds-ds paired structures) and ss-ds paired (duplex DNA paired with the single-stranded DNA) structures, indicating the presence of a pairing protein in the fraction. However, alpha- and sigma-structures were not observed. The other class of products, seen as discrete bands, were identified biochemically and by electron microscopy as ligated products. A DNA ligase-adenylate adduct of molecular weight 100 kDa was formed by the fraction. Both 5' to 3' and 3' to 5' exonucleases were absent and hence did not contribute to the formation of the products.
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Affiliation(s)
- S Acharya
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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9
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10
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Angov E, Camerini-Otero RD. The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization. J Bacteriol 1994; 176:1405-12. [PMID: 8113181 PMCID: PMC205206 DOI: 10.1128/jb.176.5.1405-1412.1994] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have cloned, expressed, and purified the RecA analog from the thermophilic eubacterium Thermus aquaticus YT-1. Analysis of the deduced amino acid sequence indicates that the T. aquaticus RecA is structurally similar to the Escherichia coli RecA and suggests that RecA-like function has been conserved in thermophilic organisms. Preliminary biochemical analysis indicates that the protein has an ATP-dependent single-stranded DNA binding activity and can pair and carry out strand exchange to form a heteroduplex DNA under reaction conditions previously described for E. coli RecA, but at 55 to 65 degrees C. Further characterization of a thermophilically derived RecA protein should yield important information concerning DNA-protein interactions at high temperatures. In addition, a thermostable RecA protein may have some general applicability in stabilizing DNA-protein interactions in reactions which occur at high temperatures by increasing the specificity (stringency) of annealing reactions.
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Affiliation(s)
- E Angov
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892
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11
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Cole AD, Kmiec EB. ATP-independent DNA renaturation catalyzed by a protein from Ustilago maydis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 220:75-82. [PMID: 8119300 DOI: 10.1111/j.1432-1033.1994.tb18600.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A protein that catalyzes the renaturation of complementary strands of DNA has been purified from mitotic cells of the lower eukaryote Ustilago maydis. The most highly purified fraction contains a polypeptide with a molecular mass of 20 kDa as determined by SDS/PAGE and glycerol gradient sedimentation. DNA reannealing is enhanced by the presence of a divalent cation but does not require ATP nor any other nucleotide triphosphate. Reassociation proceeds with fast kinetics as more than 60% of the DNA is reannealed within 4 min at a 30:1 nucleotide/protein monomer ratio, results which suggest that the protein acts in a stoichiometric fashion. Amino acid analysis revealed that the protein contained an elevated level of basic residues and low levels of tryptophan and tyrosine. The protein binds to an oligonucleotide of ten residues but not to one having only five. As judged by agarose gel assays, the protein does not catalyze strand-transfer reactions but does promote the annealing of a 58-residue polynucleotide onto single-stranded circles and gapped linear duplexes. These latter reactions are dependent on the presence of DNA sequence similarity between the pairing partners.
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Affiliation(s)
- A D Cole
- Department of Pharmacology, Jefferson Cancer Institute, Thomas Jefferson University, Philadelphia, PA 19107
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12
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Kmiec EB, Holloman WK. ATP-dependent DNA renaturation and DNA-dependent ATPase reactions catalyzed by the Ustilago maydis homologous pairing protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:865-75. [PMID: 8112338 DOI: 10.1111/j.1432-1033.1994.tb18568.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Purification of the ATP-dependent homologous pairing activity from Ustilago maydis yields a protein preparation that is enriched for a 70-kDa polypeptide as determined by SDS-gel electrophoresis. The protein responsible for the ATP-dependent pairing activity, using renaturation of complementary single strands of DNA as an assay, has a Stokes radius of 3.6 nm and a sedimentation coefficient of 4.3 S consistent with the interpretation that the activity arises from a monomeric globular protein of 70 kDa. Including heparin-agarose and FPLC gel filtration chromatography steps in the previously published protocol improves the purification of the protein. ATP and Mg2+ are necessary cofactors for optimal DNA renaturation activity. ADP inhibits the reaction. Analysis of the ATP-dependent renaturation kinetics indicates the reaction proceeds through a first-order mechanism. The protein has an associated DNA-dependent ATPase as indicated by co-chromatography with the purified ATP-dependent renaturation activity through an FPLC gel-filtration column. Single-stranded DNA and Mg2+ are required for optimal ATP hydrolytic activity, although a number of other polynucleotides and divalent cations can substitute to varying degrees. Hydrolysis of ATP is activated in a sigmoidal manner with increasing amounts of the protein. At ATP concentrations below 0.1 mM the ATPase activity exhibits positive cooperativity as indicated from the Hill coefficient of 1.8 determined by steady-state kinetic analysis of the reaction. ADP and adenosine 5'-[beta,gamma-imido]triphosphate are inhibitors of the ATPase activity although they appear to exert their inhibitory effects through different modes. These results are interpreted as evidence for protein-protein interactions.
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Affiliation(s)
- E B Kmiec
- Department of Pharmacology, Jefferson Cancer Institute, Thomas Jefferson University, Philadelphia
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13
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Jessberger R, Podust V, Hübscher U, Berg P. A mammalian protein complex that repairs double-strand breaks and deletions by recombination. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)82439-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Camerini-Otero RD, Hsieh P. Parallel DNA triplexes, homologous recombination, and other homology-dependent DNA interactions. Cell 1993; 73:217-23. [PMID: 8477443 DOI: 10.1016/0092-8674(93)90224-e] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- R D Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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15
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Affiliation(s)
- E C Conley
- Department of Biochemistry, University of Leicester, UK
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16
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Mishina Y, Shimokawa T, Kawasaki K, Arai N, Shibata T, Koyama H. Identification of two types of homologous DNA pairing activity in mouse cells. Biochem Biophys Res Commun 1992; 185:987-92. [PMID: 1627150 DOI: 10.1016/0006-291x(92)91724-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have identified two types of homologous DNA pairing activity in mouse cell extracts by a strand-transfer assay. Both activities are separated from each other by anion-exchange chromatography; neither of them needs ATP. One requires magnesium ion and is stimulated by Escherichia coli single-stranded DNA binding protein, whereas the other does not require the ion and shows a higher affinity for a left-handed Z-DNA.
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MESH Headings
- Adenosine Triphosphate/metabolism
- Animals
- Chromatography, Affinity
- Chromatography, Ion Exchange
- Clone Cells
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/metabolism
- Escherichia coli/metabolism
- Magnesium/metabolism
- Mammary Neoplasms, Experimental
- Mice
- Substrate Specificity
- Tumor Cells, Cultured
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Affiliation(s)
- Y Mishina
- Kihara Institute for Biological Research, Yokohama City University, Japan
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17
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Ferrin LJ, Camerini-Otero RD. Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage. Science 1991; 254:1494-7. [PMID: 1962209 DOI: 10.1126/science.1962209] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Current methods for sequence-specific cleavage of large segments of DNA are severely limited because of the paucity of possible cleavage sites. A method is described whereby any Eco RI site can be targeted for specific cleavage. The technique is based on the ability of RecA protein from Escherichia coli to pair an oligonucleotide to its homologous sequence in duplex DNA and to form a three-stranded complex. This complex is protected from Eco RI methylase; after methylation and RecA protein removal, Eco RI restriction enzyme cleavage was limited to the site previously protected from methylation. When pairs of oligonucleotides are used, a specific fragment can be cleaved out of genomes. The method was tested on lambda phage, Escherichia coli, and human DNA. Fragments exceeding 500 kilobases in length and yields exceeding 80 percent could be obtained.
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Affiliation(s)
- L J Ferrin
- Genetics and Biochemistry Branch, National Institute of Diabetics and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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18
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Abstract
Processes fundamental to all models of genetic recombination include the homologous pairing and subsequent exchange of DNA strands. Biochemical analysis of these events has been conducted primarily on the recA protein of Escherichia coli, although proteins which can promote such reactions have been purified from many sources, both prokaryotic and eukaryotic. The activities of these homologous pairing and DNA strand exchange proteins are either ATP-dependent, as predicted based on the recA protein paradigm, or, more unexpectedly, ATP-independent. This review examines the reactions promoted by both classes of proteins and highlights their similarities and differences. The mechanistic implications of the apparent existence of 2 classes of strand exchange protein are discussed.
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Affiliation(s)
- A K Eggleston
- Department of Cell, Molecular, and Structural Biology, Northwestern University Medical School, IL 60611
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19
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Hsieh P, Camerini-Otero CS, Camerini-Otero RD. Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev 1990; 4:1951-63. [PMID: 2276627 DOI: 10.1101/gad.4.11.1951] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We show that recombinases form joint molecules over very short regions of homology. When these molecules are deproteinized the three strands are in a structure that is surprisingly resistant to dissociation by branch migration, even at elevated temperatures. The joint molecules dissociate at temperatures comparable to those required to melt DNA duplexes of the same length and sequence. We also show that nonenzymatically formed structures of the same length and sequence, which have a free third strand ready to branch migrate, dissociate at much lower temperatures. These results provide compelling evidence that the three DNA strands in the region of pairing are hydrogen bonded to each other. Our observations suggest that such a novel three-stranded DNA molecule, or a structure very similar to it, may be the intermediate in general recombination that is used in the recognition of sequence homology. We discuss some of the structural features implicit in this molecule containing any base sequence and compare them with those manifest in true DNA triple helices containing special sequence motifs.
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Affiliation(s)
- P Hsieh
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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20
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Rao BJ, Jwang B, Radding CM. RecA protein reinitiates strand exchange on isolated protein-free DNA intermediates. An ADP-resistant process. J Mol Biol 1990; 213:789-809. [PMID: 2141651 DOI: 10.1016/s0022-2836(05)80264-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efficient homologous pairing de novo of linear duplex DNA with a circular single strand (plus strand) coated with RecA protein requires saturation and extension of the single strand by the protein. However, strand exchange, the transfer of a strand from duplex DNA to the nucleoprotein filament, which follows homologous pairing, does not require the stable binding of RecA protein to single-stranded DNA. When RecA protein was added back to isolated protein-free DNA intermediates in the presence of sufficient ADP to inhibit strongly the binding of RecA protein to single-stranded DNA, strand exchange nonetheless resumed at the original rate and went to completion. Characterization of the protein-free DNA intermediate suggested that it has a special site or region to which RecA protein binds. Part of the nascent displaced plus strand of the deproteinized intermediate was unavailable as a cofactor for the ATPase activity of RecA protein, and about 30% resisted digestion by P1 endonuclease, which acts preferentially on single-stranded DNA. At the completion of strand exchange, when the distal 5' end of the linear minus strand had been fully incorporated into heteroduplex DNA, a nucleoprotein complex remained that contained all three strands of DNA from which the nascent displaced strand dissociated only over the next 50 to 60 minutes. Deproteinization of this intermediate yielded a complex that also contained three strands of DNA in which the nascent displaced strand was partially resistant to both Escherichia coli exonuclease I and P1 endonuclease. The deproteinized complex showed a broad melting transition between 37 degrees C and temperatures high enough to melt duplex DNA. These results show that strand exchange can be subdivided into two stages: (1) the exchange of base-pairs, which creates a new heteroduplex pair in place of a parental pair; and (2) strand separation, which is the physical displacement of the unpaired strand from the nucleoprotein filament. Between the creation of new heteroduplex DNA and the eventual separation of a third strand, there exists an unusual DNA intermediate that may contain three-stranded regions of natural DNA that are several thousand bases in length.
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Affiliation(s)
- B J Rao
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510
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