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Shibata T, Ikawa S, Iwasaki W, Sasanuma H, Masai H, Hirota K. Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA. Nucleic Acids Res 2024; 52:2565-2577. [PMID: 38214227 PMCID: PMC10954442 DOI: 10.1093/nar/gkad1260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
RecA protein and RecA/Rad51 orthologues are required for homologous recombination and DNA repair in all living creatures. RecA/Rad51 catalyzes formation of the D-loop, an obligatory recombination intermediate, through an ATP-dependent reaction consisting of two phases: homology recognition between double-stranded (ds)DNA and single-stranded (ss)DNA to form a hybrid-duplex core of 6-8 base pairs and subsequent hybrid-duplex/D-loop processing. How dsDNA recognizes homologous ssDNA is controversial. The aromatic residue at the tip of the β-hairpin loop (L2) was shown to stabilize dsDNA-strand separation. We tested a model in which dsDNA strands were separated by the aromatic residue before homology recognition and found that the aromatic residue was not essential to homology recognition, but was required for D-loop processing. Contrary to the model, we found that the double helix was not unwound even a single turn during search for sequence homology, but rather was unwound only after the homologous sequence was recognized. These results suggest that dsDNA recognizes its homologous ssDNA before strand separation. The search for homologous sequence with homologous ssDNA without dsDNA-strand separation does not generate stress within the dsDNA; this would be an advantage for dsDNA to express homology-dependent functions in vivo and also in vitro.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Sasanuma
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
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2
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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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3
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Shibata T, Iwasaki W, Hirota K. The intrinsic ability of double-stranded DNA to carry out D-loop and R-loop formation. Comput Struct Biotechnol J 2020; 18:3350-3360. [PMID: 33294131 PMCID: PMC7677664 DOI: 10.1016/j.csbj.2020.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/03/2022] Open
Abstract
Double-stranded (ds)DNA, not dsRNA, has an ability to form a homologous complex with single-stranded (ss)DNA or ssRNA of homologous sequence. D-loops and homologous triplexes are homologous complexes formed with ssDNA by RecA/Rad51-family homologous-pairing proteins, and are a key intermediate of homologous (genetic/DNA) recombination. R-loop formation independent of transcription (R-loop formation in trans) was recently found to play roles in gene regulation and development of mammals and plants. In addition, the crRNA-Cas effector complex in CRISPR-Cas systems also relies on R-loop formation to recognize specific target. In homologous complex formation, ssDNA/ssRNA finds a homologous sequence in dsDNA by Watson-Crick base-pairing. crRNA-Cas effector complexes appear to actively melt dsDNA to make its bases available for annealing to crRNA. On the other hand, in D-loop formation and homologous-triplex formation, it is likely that dsDNA recognizes the homologous sequence before the melting of its double helix by using its intrinsic molecular function depending on CH2 at the 2'-position of the deoxyribose, and that the major role of RecA is the extension of ssDNA and the holding dsDNA at a position suitable for homology search. This intrinsic dsDNA function would also play a role in R-loop formation. The dependency of homologous-complex formation on 2'-CH2 of the deoxyribose would explain the absence of homologous complex formation by dsRNA, and dsDNA as sole genome molecule in all cellular organisms.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi, Yokohama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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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: 36] [Impact Index Per Article: 7.2] [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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Lu D, Danilowicz C, Tashjian TF, Prévost C, Godoy VG, Prentiss M. Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem 2019; 294:8606-8616. [PMID: 30975899 PMCID: PMC6544866 DOI: 10.1074/jbc.ra119.007554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/10/2019] [Indexed: 11/21/2022] Open
Abstract
DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu. We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with ≥50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.
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Affiliation(s)
- Daniel Lu
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138
| | - Claudia Danilowicz
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138
| | - Tommy F Tashjian
- Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UMR 9080, Institut de Biologie Physico-chimique (IBPC), Paris 75005, France
| | - Veronica G Godoy
- Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138.
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6
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Chen J, Tang Q, Guo S, Lu C, Le S, Yan J. Parallel triplex structure formed between stretched single-stranded DNA and homologous duplex DNA. Nucleic Acids Res 2017; 45:10032-10041. [PMID: 28973442 PMCID: PMC5622322 DOI: 10.1093/nar/gkx628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/11/2017] [Indexed: 02/01/2023] Open
Abstract
The interaction between the single-stranded DNA and the homologous duplex DNA is essential for DNA homologous repair. Here, we report that parallel triplex structure can form spontaneously between a mechanically extended ssDNA and a homologous dsDNA in protein-free condition. The triplex has a contour length close to that of a B-form DNA duplex and remains stable after force is released. The binding energy between the ssDNA and the homologous dsDNA in the triplex is estimated to be comparable to the basepairing energy in a B-form dsDNA. As ssDNA is in a similar extended conformation within recombinase-coated nucleoprotein filaments, we propose that the parallel triplex may form and serve as an intermediate during recombinase-catalyzed homologous joint formation.
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Affiliation(s)
- Jin Chen
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Qingnan Tang
- Department of Physics, National University of Singapore, 117542, Singapore
| | - Shiwen Guo
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Chen Lu
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, 117546, Singapore
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, 117542, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore.,Department of Physics, National University of Singapore, 117542, Singapore.,Centre for Bioimaging Sciences, National University of Singapore, 117546, Singapore
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7
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Danilowicz C, Hermans L, Coljee V, Prévost C, Prentiss M. ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences. Nucleic Acids Res 2017; 45:8448-8462. [PMID: 28854739 PMCID: PMC5737215 DOI: 10.1093/nar/gkx582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/05/2017] [Indexed: 01/30/2023] Open
Abstract
During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with >100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchange was believed to occur after testing ∼20-30 bp. If that were true, pairings between different copies of long repeated sequences would usually become irreversible. Our experiments reveal that in the presence of ATP hydrolysis even 75 bp sequence-matched strand exchange products remain quite reversible. Experiments also indicate that when ATP hydrolysis is present, flanking heterologous dsDNA regions increase the reversibility of sequence matched strand exchange products with lengths up to ∼75 bp. Results of molecular dynamics simulations provide insight into how ATP hydrolysis destabilizes strand exchange products. These results inspired a model that shows how pairings between long repeated sequences could be efficiently rejected even though most homologous pairings form irreversible products.
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Affiliation(s)
| | - Laura Hermans
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Vincent Coljee
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS UMR 9080, IBPC, Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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Bellio P, Di Pietro L, Mancini A, Piovano M, Nicoletti M, Brisdelli F, Tondi D, Cendron L, Franceschini N, Amicosante G, Perilli M, Celenza G. SOS response in bacteria: Inhibitory activity of lichen secondary metabolites against Escherichia coli RecA protein. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2017; 29:11-18. [PMID: 28515022 DOI: 10.1016/j.phymed.2017.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown. PURPOSE Twenty-seven secondary metabolites classified as anthraquinones, depsides, depsidones, dibenzofurans, diphenyl-butenolides, paraconic acids, pseudo-depsidones, triterpenes and xanthones, were investigated for their ability to inhibit RecA from Escherichia coli. They were isolated in various Chilean regions from 14 families and 19 genera of lichens. METHODS The ATP hydrolytic activity of RecA was quantified detecting the generation of free phosphate in solution. The percentage of inhibition was calculated fixing at 100µM the concentration of the compounds. Deeper investigations were reserved to those compounds showing an inhibition higher than 80%. To clarify the mechanism of inhibition, the semi-log plot of the percentage of inhibition vs. ATP and vs. ssDNA, was evaluated. RESULTS Only nine compounds showed a percentage of RecA inhibition higher than 80% (divaricatic, perlatolic, alpha-collatolic, lobaric, lichesterinic, protolichesterinic, epiphorellic acids, sphaerophorin and tumidulin). The half-inhibitory concentrations (IC50) calculated for these compounds were ranging from 14.2µM for protolichesterinic acid to 42.6µM for sphaerophorin. Investigations on the mechanism of inhibition showed that all compounds behaved as uncompetitive inhibitors for ATP binding site, with the exception of epiphorellic acid which clearly acted as non-competitive inhibitor of the ATP site. Further investigations demonstrated that epiphorellic acid competitively binds the ssDNA binding site. Kinetic data were confirmed by molecular modelling binding predictions which shows that epiphorellic acid is expected to bind the ssDNA site into the L2 loop of RecA protein. CONCLUSION In this paper the first RecA ssDNA binding site ligand is described. Our study sets epiphorellic acid as a promising hit for the development of more effective RecA inhibitors. In our drug discovery approach, natural products in general and lichen in particular, represent a successful source of active ligands and structural diversity.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Letizia Di Pietro
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Alisia Mancini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Marisa Piovano
- Department of Chemistry, Universidad Técnica Federico Santa María, Casilla 110 V, Valparaíso, 6, Chile
| | - Marcello Nicoletti
- Department of Environmental Biology, University Sapienza, P.le A. Moro, 00185, Rome, Italy
| | - Fabrizia Brisdelli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena e Reggio Emilia, Via Campi 103, 41100, Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Nicola Franceschini
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of l'Aquila, Via Vetoio, 1, 67100 l'Aquila, Italy.
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9
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Zhang YW, Nong DG, Dou SX, Li W, Yan Y, Xi XG, Xu CH, Li M. Iterative homology checking and non-uniform stepping during RecA-mediated strand exchange. Biochem Biophys Res Commun 2016; 478:1153-7. [PMID: 27543204 DOI: 10.1016/j.bbrc.2016.08.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 08/14/2016] [Indexed: 12/11/2022]
Abstract
Recombinase-mediated homologous recombination (HR) in which strands are exchanged between two similar or identical DNA molecules is essential for maintaining genome fidelity and generating genetic diversity. It is believed that HR comprises two distinct stages: an initial alignment with stringent homology checking followed by stepwise heteroduplex expansion. If and how homology checking takes place during heteroduplex expansion, however, remains unknown. In addition, the number of base pairs (bp) involved in each step is still under debate. By using single-molecule approaches to catch transient intermediates in RecA-mediated HR with different degrees of homology, we show that (i) the expansion proceeds with step sizes of multiples of 3 bp, (ii) the step sizes follow wide distributions that are similar to that of initial alignment lengths, and (iii) each distribution can be divided into a short-scale and a long-scale part irrespective of the degree of homology. Our results suggest an iterative mechanism of strand exchange in which ssDNA-RecA filament interrogates double-stranded DNA using a short tract (6-15 bp) for quick checking and a long tract (>18 bp) for stringent sequence comparison. The present work provides novel insights into the physical and structural bases of DNA recombination.
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Affiliation(s)
- Yu-Wei Zhang
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Da-Guan Nong
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yan Yan
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China; Department of Physics, Emory University, Atlanta, GA, 30322, USA
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A & F University, Xi'an, Shaanxi, 712100, China; LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, F-94235, Cachan, France
| | - Chun-Hua Xu
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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10
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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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11
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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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12
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Qi Z, Redding S, Lee JY, Gibb B, Kwon Y, Niu H, Gaines WA, Sung P, Greene EC. DNA sequence alignment by microhomology sampling during homologous recombination. Cell 2015; 160:856-869. [PMID: 25684365 DOI: 10.1016/j.cell.2015.01.029] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/18/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022]
Abstract
Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.
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Affiliation(s)
- Zhi Qi
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Sy Redding
- Department of Chemistry, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Ja Yil Lee
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - William A Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
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13
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Jiang L, Prentiss M. RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022704. [PMID: 25215755 PMCID: PMC4972340 DOI: 10.1103/physreve.90.022704] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 06/03/2023]
Abstract
Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work suggested that RecA searches could produce stable final structures with high stringency using a slow testing process that follows an initial rapid search of ∼9-15 bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all ∼9-15 bases as separate individual units results in a longer overall searching time than testing them in groups and stages.
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14
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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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15
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Abstract
All organisms need homologous recombination (HR) to repair DNA double-strand breaks. Defects in recombination are linked to genetic instability and to elevated risks in developing cancers. The central catalyst of HR is a nucleoprotein filament, consisting of recombinase proteins (human RAD51 or bacterial RecA) bound around single-stranded DNA. Over the last two decades, single-molecule techniques have provided substantial new insights into the dynamics of homologous recombination. Here, we survey important recent developments in this field of research and provide an outlook on future developments.
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16
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Kates-Harbeck J, Tilloy A, Prentiss M. Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012702. [PMID: 23944487 PMCID: PMC4974998 DOI: 10.1103/physreve.88.012702] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Indexed: 06/02/2023]
Abstract
Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.
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Affiliation(s)
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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17
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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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18
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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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Fornander LH, Frykholm K, Reymer A, Renodon-Cornière A, Takahashi M, Nordén B. Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination. Nucleic Acids Res 2012; 40:4904-13. [PMID: 22362735 PMCID: PMC3367181 DOI: 10.1093/nar/gks140] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca2+ than of Mg2+, we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca2+ induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg2+, ADP/Mg2+ or ADP/Ca2+ does not. A high strand exchange activity is observed for the filament formed with ATP/Ca2+, whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca2+ stabilizes the loop conformation and thereby the protein–DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange.
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Affiliation(s)
- Louise H Fornander
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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20
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Abstract
Cleverly designed single-molecule FRET experiments reported in this issue of Structure by Ragunathan et al. coax RecA to reveal some of its secrets. Observing individual events identifies intermediate steps and provides clues for how to drive strand exchange forward.
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Affiliation(s)
- Claire Wyman
- Department of Radiation Oncology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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21
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Danilowicz C, Feinstein E, Conover A, Coljee VW, Vlassakis J, Chan YL, Bishop DK, Prentiss M. RecA homology search is promoted by mechanical stress along the scanned duplex DNA. Nucleic Acids Res 2011; 40:1717-27. [PMID: 22013164 PMCID: PMC3287184 DOI: 10.1093/nar/gkr855] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A RecA–single-stranded DNA (RecA–ssDNA) filament searches a genome for sequence homology by rapidly binding and unbinding double-stranded DNA (dsDNA) until homology is found. We demonstrate that pulling on the opposite termini (3′ and 5′) of one of the two DNA strands in a dsDNA molecule stabilizes the normally unstable binding of that dsDNA to non-homologous RecA–ssDNA filaments, whereas pulling on the two 3′, the two 5′, or all four termini does not. We propose that the ‘outgoing’ strand in the dsDNA is extended by strong DNA–protein contacts, whereas the ‘complementary’ strand is extended by the tension on the base pairs that connect the ‘complementary’ strand to the ‘outgoing’ strand. The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present.
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22
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Conover AJ, Danilowicz C, Gunaratne R, Coljee VW, Kleckner N, Prentiss M. Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments. Nucleic Acids Res 2011; 39:8833-43. [PMID: 21768124 PMCID: PMC3203582 DOI: 10.1093/nar/gkr561] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The RecA protein is an ATPase that mediates recombination via strand exchange. In strand exchange a single-stranded DNA (ssDNA) bound to RecA binding site I in a RecA/ssDNA filament pairs with one strand of a double-stranded DNA (dsDNA) and forms heteroduplex dsDNA in site I if homology is encountered. Long sequences are exchanged in a dynamic process in which initially unbound dsDNA binds to the leading end of a RecA/ssDNA filament, while heteroduplex dsDNA unbinds from the lagging end via ATP hydrolysis. ATP hydrolysis is required to convert the active RecA conformation, which cannot unbind, to the inactive conformation, which can unbind. If dsDNA extension due to RecA binding increases the dsDNA tension, then RecA unbinding must decrease tension. We show that in the presence of ATP hydrolysis decreases in tension induce decreases in length whereas in the absence of hydrolysis, changes in tension have no systematic effect. These results suggest that decreases in force enhance dissociation by promoting transitions from the active to the inactive RecA conformation. In contrast, increases in tension reduce dissociation. Thus, the changes in tension inherent to strand exchange may couple with ATP hydrolysis to increase the directionality and stringency of strand exchange.
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Affiliation(s)
- Alyson J Conover
- Department of Physics and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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23
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Optimizing the design of oligonucleotides for homology directed gene targeting. PLoS One 2011; 6:e14795. [PMID: 21483664 PMCID: PMC3071677 DOI: 10.1371/journal.pone.0014795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 01/27/2011] [Indexed: 11/19/2022] Open
Abstract
Background Gene targeting depends on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. A robust mechanistic model of homologous recombination is necessary to fully exploit gene targeting for therapeutic benefit. Methodology/Principal Findings In this work, our recently developed numerical simulation model for homology search is employed to develop rules for the design of oligonucleotides used in gene targeting. A Metropolis Monte-Carlo algorithm is used to predict the pairing dynamics of an oligonucleotide with the target double-stranded DNA. The model calculates the base-alignment between a long, target double-stranded DNA and a probe nucleoprotein filament comprised of homologous recombination proteins (Rad51 or RecA) polymerized on a single strand DNA. In this study, we considered different sizes of oligonucleotides containing 1 or 3 base heterologies with the target; different positions on the probe were tested to investigate the effect of the mismatch position on the pairing dynamics and stability. We show that the optimal design is a compromise between the mean time to reach a perfect alignment between the two molecules and the stability of the complex. Conclusion and Significance A single heterology can be placed anywhere without significantly affecting the stability of the triplex. In the case of three consecutive heterologies, our modeling recommends using long oligonucleotides (at least 35 bases) in which the heterologous sequences are positioned at an intermediate position. Oligonucleotides should not contain more than 10% consecutive heterologies to guarantee a stable pairing with the target dsDNA. Theoretical modeling cannot replace experiments, but we believe that our model can considerably accelerate optimization of oligonucleotides for gene therapy by predicting their pairing dynamics with the target dsDNA.
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RecA-Mediated Homology Search as a Nearly Optimal Signal Detection System. Mol Cell 2010; 40:388-96. [DOI: 10.1016/j.molcel.2010.10.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 02/18/2010] [Accepted: 09/08/2010] [Indexed: 11/18/2022]
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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: 1.9] [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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26
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Guo C, Li G, Liu Z, Sun L, Sun Y, Xu F, Zhang Y, Yang T, Li Z. Influence of Polyelectrolyte on DNA-RecA Nucleoprotein Filaments: Poly-L-Lysine Used as a Model. Chemphyschem 2009; 10:1624-9. [DOI: 10.1002/cphc.200800850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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Volodin AA, Bocharova TN, Smirnova EA, Camerini-Otero RD. Reversibility, equilibration, and fidelity of strand exchange reaction between short oligonucleotides promoted by RecA protein from escherichia coli and human Rad51 and Dmc1 proteins. J Biol Chem 2009; 284:1495-504. [PMID: 19004837 PMCID: PMC2615514 DOI: 10.1074/jbc.m800612200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 10/21/2008] [Indexed: 11/06/2022] Open
Abstract
We demonstrate the reversibility of RecA-promoted strand exchange reaction between short oligonucleotides in the presence of adenosine 5'-O-(thiotriphosphate). The reverse reaction proceeds without the dissociation of RecA from DNA. The reaction reaches equilibrium and its yield depends on the homology between the reaction substrates. We estimate the tolerance of the RecA-promoted strand exchange to individual base substitutions for a comprehensive set of possible base combinations in a selected position along oligonucleotide substrates for strand exchange and find, in agreement with previously reported estimations, that this tolerance is higher than in the case of free DNA. It is demonstrated that the short oligonucleotide-based approach can be applied to the human recombinases Rad51 and Dmc1 when strand exchange is performed in the presence of calcium ions and ATP. Remarkably, despite the commonly held belief that the eukaryotic recombinases have an inherently lower strand exchange activity, in our system their efficiencies in strand exchange are comparable with that of RecA. Under our experimental conditions, the human recombinases exhibit a significantly higher tolerance to interruptions of homology due to point base substitutions than RecA. Finding conditions where a chemical reaction is reversible and reaches equilibrium is critically important for its thermodynamically correct description. We believe that the experimental system described here will substantially facilitate further studies on different aspects of the mechanisms of homologous recombination.
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Affiliation(s)
- Alexander A Volodin
- Institute of Molecular Genetics of the Russian Academy of Sciences, Kurchatov Square, 123182 Moscow, Russia
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28
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Singleton SF, Roca AI, Lee AM, Xiao J. Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog. Tetrahedron 2007; 63:3553-3566. [PMID: 17955055 PMCID: PMC2031864 DOI: 10.1016/j.tet.2006.10.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The RecA protein of Escherichia coli plays a crucial roles in DNA recombination and repair, as well as various aspects of bacterial pathogenicity. The formation of a RecA-ATP-ssDNA complex initiates all RecA activities and yet a complete structural and mechanistic description of this filament has remained elusive. An analysis of RecA-DNA interactions was performed using fluorescently labeled oligonucleotides. A direct comparison was made between fluorescein and several fluorescent nucleosides. The fluorescent guanine analog 6-methylisoxanthopterin (6MI) demonstrated significant advantages over the other fluorophores and represents an important new tool for characterizing RecA-DNA interactions.
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Affiliation(s)
- Scott F. Singleton
- Division of Medicinal Chemistry & Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, CB 7360, Chapel Hill, NC 27599-7360, USA
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