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Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination

Published online by Cambridge University Press:  04 June 2004

Chantal Prévost  and
Masayuki Takahashi
Chantal Prévost
Affiliation:
Laboratoire de Biochimie Théorique, CNRS – UPR 9080, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France
Masayuki Takahashi
Affiliation:
Unité de Recherche sur la Biocatalyse, CNRS – FRE 2230 et Université de Nantes, Faculté des Sciences et Technologies, F-44322 Nantes Cedex 3, France
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Abstract

1. Introduction 430

2. Transformations of the RecA filament 431

2.1 The different forms of the RecA filament 431

2.2 Orientation and position of the RecA monomers in the active filament 433

2.3 Transmission of structural information along the filament 433

3. RecA-induced DNA deformations 435

3.1 Characteristics of RecA-bound DNA 435

3.2 Stretching properties of double-stranded DNA 436

3.3 DNA bound to architectural proteins 437

3.4 Implications for RecA-induced DNA deformations 438

3.5 Axial distribution of the DNA stretching deformation 438

4. Contacts between RecA and the DNA strands 440

4.1 The DNA-binding sites 440

4.2 Possible arrangement of loops L1 and L2 and the three bound strands of DNA 442

5. Strand arrangement during pairing reorganization 444

5.1 Hypotheses for DNA strand association 444

5.2 Association via major or minor grooves 446

5.3 Post-strand exchange geometries 446

6. Conclusion 447

7. Acknowledgments 448

8. References 448

Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50% and unwound by 40% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 36 , Issue 4 , November 2003 , pp. 429 - 453
Copyright
2004 Cambridge University Press

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Footnotes

Abbreviations: EM, electron microscopy; LD, linear dichroism; MtRecA, RecA protein from Mycobacterium tuberculosis; Mt-L1, Mt-L2, geometric folds of loops L1 and L2 of RecA as found in the crystal structure of MtRecA; NMR, nuclear magnetic resonance; PDB, Protein Data Bank (http://www.rcsb.org/pdb); B-DNA, biologically active form of DNA; R-DNA, parallel DNA triple helix, where the single strand interacts in the major groove of the duplex; S-DNA, stretched form of DNA, with a stretching factor of ~1·7; ST-DNA, stretched triplex DNA, where the single strand interacts in the minor groove of the duplex; TA-DNA, form of the DNA in the complex with the TATA-box binding protein; SANS, small-angle neutron scattering.