Dissociation of non-complementary second DNA from RecA filament without ATP hydrolysis: Mechanism of search for homologous DNA

Journal of Biochemistry

Volumn 121, Issue 6, 1997, Pages 1070-1075

  Ellouze, Christine ^a   Nordén, Bengt ^b   Takahashi, Masayuki ^a  

^a INSTITUT CURIE   (France)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

DNA binding; Homologous recombination; RecA protein; Search of homologous DNA; Strand exchange

Indexed keywords

ADENOSINE TRIPHOSPHATE; COMPLEMENTARY DNA; DNA; RECA PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FLUORESCENCE ANALYSIS; HYDROLYSIS; KINETICS; PROTEIN DNA INTERACTION; SEQUENCE HOMOLOGY;

EID: 0030743648     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a021696     Document Type: Article

References (33)

1. Clark, A.J. and Margulies, A.D. (1965) Isolation and characterization of recombination-deficient mutants of Escherichia coli K12. Proc. Natl. Acad. Sci. USA 53, 451-459
2. Smith G.R. (1989) Homologous recombination in E. coli: Multiple pathways for multiple reasons. Cell 58, 807-809
3. Roca, A.I. and Cox, M.M. (1990) The RecA protein: structure and function. Critic. Rev. Biochem. Mol. Biol. 25, 415-456
4. Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K., Lauder, S.D., and Rehrauer, W.M. (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58, 401-465
5. McEntee, K., Weinstock, G.M., and Lehman, I.R. (1979) Initiation of general recombination catalyzed in vitro by the recA protein of Escherichia coli. Proc. Natl. Acad. Sci. USA 76, 2615-2619
6. Shibata, T., DasGupta, C., Cunningham, R.P., and Radding, C.M. (1979) Purified Escherichia coli RecA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc. Natl. Acad. Sci. USA 76, 1638-1642
7. Shinohara, A., Ogawa, H., Matsuda, Y., Ushio, N., Ikeo, K., and Ogawa, T. (1993) Cloning of human, mouse and fission yeast genes homologous to Rad51 and recA. Nature Genetics 4, 239-243
8. Maeshima, K., Morimatsu, K., Shinohara, A., and Horii, T. (1995) Rad51 homologues in Xenopus laevis: Two distinct genes are highly expressed in ovary and testis. Gene 160, 195-200
9. Griffith, J.D. and Harris, L.D. (1988) DNA strand exchanges. CRC Crit. Rev. Biochem. 23, S43-S86
10. Takahashi, M. (1989) Analysis of DNA-RecA protein interactions involving the protein self-association reaction. J. Biol. Chem. 264, 288-295
11. Williams, R.C. and Spengler, S.J. (1986) Fibers of RecA protein and complexes of RecA protein and single-stranded φX174 DNA as visualized by negative-stain electron microscopy. J. Mol. Biol. 187, 109-118
12. Takahashi, M., Kubista, M., and Nordén, B. (1989) Binding stoichiometry and structure of RecA-DNA complexes studied by the linear dichroism and fluorescence spectroscopy. Evidence for multiple heterogeneous DNA coordination. J. Mol. Biol. 205, 137-147
13. Zlotnick, A., Mitchell, R.S., Steed, R.K., and Brenner, S.L. (1993) Analysis of two distinct single-stranded binding sites on the recA nucleoprotein filament. J. Biol. Chem. 268, 22525-22530
14. Müller, B., Koller, T., and Stasiak, A. (1990) Characterization of the DNA binding activity of stable RecA-DNA complexes: interaction between two DNA binding sites within RecA helical filaments. J. Mol. Biol. 212, 97-112
15. Takahashi, M. and Nordén, B. (1992) Coordination and internal exchange of two DNA molecules in a RecA filament in presence of ATP hydrolysis. Structural information of ATP-RecA-DNA complexes from linear dichroism spectroscopy. Eur. J. Biochem. 210, 87-92
16. Honigberg, S.M., Rao, B.J., and Radding, C.M. (1986) Ability of RecA protein to promote a search for rare sequences in duplex DNA. Proc. Natl. Acad. Sci. USA 83, 9586-9590
17. Revet, B.M.J., Sena, E.P., and Zarling, D.A. (1993) Homologous DNA targeting with RecA protein-coated short DNA probes and electron microscope mapping on linear duplex molecules. J. Mol. Biol. 232, 779-791
18. Menetski, J., Bear D.G., and Kowalczykowski, S.C. (1990) Stable DNA heteroduplex formation catalyzed by the Escherichia coli RecA protein in the absence of ATP hydrolysis. Proc. Natl. Acad. Sci. USA 87, 21-25
19. Chabbert, M., Lami, H., and Takahashi, M. (1991) Cofactor induced orientation of the DNA bases in single-stranded DNA, complexed with RecA protein: A fluorescence anisotropy and time-decay study. J. Biol. Chem. 266, 5395-5400
20. Record, M.T., Jr., Anderson, C.F., and Lohman, T.M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11, 103-178
21. Nordén, B., Kubista, M., and Kurucsev, T. (1992) Linear dichroism spectroscopy of nucleic acids. Q. Rev. Biophys. 25, 51-170
22. Takahashi, M. and Nordén, B. (1994) Structure of RecA-DNA complex and mechanism of DNA strand exchange reaction in homologous recombination. Adv. Biophys. 30, 1-35
23. Takahashi, M. and Hagmar, P. (1991) Use of ion exchange chromatography for the study of RecA-DNA interactions. FEBS Lett. 279, 270-272
24. Ledneva, R.K., Razjivim, A.P., Kost, A.A., and Bogdanov, A.A. (1978) Interaction of tobacco mosaic virus protein with synthetic polynucleotides containing a fluorescent label. Nucleic Acids Res. 5, 4225-4243
25. Nordén, B. and Seth, S. (1985) Critical aspects on measurement of circular and linear dichroism. A device for absolute calibration. Appl. Spectrosc. 39, 647-655
26. Takahashi, M., Kubista, M., and Nordén, B. (1987) Linear dichroism study of RecA-DNA complexes: Structural evidence and stoichiometries. J. Biol. Chem. 262, 8109-8111
27. Kubista, M., Nordén, B., and Takahashi, M. (1994) Properties of RecA complexes with homopolymeric DNA strands depend on sequence complementarity: implications for the mechanism of strand exchange. Nucleosides Nucleotides 13, 753-772
28. Mazin, A.V. and Kowalczykowski, S.C. (1996) The specificity of the secondary DNA binding site of RecA protein defines its role in DNA strand exchange. Proc. Natl. Acad. Sci. USA 93, 10673-10678
29. Wittung, P., Nordén, B., Kim, S.K., and Takahashi, M. (1994) Interactions between DNA molecules bound to RecA filament: effects of base complementarity. J. Biol. Chem. 269, 5799-5803
30. Rao, B.J. and Radding, C.M. (1993) Homologous recognition promoted by RecA protein via non-Watson-Crick bonds between identical DNA strands. Proc. Natl. Acad. Sci. USA 90, 6646-6650
31. Wittung, P., Bazemore, L.R., Takahashi, M., Nordén, B., and Radding, C. (1996) Second-site RecA-DNA interactions: Lack of identical recognition. Biochemistry 35, 15349-15355
32. Mazur, S.J. and Record, M.T., Jr. (1989) Association kinetics of site-specific protein-DNA interactions: roles of nonspecific DNA sites and of the molecular location of the specific site. Biopolymers 28, 929-953
33. Kabata, H., Kurosawa, O., Arai, I., Washizu, M., Margarson, S.A., Glass, R.E., and Shimamoto, N. (1993) Visualization of single molecules of RNA polymerase sliding along DNA. Science 262, 1561-1563