Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1993 Jul 15;90(14):6646–6650. doi: 10.1073/pnas.90.14.6646

Homologous recognition promoted by RecA protein via non-Watson-Crick bonds between identical DNA strands.

B J Rao 1, C M Radding 1
PMCID: PMC46989  PMID: 8341681

Abstract

The RecA protein of Escherichia coli forms a nucleoprotein filament that promotes homologous recognition and subsequent strand exchange between a single strand and duplex DNA via a three-stranded intermediate. Recognition of homology within three-stranded nucleoprotein complexes, which is probably central to genetic recombination, is not well understood as compared with the mutual recognition of complementary single strands by Watson-Crick base pairing. Using oligonucleotides, we examined the determinants of homologous recognition within RecA nucleoprotein filaments. Filaments that contained a single strand of DNA recognized homology not only in a complementary oligonucleotide but also in an identical oligonucleotide, whether their respective sugar-phosphate backbones were antiparallel or parallel, and a filament that contained duplex DNA showed the same polymorphic versatility in the recognition of homology. Recognition of self by a filament that contains a single strand reveals that RecA filaments can recognize homology via non-Watson-Crick hydrogen bonds. Recognition of multiple forms of the same sequence by duplex DNA in the filament shows that it primarily senses base-sequence homology, and suggests that recognition can be accomplished prior to the establishment of new Watson-Crick base pairs in heteroduplex products. However, unlike the initial recognition of homology, strand exchange is stereospecific, requiring the proper antiparallel orientation of complementary strands.

Full text

PDF
6646

Images in this article

6647Fig. 1
on p.6647
6648Fig. 4
on p.6648
6649Fig. 5
on p.6649

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adzuma K. Stable synapsis of homologous DNA molecules mediated by the Escherichia coli RecA protein involves local exchange of DNA strands. Genes Dev. 1992 Sep;6(9):1679–1694. doi: 10.1101/gad.6.9.1679. [DOI] [PubMed] [Google Scholar]
  2. Antao V. P., Gray C. W., Gray D. M., Ratliff R. L. Circular dichroism of two conformations of poly[d(G-C)] induced by low pH. Nucleic Acids Res. 1986 Dec 22;14(24):10091–10112. doi: 10.1093/nar/14.24.10091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cassuto E., West S. C., Mursalim J., Conlon S., Howard-Flanders P. Initiation of genetic recombination: homologous pairing between duplex DNA molecules promoted by recA protein. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3962–3966. doi: 10.1073/pnas.77.7.3962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chow S. A., Rao B. J., Radding C. M. Reversibility of strand invasion promoted by recA protein and its inhibition by Escherichia coli single-stranded DNA-binding protein or phage T4 gene 32 protein. J Biol Chem. 1988 Jan 5;263(1):200–209. [PubMed] [Google Scholar]
  5. Cooney M., Czernuszewicz G., Postel E. H., Flint S. J., Hogan M. E. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science. 1988 Jul 22;241(4864):456–459. doi: 10.1126/science.3293213. [DOI] [PubMed] [Google Scholar]
  6. Cruse W. B., Egert E., Kennard O., Sala G. B., Salisbury S. A., Viswamitra M. A. Self base pairing in a complementary deoxydinucleoside monophosphate duplex: crystal and molecular structure of deoxycytidylyl-(3'-5')-deoxyguanosine. Biochemistry. 1983 Apr 12;22(8):1833–1839. doi: 10.1021/bi00277a014. [DOI] [PubMed] [Google Scholar]
  7. Cunningham R. P., DasGupta C., Shibata T., Radding C. M. Homologous pairing in genetic recombination: recA protein makes joint molecules of gapped circular DNA and closed circular DNA. Cell. 1980 May;20(1):223–235. doi: 10.1016/0092-8674(80)90250-0. [DOI] [PubMed] [Google Scholar]
  8. DasGupta C., Shibata T., Cunningham R. P., Radding C. M. The topology of homologous pairing promoted by RecA protein. Cell. 1980 Nov;22(2 Pt 2):437–446. doi: 10.1016/0092-8674(80)90354-2. [DOI] [PubMed] [Google Scholar]
  9. Edwards E. L., Patrick M. H., Ratliff R. L., Gray D. M. A.T and C.C+ base pairs can form simultaneously in a novel multistranded DNA complex. Biochemistry. 1990 Jan 23;29(3):828–836. doi: 10.1021/bi00455a033. [DOI] [PubMed] [Google Scholar]
  10. Flory J., Tsang S. S., Muniyappa K. Isolation and visualization of active presynaptic filaments of recA protein and single-stranded DNA. Proc Natl Acad Sci U S A. 1984 Nov;81(22):7026–7030. doi: 10.1073/pnas.81.22.7026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Howard-Flanders P., West S. C., Stasiak A. Role of RecA protein spiral filaments in genetic recombination. Nature. 1984 May 17;309(5965):215–219. doi: 10.1038/309215a0. [DOI] [PubMed] [Google Scholar]
  12. Hsieh P., Camerini-Otero C. S., Camerini-Otero R. D. Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev. 1990 Nov;4(11):1951–1963. doi: 10.1101/gad.4.11.1951. [DOI] [PubMed] [Google Scholar]
  13. Jain S. K., Inman R. B., Cox M. M. Putative three-stranded DNA pairing intermediate in recA protein-mediated DNA strand exchange: no role for guanine N-7. J Biol Chem. 1992 Feb 25;267(6):4215–4222. [PubMed] [Google Scholar]
  14. Letai A. G., Palladino M. A., Fromm E., Rizzo V., Fresco J. R. Specificity in formation of triple-stranded nucleic acid helical complexes: studies with agarose-linked polyribonucleotide affinity columns. Biochemistry. 1988 Dec 27;27(26):9108–9112. doi: 10.1021/bi00426a007. [DOI] [PubMed] [Google Scholar]
  15. Moser H. E., Dervan P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987 Oct 30;238(4827):645–650. doi: 10.1126/science.3118463. [DOI] [PubMed] [Google Scholar]
  16. Praseuth D., Perrouault L., Le Doan T., Chassignol M., Thuong N., Hélène C. Sequence-specific binding and photocrosslinking of alpha and beta oligodeoxynucleotides to the major groove of DNA via triple-helix formation. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1349–1353. doi: 10.1073/pnas.85.5.1349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pugh B. F., Cox M. M. Stable binding of recA protein to duplex DNA. Unraveling a paradox. J Biol Chem. 1987 Jan 25;262(3):1326–1336. [PubMed] [Google Scholar]
  18. Rao B. J., Chiu S. K., Radding C. M. Homologous recognition and triplex formation promoted by RecA protein between duplex oligonucleotides and single-stranded DNA. J Mol Biol. 1993 Jan 20;229(2):328–343. doi: 10.1006/jmbi.1993.1038. [DOI] [PubMed] [Google Scholar]
  19. Rao B. J., Dutreix M., Radding C. M. Stable three-stranded DNA made by RecA protein. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):2984–2988. doi: 10.1073/pnas.88.8.2984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rao B. J., Jwang B., Radding C. M. RecA protein reinitiates strand exchange on isolated protein-free DNA intermediates. An ADP-resistant process. J Mol Biol. 1990 Jun 20;213(4):789–809. doi: 10.1016/S0022-2836(05)80264-5. [DOI] [PubMed] [Google Scholar]
  21. Robinson H., van der Marel G. A., van Boom J. H., Wang A. H. Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs. Biochemistry. 1992 Nov 3;31(43):10510–10517. doi: 10.1021/bi00158a014. [DOI] [PubMed] [Google Scholar]
  22. Rosselli W., Stasiak A. Energetics of RecA-mediated recombination reactions. Without ATP hydrolysis RecA can mediate polar strand exchange but is unable to recycle. J Mol Biol. 1990 Nov 20;216(2):335–352. doi: 10.1016/S0022-2836(05)80325-0. [DOI] [PubMed] [Google Scholar]
  23. Schwindinger W. F., Warner J. R. DNA sequence analysis on the IBM-PC. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):601–604. doi: 10.1093/nar/12.1part2.601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shibata T., Cunningham R. P., Radding C. M. Homologous pairing in genetic recombination. Purification and characterization of Escherichia coli recA protein. J Biol Chem. 1981 Jul 25;256(14):7557–7564. [PubMed] [Google Scholar]
  25. Stasiak A. Three-stranded DNA structure; is this the secret of DNA homologous recognition? Mol Microbiol. 1992 Nov;6(22):3267–3276. doi: 10.1111/j.1365-2958.1992.tb02194.x. [DOI] [PubMed] [Google Scholar]
  26. Umlauf S. W., Cox M. M., Inman R. B. Triple-helical DNA pairing intermediates formed by recA protein. J Biol Chem. 1990 Oct 5;265(28):16898–16912. [PubMed] [Google Scholar]
  27. West S. C., Cassuto E., Howard-Flanders P. recA protein promotes homologous-pairing and strand-exchange reactions between duplex DNA molecules. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2100–2104. doi: 10.1073/pnas.78.4.2100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Westhof E., Sundaralingam M. X-ray-structure of a cytidylyl-3',5'-adenosine-proflavine complex: a self-paired parallel-chain double helical dimer with an intercalated acridine dye. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1852–1856. doi: 10.1073/pnas.77.4.1852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. van Wezenbeek P. M., Hulsebos T. J., Schoenmakers J. G. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd. Gene. 1980 Oct;11(1-2):129–148. doi: 10.1016/0378-1119(80)90093-1. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES