The function of the secondary DNA-binding site of RecA protein during DNA strand exchange

Alexander V. Mazin, Stephen C. Kowalczykowski

Research output: Contribution to journalArticlepeer-review

84 Scopus citations


RecA protein features two distinct DNA-binding sites. During DNA strand exchange, the primary site binds to single-stranded DNA (ssDNA), forming the helical RecA nucleoprotein filament. The weaker secondary site binds double-stranded DNA (dsDNA) during the homology search process. Here we demonstrate that this site has a second important function. It binds the ssDNA strand that is displaced from homologous duplex DNA during DNA strand exchange, stabilizing the initial heteroduplex DNA product. Although the high affinity of the secondary site for ssDNA is essential for DNA strand exchange, it renders DNA strand exchange sensitive to an excess of ssDNA which competes with dsDNA for binding. We further demonstrate that single-stranded DNA-binding protein can sequester ssDNA, preventing its binding to the secondary site and thereby assisting at two levels: it averts the inhibition caused by an excess of ssDNA and prevents the reversal of DNA strand exchange by removing the displaced strand from the secondary site.

Original languageEnglish (US)
Pages (from-to)1161-1168
Number of pages8
JournalEMBO Journal
Issue number4
StatePublished - Feb 4 1998
Externally publishedYes


  • DNA-protein interactions
  • Genetic recombination
  • Homologous pairing

ASJC Scopus subject areas

  • General Immunology and Microbiology
  • General Biochemistry, Genetics and Molecular Biology
  • Molecular Biology
  • General Neuroscience


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