Genetic recombination is a multistep process involving many gene products. In order to dissect the biochemical steps involved we have chosen to focus on a key early step: strand exchange between homologous parental DNAs. To date, the ability to carry out a strand exchange between a linear duplex DNA and a homologous circular single-strand DNA is unique to recombination proteins. The product of this strand exchange reaction is a joint molecule composed of a single-strand circle joined to one end of a linear duplex. Three proteins responsible for this step have been purified: uvsx from phage T4; Rec A from E. coli; and rec 1 from U. maydis. Over the last two years we have reported the partial purification and characterization of similar strand-exchange proteins or recombinases from nuclear extracts of human cells and tissues and embryos of D. melanogaster. The proteins have two noteworthy characteristics: (I) they do not require ATP (unlike Rec A and rec 1); and (2) their direction of strand displacement (3' to 5') was similar to that of rec 1 but opposite to that of Rec A. Recently, we have used a variety of assays to show that both E. coli Rec A and human recombinase can form stable joint molecules from substrates that share very small regions of homology (as little as 13 bp in one case). This finding has two important implications. First, these proteins can recognize and pair in vitro very short regions of homology. This result is consistent with data from both prokaryotic and eukaryotic systems that demonstrate that genetic recombination in vivo can utilize exceedingly short stretches of DNA homology. Second, the surprising stability, both to deproteinizing agents and to temperature, of joint molecules containing short hydrogen-bonded regions, suggests that these structures do not have a displaced strand that is free to participate in branch migration.
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