In vitro selection of preferred DNA pairing sequences by the Escherichia coli RecA protein.

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Abstract
The RecA protein and other DNA strand exchange proteins are characterized by their ability to bind and pair DNA in a sequence-independent manner. In vitro selection experiments demonstrate, unexpectedly, that RecA protein has a preferential affinity for DNA sequences rich in GT composition. Such GT-rich sequences are present in loci that display increased recombinational activity in both eukaryotes and prokaryotes, including the Escherichia coli recombination hotspot, chi (5'-GCTGGTGG-3'). Interestingly, these selected sequences, or chi-containing substrates, display both an enhanced rate and extent of homologous pairing in RecA protein-dependent homologous pairing reactions. Thus, the binding and pairing of DNA by RecA protein is composition-dependent, suggesting that a component of the elevated recombinational activity of chi and increased genomic rearrangements at certain DNA sequences in eukaryotes is contributed by enhanced DNA pairing activity.