Distribution of Chi-stimulated recombinational exchanges and heteroduplex endpoints in phage lambda.

Abstract The recombination hotspot Chi, 5' G-C-T-G-G-T-G-G 3', stimulates the RecBCD recombination pathway of Escherichia coli. We have determined, with precision greater than previously reported, the distribution of Chi-stimulated exchanges around a Chi site in phage lambda. Crosses of lambda phages with single base-pair mutations surrounding a Chi site were conducted in and analyzed on mismatch correction-impaired hosts to preserve heteroduplex mismatches for analysis. Among phages recombinant for flanking markers, Chi stimulated exchanges most intensely in the intervals immediately adjacent to the Chi site, both to its right and to its left. Stimulation fell off abruptly to the right but gradually to the left (with respect to the orientation of the Chi sequence written above). We have also determined that Chi stimulated the formation of heteroduplex DNA, which frequently had one endpoint to the right of Chi and the other endpoint to the left. These data support a model of Chi-stimulated recombination in which RecBCD enzyme cuts DNA immediately to the right of Chi and unwinds DNA to the left of Chi; segments of unwound single-stranded DNA are sometimes, but not always, degraded before synapsis with homologous DNA.