Dissociation kinetics of RecA protein-three-stranded DNA complexes reveals a low fidelity of RecA-assisted recognition of homology

Abstract

We determined that the incorporation of one mismatch into RecA mediated synaptic complexes between oligonucleotide single-stranded DNAs and target duplex DNAs destabilizes the complex by 0.8 to 1.9 kcal/mol. This finding supports our previous result, that RecA binding per se can significantly decrease the loss in free energy associated with mismatch incorporation even in the absence of ATP hydrolysis. We show that the specificity is mostly driven by the dissociation process. We found that the relative destabilization induced by different mismatches depends on their position. Thus, while there is a good correlation between the ranking order of mismatches at the 5′ end of synaptic complexes and mismatches in heteroduplexes (D-loops), there is no correlation between the ranking order for mismatches at the 3′ end and mismatches in various DNA structures. This difference between the 5′ and 3′ ends of synaptic complexes agrees well with the established 5′ to 3′ polarity of the strand exchange promoted by RecA protein. The lack of a correlation between mismatches at the 3′ end of synaptic complexes and mismatches in D-loops suggests the intermediate is probably not a canonical protein-free D-loop.