Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails

Abstract During repair of double-strand breaks, recombinases form D-loops in which one strand of the broken chromosome base pairs with a strand from an unbroken chromosome. Thus, the double-stranded DNA (dsDNA) in the unbroken chromosome must melt. Rapid repair requires quick melting. In this work, we present experimental results suggesting that both RecA and ScDmc1 form D-loops that distort the structure of long homoduplex tails in regions adjacent to recombinase-bound D-loops. The observed distortion is not simply due to attempted D-loop extension, but it is consistent with local melting of homoduplex tail regions adjacent to recombinase-bound D-loops. Our experiments indicate that the distortion arises from a collective interaction involving torsional stress that extends along RecA-bound D-loops from one homoduplex tail to the other. Furthermore, molecular dynamics simulations show melting in homoduplex tail regions adjacent to RecA-bound D-loops. Finally, we speculate that the destabilization in the base pairing in homoduplex tails flanking D-loops facilitates the extension of D-loops and underlies the previously observed extension of D-loops through 10 contiguous heterologous bases.