A mechanism for RecA-promoted sequence homology recognition and strand exchange between single-stranded DNA and duplex DNA, via triple-helical intermediates

A central function of RecA protein during homologous recombination is to pr omote sequence recognition and strand exchange between a stretched and unwo und single-stranded DNA, to which it is complexed, and a duplex DNA. By stu dying the properties of DNA under the conditions of deformation imposed by RecA, we propose a model for recognition and strand exchange at the atomic level, via unusual triple-helical intermediates. In this mode], association takes place within a stretched and unwound triple helix of a new type, whe re the invading single strand occupies the minor groove of the duplex in a parallel orientation. Our calculations indicate that strand exchange within this structure is exothermic and results in a triple helix where the third strand interacts in the major groove, the so-called R-DNA triple helix. Pr eliminary calculations suggest that sequence homology recognition within th e tripler of association is partial and that it is completed during strand exchange and product formation.