Radioprobing of a RecA-three-stranded DNA complex with iodine 125: Evidence for recognition of homology in the major groove of the target duplex

A fundamental problem in homologous recombination is how homology between D NAs is recognized. In all current models, a recombination protein loads ont o a single strand of DNA and scans another duplex for homology. When homolo gy is found, a synaptic complex is formed, leading to strand exchange and a heteroduplex. A novel technique based on strand cleavage by the Auger radi odecay of iodine 125, allows us to determine the distances between I-125 on the incoming strand and the target sugars of the duplex DNA strands in an Escherichia coli RecA protein-mediated synaptic complex. Analysis of these distances shows that the complex represents a post-strand exchange intermed iate in which the heteroduplex is located in the center, while the outgoing strand forms a relatively wide helix intertwined with the heteroduplex and located in its minor groove. The structure implies that homology is recogn ized in the major groove of the duplex. (C) 2000 Academic Press.