In order to dissect the biochemical steps involved in genetic recombination we have chosen to focus on a key early step: strand exchange between homologous single-stranded and duplex parental DNAs. We have established a new paradigm for this homologous pairing. In essence, that recombinases such as the E. coli RecA protein can form a novel DNA triplex (R-form DNA) in which the third strand may have any arbitrary sequence and must have a parallel orientation with respect to the phosphodiester backbone of the, identical strand in the duplex. We have also been able to isolate synaptic complexes consisting of all the three strands and RecA. In order to understand the mechanism and structures involved in greater detail we have determined that a 20 amino acid peptide from RecA has some of the activities of RecA. Most remarkably, this short 20 amino acid peptide spanning the disordered or mobile loop L2 of RecA is capable of carrying out the hallmark reactions mediated by the whole RecA protein: pairing (targeting) of a single-stranded DNA to its homologous site on duplex DNA and forming homology-dependent stable joint molecules. In the course of the reaction the peptide binds to both substrates, unstacks the single-stranded DNA and assumes a beta-structure. Efforts are now underway to determine the three-dimensional structure of this peptide when bound to DNA. The synaptic complexes have also been used to develop a method for the selective cleavage of human DNA (RecA-Assisted Restriction Endonuclease (RARE) cleavage). We have shown that RARE can be used to map Sequences in genomic DNA of increasing complexity, including human DNA. Recently, we have developed a new technique, RecA-Assisted Cloning (RAC), that is functionally the reverse of RARE in that uses RecA and oligonucleotides to direct sequence-specific ligation of genomic DNA.
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