Homologous genetic recombination as an intrinsic dynamic property of a DNAstructure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material

Heteroduplex joints are general intermediates of homologous genetic recombi nation in DNA genomes, A heteroduplex joint is formed between a single-stra nded region (or tail), derived from a cleaved parental double-stranded DNA, and homologous regions in another parental double-stranded DNA, in a react ion mediated by the RecA/Rad51-family of proteins. In this reaction, a RecA /Rad51-family protein first forms a filamentous complex with the single-str anded DNA, and then interacts with the double-stranded DNA in a search for homology, Studies of the three-dimensional structures of single-stranded DN A bound either to Escherichia coli RecA or Saccharomyces cerevisiae Rad51 h ave revealed a novel extended DNA structure. This structure contains a hydr ophobic interaction between the 2 ' methylene moiety of each deoxyribose an d the aromatic ring of the following base, which allows bases to rotate hor izontally through the interconversion of sugar puckers. This base rotation explains the mechanism of the homology search and base-pair switch between double-stranded and singlestranded DNA during the formation of heteroduplex joints, The pivotal role of the 2 ' methylene-base interaction in the hete roduplex joint formation is supported by comparing the recombination of RNA genomes with that of DNA genomes, Some simple organisms with DNA genomes i nduce homologous recombination when they encounter conditions that are unfa vorable for their survival. The extended DNA structure confers a dynamic pr operty on the otherwise chemically and genetically stable double-stranded D NA, enabling gene segment rearrangements without disturbing the coding fram e (i.e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA.