Sequence Recognition by a Pseudorotational Cycle of Sugar Puckers: A Base Pair Switching Model via N-E Sugar Pucker Conversion for Homologous Recombination

A triplex DNA model bound to a helical filament of homologous recombination protein, such as Escherichia coli RecA, is presented. This model suggests that a function of the nucleoprotein filament could be at least partly attributed to the lowering of transition energy of duplex DNA structure having the E-type sugar puckers. Key events during homologous recombination such as sequence recognition, base pair switching and elongation/contraction of the helical pitch may correlate with the pseudo-rotation angle of sugar puckers along the N-, E-, S- and W-types. A conformational change of sugar puckers during the reaction is resolved into two motions by introducing a pair of parameters, μ 1 and ν 3 , which defines a swing orientation of bases and a torsional angle of phosphate backbones, respectively.