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bioRxiv · 10.1101/2021.10.21.464190

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

Nishinaka, T.
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Abstract

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, 1 and {nu}3, which defines a swing orientation of bases and a torsional angle of phosphate backbones, respectively.

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Nishinaka, T.. 2021-10-21. Sequence Recognition by a Pseudorotational Cycle of Sugar Puckers: A Base Pair Switching Model via N-E Sugar Pucker Conversion for Homologous Recombination. https://doi.org/10.1101/2021.10.21.464190

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