Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

摘要: Homologous recombination is a fundamental process enabling the repair of double-strand breaks with high degree fidelity. In prokaryotes, it carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to ssDNA and exchange strands. Due highly dynamic character this its rapid propagation along filament, sequence recognition strand mechanism remains unknown at structural level. The recently published structure RecA/DNA filament active for (Chen et al., Mechanism from RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides starting point new exploration system. Here, we investigate possible geometries association early encounter complex between RecA/ssDNA double-stranded (dsDNA). huge size system dense packing, use reduced representation protein together state-of-the-art molecular modeling methods, including systematic docking virtual reality simulations. results indicate access RecA-bound while initially retaining Watson-Crick pairing. They emphasize importance L2 loop mobility both exchange.