Abstract
RecA protein lies at the core of DNA repair mechanism. RecA forms a helical-structured filament on a single-strand DNA (ssDNA) as an intermediate of homologous recombination. Recent crystal structure of RecA filament with embedded ssDNA found that each RecA monomer in the filament is bound to a group of three nucleotides, simultaneously forming a gap between neighboring groups. Thus, there are three possibilities (phases) in the binding of RecA according to the relative position of the gap in the substrate ssDNA. We developed a single-molecule fluorescence based assay to identify the phase of individual RecA filament. On a polythymine substrate, RecA filaments were formed randomly in the three phases. Each RecA filament changed its phase via migration along the substrate ssDNA for which the energy from ATP hydrolysis was required. On the other hand, the RecA filament was arrested into a single phase when the poly thymine was replaced by TGG repeats. Our results provide a new insight into the molecular mechanism of sequence specific RecA filament dynamics.
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