Escherichia coli rep helicase unwinds DNA by an active mechanism

DNA helicases unwind duplex DNA to form the single-stranded (ss) DNA intermediates required for replication, recombination, and repair in reactions that require nucleoside 5'-triphosphate hydrolysis. Helicases generally require a ss-DNA flanking the duplex in order to initiate unwinding in vitro; however, the precise function of the ss-DNA is not understood. If a helicase unwinds DNA by a "passive" mechanism, it would bind to and translocate unidirectionally along the ss-DNA and facilitate duplex unwinding by translocating onto the ss-DNA that is formed transiently by thermal fluctuations in the duplex. We have examined the kinetics of DNA unwinding by Escherichia coli Rep protein (a 3' to 5' helicase) by rapid quench-flow methods using a series of novel, nonnatural DNA substrates possessing 3' flanking ss-DNA within which is embedded either a segment of ss-DNA possessing reversed backbone polarity or a non-DNA [poly(ethylene glycol)] spacer, either of which should block unwinding by a passive helicase. The E. coli Rep helicase effectively unwinds these DNA substrates, ruling out a passive mechanism of unwinding. Instead, the results are consistent with an "active" rolling mechanism during which Rep binds to ss-DNA and duplex DNA simultaneously.