Uptake and processing of duplex DNA by RecA nucleoprotein filaments: insights provided by a mixed population of dynamic and static intermediates.

In the polarized strand exchange that is promoted by Escherichia coli RecA protein, when the initiating end of a duplex DNA molecule is blocked by heterology, the homologous distal end nonetheless forms a joint with single-stranded DNA, but strand exchange in that joint cannot be completed because the strand that would otherwise be displaced lacks a free 5' end. Instead, 2/3 to 3/4 of such distal joints cyclically form and dissociate. Dissociation requires the hydrolysis of ATP (Burnett et al., 1994). Observations on DNase protection revealed that consistent with their dynamic nature, these joints were heterogeneous in length, extending from the labeled distal end of the duplex up to 600 base pairs within the homologous region. Switching of base pairs was undetectable in this fraction of distal joints. However, the other 1/3 to 1/4 of distal joints, which did not cycle, were as long as the entire homologous region (6 kb), and underwent complete switching of base pairs. The formation of these static joints occurred at a rate in excess of 100 bp per second, without requiring hydrolysis of ATP. These and earlier observations suggest that the RecA filament containing single-stranded DNA rapidly incorporates duplex DNA into a coaxial three-stranded helix by a passive process, whereas additional energy is required to convert the three-stranded intermediate into products or back into substrates, both of which involve the unwinding of many turns of three-stranded helix.