Figure 7.

Late-stage snapshots in stereoview (at ~2.5 ns) from the unconstrained trajectories started from the pretranslocated states in the (A) open and (B) closed complex, aligned with respect to the posttranslocated reference state (shown in silver). The labels show the nucleotide numbering of Figure 4 and the dotted lines indicate the base paring between the RNA and DNA. In (A), nucleotides have mostly restored the original positions of the posttranslocated state, except the −1 nucleotide pairs (RNA3′-end), which remain close to the pretranslocated positions because of the steric hindrance of the O′-helix (light blue) blocking the forward translocation of the +1 nucleotide. In (B), most of nucleotides remain stable near the pretranslocated positions. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]