Could the bridging OH- ion initiate hammerhead cleavage?
In the simulated MD trajectories, where the hammerhead conformations are always close to the crystal structure, the [mu]-hydroxo bridge was never seen in a favourable position for the direct activation of the cleavage-site 2′-hydroxyl. As such, this observation is not surprising since the conformational sampling is done around the equilibrium state, from which input of activation energy is required in order to reach the transition state. Simulations performed at higher temperatures up to 350 K followed by rapid cooling led at times to only slightly shorter distances between the 2′-hydroxyl oxygen atom and the cleavable phosphate (data not shown). However, when a flip of the ribose pucker from C3′-endo to C2′-endo at the C17 residue which holds the cleavable 3′-phosphate was induced during the simulations, the reactive-site 2′-hydroxyl moved in close proximity to both the attacked phosphorous atom and the [mu]-bridging OH- ion (Fig. 4 ). At the same time, the 2′-hydroxyl comes within hy
