Large-scale bending
Using the DNA-segment method only, initial attempts at docking the DBDs onto I1 or I2 were not satisfactory. A second type of DNA conformation change was applied to conduct large-scale bending of DNA using Web 3DNA 2.0, a web-based server23 designed to manipulate DNA conformations. The software generates rigid-body values (three translations and three rotations) of a single base pair (bp) and six step parameters for neighboring bps. It allows modification of the bp and step parameters to build customized DNA structures.
To calculate the bp step parameters to bend DNA within a plane, we followed the recommendations in Calladine et al .24 DNA roll angles were modified gradually at each bp step in the relevant region in which the roll angle Rn at step n is given by , where a
larger A results in a greater total bend angle and b introduces a phase angle to position the maximum roll angle at the desired location along the DNA. This formula makes the approximation that a full helical twist of B‑DNA contains 10 bp/turn and that the roll angle has the same period of 10 steps (also see Discussion). Values for A and b were selected empirically by presenting HDOCK with a variety of bent DNA structures and choosing the docked structure with the best surface complementarity.