Figure 7.

MD investigation of G-quadruplex G-tetrad stacking interfaces: 5-ns trajectories of stacked propeller G-quadruplexes formed by the sequences d[(G₃T)₃G₃] were run for (A) 5′–5′ and (B) 3′–3′ stacked G-quadruplexes. The trajectories of three different starting geometries of G-quadruplex stacking arrangements (Interface θ_tet varying by ∼30°) are shown. (C) Long 100-ns trajectories were computed for a 5′–5′ and a 3′–3′ stacked G-quadruplex complex. Average relative rotation (θ_tet) of the four interface guanine stacks was characterized at regular intervals.