Sequence dependency of canonical base pair opening in the DNA double helix
Fig 1
Enhanced sampling of base pair opening by adaptively biasing along dN1N3.
The opening of a base pair can be described either by the distance coordinate dN1N3 or by two dihedral angles θ, one for each base (A). The closed state (gray configuration) is characterized by θ ≈ 0 and small dN1N3. Open configurations (black) have larger dN1N3 values and negative or positive θ values, depending on the direction of opening. Here, we improve sampling of the opening event by applying a bias along dN1N3 using the adaptive biasing method AWH. Example trajectories are shown for one such simulation, for the case of opening of an AT base pair (B). Both θ angles are sampled simultaneously, according to their Boltzmann distribution at each given value of dN1N3. After exiting an initial stage of the method (dashed vertical line), sampling of dN1N3 is expected to be roughly uniform and its dynamics diffusive.