Figure 3.

Hydrogen bonding and stacking for (CC)12 simulated in explicit solvent at 200 mM NaCl restrained at σ = 0.068 (A) and at σ = 0.068 (B). In each case, the structures are stable and show good correspondence with the implicit solvent simulation, with very little loss of canonical interactions. In the under-twisted case we see some increase of non-canonical hydrogen bonds but these do not correspond with a loss of canonical hydrogen bonds and hence are unlikely to be a conformational change. In the over-twisted case, the DNA remains virtually unchanged for the entire simulation in terms of base pair interactions. Red indicates a loss of >1 canonical hydrogen bond and grey indicates a relatively unchanged interaction landscape.