Effect of backbone ζ torsion angle on low energy single base opening in B-DNA crystal structures

The effect of backbone ζ torsion angle on low energy single base opening in the available B-DNA crystal duplex structures has been studied. This work is based on our earlier method in which ζ torsion angle (C3ʹ–O3ʹ–P–O5ʹ) has been identified as the reaction coordinate for the opening process. Our results show a strong correlation between the magnitude of base displacement and the equilibrium ζeq angle. In all the crystal structures studied, the magnitude follows a periodic pattern with largest value at ζeq∼−100° and minimum at ∼−217°. The effect of other backbone torsion angles on base opening is also discussed.