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

The effect of backbone zeta 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 zeta torsion angle (C3'-O3'-P-O5') has been identified as the reaction coordinate for the opening process. Our results shaw a strong correlation between the magnitude of base displacement and the equilibrium zeta(eq) angle. In all the crystal structures studied, the magnitude follows a periodic pattern with largest value at zeta(eq) similar to -100 degrees and minimum at similar to -217 degrees. The effect of other backbone torsion angles on base opening is also discussed. (C) 1998 Elsevier Science B.V. All rights reserved.