B-DNA와 Z-DNA 사이의 전이에 관한 mesoscopic 모델

Abstract

It is known that the left-handed DNA, called Z-DNA, exists in various situations of specific sequences and ionic environments. Transition between the right-handed B-DNA, the regular form in cell, and the Z-DNA is critical in regulating gene regulation. Within the mesoscopic model for double strand(ds) DNA recently developed, where the ds stacking is implemented by base-pairing, diagonal and stretching interactions, we incorporate a geometrical feature, i.e., the tilting angle of base plane, and the associated energy. This breaks the symmetry of the energy profile, otherwise symmetric, with respect to helical angles, showing the energy minimum at the positive (angle) of the B-DNA as well as the meta-stability of Z-DNA, when B-DNA potential parameters obtained by the B-DNA geometry are used in the energy model. On the other hand, when Z-DNA geometry is used to obtain the Z-DNA potential parameters, the energy profile indeed shows the minimum at the negative helical angle characteristic of Z-DNA. We find the potential parameters, the ranges and stiffness of the interactions, are all slightly smaller than those of B-DNA. We explain this difference within a simple argument based on the electrostatics of different ionic environments of B and Z-DNAs. It demonstrates the validity of our model that it can describe some physical condition or Z-DNA and the B-Z transition in an analytical manner.