Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix
Biopolymers 18(4): 959-980
An algorithm is developed that enables the routine determination of backbone conformations of nucleic acids. All atomic positions including H are specified in accord with experimental bond lengths and angles but with theoretically determined conformational angles. For 2 Watson-Crick base pairs at a separation of 3.38 .ANG. and perpendicular to a common helical axis, minimum energy configurations are found for all 10 combinations at helical angles of .alpha. .apprx. 36-38.degree., corresponding to the B-DNA structure with C(2')-endo sugar puckers. Backbone configurations exist only within the range 35.5.degree. .ltoreq. .alpha. .ltoreq. 42.degree., which suggests the origin of the 10-fold helix. Calculated stacking energies for the B-DNA structure increases for each of the clustered groups of base pairs: G .cntdot. C with G .cntdot. C, G .cntdot. C with A .cntdot. T and A .cntdot. T with A .cntdot. T. They are in approximate agreement with experimental observations. The counterclockwise helix is examined, and physically meaningful structures are found only when the helical axes of successive base pairs are disjointed.