FLEXIBILITY OF THE B-DNA BACKBONE - EFFECTS OF LOCAL AND NEIGHBORING SEQUENCES ON PYRIMIDINE-PURINE STEPS

The structurally correlated dihedral angles epsilon and zeta are known for their large variability within the B-DNA backbone. We have used m olecular modelling to study both energetic and mechanical features of these variations which can produce BI/BII transitions, Calculations we re carried out on DNA oligomers containing either YpR or RpY dinucleot ides steps within various sequence environments. The results indicate that CpA and CpG steps favour the BI/BII transition more than TpA or a ny RpY step. The stacking energy and its intra-and inter-strand compon ents explain these effects, Analysis of neighbouring base pairs reveal s that BI/BII transitions of CpG and CpA are easiest within (Y)(n)(R)( n) sequences. These can also induce a large vibrational amplitude for TpA steps within the BI conformation.