Influence of sequence on the conformation of the B-DNA helix

We have tried to ascertain whether the variability found in the conformational features of the 10 base steps in B-DNA is mainly due to the flanking sequences or to interactions with the environment. From an analysis of the twist parameter of the base-pair steps available from crystals of oligonucleotides and protein/oligonucleotide complexes, we conclude that in most cases the flanking sequences show little influence: the conformation of a DNA region results from the combination of the independent intrinsic features of each base step (average conformation and intrinsic variability), modulated by their interactions with the environment. Only in some cases (YR steps, in particular CG and CA/TG) does it appear that flanking sequences have an influence on the conformation of the central base step. The values obtained allow an approximation to the parameters expected for repetitive DNA sequences. In particular, it is found that poly[d(AG/CT)] should have a strongly alternating conformation, in agreement with recently reported oligonucleotide structures.