INFLUENCE OF SEQUENCE ON THE CONFORMATION OF THE B-DNA HELIX

We have tried to ascertain whether the variability found in the confor mational features of the 10 base steps in B-DNA is mainly due to the f lanking sequences or to interactions with the environment. From an ana lysis of the twist parameter of the base-pair steps available from cry stals of oligonucleotides and protein/oligonucleotide complexes, we co nclude 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 conformatio n 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 conf ormation of the central base step, The values obtained allow an approx imation to the parameters expected for repetitive DNA sequences, In pa rticular, it is found that poly[d(AG/CT)] should have a strongly alter nating conformation, in agreement with recently reported oligonucleoti de structures.