Structural basis of DNA flexibility

It has been recently shown by us, on the basis of crystal structure databas e that the flexibility of B-DNA double helices depends significantly on the ir base sequence. Our model building studies Further indicated that the exi stence of bifurcated cross-strand hydrogen bonds between successive base pa irs is possibly the main factor behind the sequence directed DMA flexibilit y. These cross-strand hydrogen bonds are, of course, weaker than the usual Watson-Crick hydrogen bonds and their bond geometry is characterized by rel atively larger bond lengths and smaller bond angles. We have tried to impro ve our model structures by incorporating non-planarity of the amino groups in DNA bases due to the presence of lone pair electrons at the nitrogen ato ms. Energy minimization studies have been carried out by using different qu antum chemical methods, whereby it is found that in all cases of N-H . . .O type cross-strand hydrogen bonds, the bond geometry improves significantly . In the cases of N-H . . .N type hydrogen bonds, however, no such consiste nt improvements can be noticed. Perhaps the true picture would emerge only if all the other interactions present in the DNA macromolecule could be app ropriately taken into account.