Sequence-dependent harmonic deformability of nucleic acids inferred from atomistic molecular dynamics

Abstract

This chapter is concerned with a method of deducing coarse-grained confrormation and harmonic stiffness of nucleic acids from unrestrained atomistic molecular dynamics. It contains a brief introduction and a review of recent computational studies. The length scales of individual base pairs, basepair steps, and longer oligonucleotides are discussed. The results are compared with analogous data based on experimental investigations. Finally, limitations and challenges of the approach are exposed. © 2006 Springer.