CICADA Interface with AMBER. An Application on Oligonucleotides and their Fragments

Abstract

The potential energy hypersurfaces (PES) of several nucleotide fragments were analyzed by the conformational search algorithm CICADA interfaced with the molecular mechanics program AMBER, version 4.0. The low energy conformers for dimethylphosphate, dinucleoside monophosphate fragments, and deoxyadenosine are described. Calculated relative and absolute flexibilities of single conformers, molecular fragments as well as entire molecules are introduced. The comparison of the results with the literature data shows good ability of the CICADA-AMBER combination to describe conformational space. It is revealed that the number of low energy conformers as well as flexibility decreases as the size of the molecule increases. The conformational behavior of freely rotatable single bonds, specially those within a sugar ring, is more “sharp” in larger structures.