The Structure of DNA Fragments: Quantum Chemical Modeling

Abstract

We have briefly described the results of quantum–chemical investigations of DNA mini-helixes that are composed of three and five pairs of 2´-deoxyribonucleotides. The analysis of the helicity suggests that the helical conformations adopt geometrical parameters, which are close to those of the A- and B-DNA forms, even when the mini-helix is composed of just three DNA base pairs. We also have found that (dA)5⸱(dT)5 anion forms a DNA duplex that possesses an intermediate form between a helix and a ladder when it is placed in a vacuum. The presence of compensative Na+ counterions or explicit micro-hydration of minor and major groves stabilizes a B-DNA mini-helix. . Such factor as water volume plays a minor role. Slightly different behavior has been found in the case of the (dG)5⸱(dC)5 duplex. In this case, it is observed the formation of B-type mini-helixes even for (dG)5⸱(dC)5 anion placed in a vacuum. This is due to an additional stabilization originating from the appearance of an extra hydrogen bond, compared with an AT base pair.

Keywords: DNA structure, DNA mini-helixes, micro-hydration, macro-hydration, DFT