Sequence dependent intrinsic deformability of the DNA base amino groups. An ab initio quantum chemical analysis

Abstract

An accurate description of the interactions between DNA bases is of fundamental importance in the theoretical analysis of DNA structure, flexibility and dynamics. These base-base interactions are significantly influenced by the properties of the DNA base amino groups. In the present paper we show that, in constrast to the empirical force fields, ab initio calculations predict non-planar geometries for the DNA base amino groups. We compare the amino group non-planarity of cytosine, adenine, guanine, the guanine amino tautomer, 2-aminoadenine, 5-methylcytosine and the guanine formamidine hydrogen bonded complex, at the HF/6–31G(NH 2 ∗) level of theory. In addition, the geometry of cytosine is optimized at the MP2/6–31G ∗, MP2/6–31G(NH ∗ 2), HF/6–31G ∗, HF/4–21G(NH ∗ 2) and HF/6–31G levels of theory to estimate the role of electron correlation and polarization functions in the amino group geometry. It is shown that the gradient geometry optimization with inclusion of electron correlation significantly increases the non-planarity of the cytosine amino group compared to the HF level of calculations. The influence of non-planar DNA base amino groups on the conformational variability of DNA is briefly discussed.