INTERACTIONS BETWEEN AMINO-GROUPS IN DNA - AN AB-INITIO STUDY AND A COMPARISON WITH EMPIRICAL POTENTIALS

An ab initio quantum chemical analysis of the close amino group contac ts, existing in many DNA crystal structures, is presented. The calcula tions are made at the Hartree-Fock (HF) level with medium 6-31G and 6 -31G(NH2) basis sets as well as with inclusion of correlation energy using the second order Moller-Plesset theory (MP2) with the 6-31G bas is set. We demonstrate that the model system (methylamine dimer, cytos ine dimer) amino groups are forced to adopt significantly non-planar g eometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyz e the amino group contacts occurring in the DNA double helices. We pro pose that the mutual amino group interactions contribute to the confor mational variability of the CpG and ApT B-DNA steps.