Geometries, Charges, Dipole Moments and Interaction Energies of Normal, Tautomeric and Novel Bases

Abstract

Ab initio molecular orbital calculations with the STO–3G and 4–31G basis sets are performed to study the geometries and interactions of natural and “novel” Watson-Crick base pairs, as well as some non-Watson-Crick base pairs. First the optimized geometries of bases are determined using the STO-3G basis set and then for the base pairs with the STO-3G and 4–31G basis sets. Interaction energies of these base pairs are evaluated, and their relative stabilities are discussed. Hydrogen bond features, partial charges and dipole moments of the base pairs are described. The calculated stabilities are in reasonable agreement with the limited available experimental data from thermal melting studies. Hydrogen bond geometries at the 4- 31G level are in good agreement with the crystal structure data. The order of relative stabilities is found to be:

iG:iC > G:C > G:T^* > rG:rC > A^*:C > Am:U > π:κ > χ:κ > G^*:T > A:C^* > A:U = A:T

where, A^*, T^*, G^* and C^* are tautomers, iG and iC are iso-G and iso-C, Am is 2-amino adenine, χ is xanthosine, κ is 2,4-diaminopyrimidine, π is 7-methyl oxoformycin B, rG is modified guanine with substitutions at positions 5 and 7, and rC is modified cytosine with a substitution at position 6. Pairing strengths with modified bases may affect the efficiency of protein production.