GEOMETRIES, CHARGES, DIPOLE-MOMENTS AND INTERACTION ENERGIES OF NORMAL, TAUTOMERIC AND NOVEL BASES

Ab initio molecular orbital calculations with the STO-3G and 4-31G bas is sets are performed to study the geometries and interactions of natu ral and ''novel'' Watson-Crick base pairs, as well as some non-Watson- Crick base pairs. First the optimized geometries of bases are determin ed using the STO-3G basis set, and then for the base pairs with the ST O-3G and 4-31G basis sets. Interaction energies of these base pairs ar e evaluated, and their relative stabilities are discussed. Hydrogen bo nd 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 wit h the crystal structure data. The order of relative stabilities is fou nd to be: iG:iC > G:C. G:T > rG:rC > A*:C > Am:U > pi:kappa K > chi:k appa > G:T > A:C* > U = AT where, A*, T*, G* and C* are tautomers, iG and iC are iso-G and iso-CI Am is 2-amino adenine, chi is xanthosine, kappa is 2,4-diaminopyrimidine, pi is 7-methyloxoformycin B, rG is mo dified guanine with substitutions at positions 5 and 7, and rC is modi fied cytosine with a substitution at position 6. Pairing strengths wit h modified bases may affect the efficiency of protein production.