Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

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Abstract

Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries of 10 stacked nucleic acid−base pairs: A···A, C···C, G···G, U···U, A···C, G···A, A···U, G···C, C···U, and G···U; in some cases uracil was replaced by thymine. The most stable stacked pair is the G···G dimer (−11.3 kcal/mol), and the least stable is the uracil dimer (−6.5 kcal/mol). The interaction energies of H-bonded base pairs range from −25.8 kcal/mol (G···C) to −10.6 kcal/mol (T···T). The stability of stacked pairs originates in the electron correlation, while all the H-bonded pairs are dominated by the HF energy. The mutual orientation of the stacked bases is, however, primarily determined by the HF interaction energy. The ab initio base stacking energies are well reproduced by the empirical potential calculations, provided the atomic charges are derived by the same method as used in the ab initio calculations. Some contributions previously postulated to significantly influence base stacking (induction interactions, π−π interactions) were not found. Base stacking was also investigated in six B-DNA and two Z-DNA base pair steps; their geometries were taken from the oligonucleotide crystal data. The many-body correction was estimated at the HF/MINI-1 level. The sequence-dependent variations of the total base pair step stacking energies range from −9.9 to −14.7 kcal/mol. The range of the calculated many-body corrections to the stacking energy is 2 kcal/mol. The ab initio calculations exclude the consideration that the unusual conformational properties of the CpA(TpG) steps might be associated with attractive induction interactions of the exocyclic groups of DNA bases and the aromatic rings of bases.

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