Biopolym. Cell. 2004; 20(1-2):71-76.
The study of the canonical Watson-Crick DNA base pairs by Moller-Plesset perturbation method: the nature of their stability
1Danilov V. I., 2Anisimov V. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Department of Pharmaceutical Sciences, School of Pharmacy,
    University of Maryland
    620 W. Lexington St., Baltimore, MD 21201


Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Moller-Plesset (MP2) perturbation method at the 6-31G* and 6-31G*(0.25) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs. Morokuma-Kitaura (MK) and reduced variational space (RVS) methods of the decomposition for molecular Hartree-Fock interaction energies were used for the investigation of the hydrogen bonding in the Watson-Crick base pairs in question. It is shown that the stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time the polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases.


[1] Hobza, P., Sponer, J. Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations (2002) Journal of the American Chemical Society, 124 (39), pp. 11802-11808.
[2] Sponer, J., Leszczynski, J., Hobza, P. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases (2002) Biopotymers (Nucl. Acids Sci.), 61, p. 331.
[3] Guerra, C.F., Bickelhaupt, F.M., Snijders, J.G., Baerends, E.J. The nature of the hydrogen bond in DNA base pairs: The role of charge transfer and resonance assistance (1999) Chemistry - A European Journal, 5 (12), pp. 3581-3594.
[4] Guerra, F., C., Bickelhaupt, F.M., Snijders, J.G., Baerends, E.J. Hydrogen bonding in DNA base pairs: Reconciliation of theory and experiment (2000) Journal of the American Chemical Society, 122 (17), pp. 4117-4128.
[5] Saniamwia, R., Vazquez, A. Structural and electronic property changes of the nucleic bases upon base pair formation (1994) J. Comput. Chem, 15, pp. 981-996.
[6] Fellers, R.S., Barsky, D., Gygi, F., Colvin, M. An ab initio study of DNA base pair hydrogen bonding: A comparison of plane-wave versus Gaussian-type function methods (1999) Chemical Physics Letters, 312 (5-6), pp. 548-555.
[7] Lai, C.-C., Shen, C.-C., Hu, C.-H. A comparative study of hydrogen bonding using density functional theory (2001) Journal of the Chinese Chemical Society, 48 (2), pp. 145-152.
[8] Artacho, E., Machado, M., S?nchez-Portal, D., Ordej?n, P., Soler, J.M. Electrons in dry DNA from density functional calculations (2003) Molecular Physics, 101 (11), pp. 1587-1594.
[9] Sherer, E.C., York, D.M., Cramer, C.J. Fast approximate methods for calculating nucleic acid base pair interaction energies (2003) Journal of Computational Chemistry, 24 (1), pp. 57-67.
[10] Preuss, M., Schmidt, W.G., Seino, K., Furthm?ller, J., Bechstedt, F. Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials (2004) Journal of Computational Chemistry, 25 (1), pp. 112-122.
[11] Kurita, N., Araki, M., Nakao, K., Kobayashi, K. Efficiency of the MO method using a Slater-type basis set and non-local density functional formalism for describing DNA base stacking energy (1999) Chemical Physics Letters, 313 (3-4), pp. 693-700.
[12] Ogawa, T., Kurita, N., Sekino, H., Kitao, O., Tanaka, S. Hydrogen bonding of DNA base pairs by consistent charge equilibration method combined with universal force field (2003) Chemical Physics Letters, 374 (3-4), pp. 271-278.
[13] Danilov, V.I., Anisimov, V.M. The nature of the stability of Watson-Crick nucleic acids base pairs. Ab initio Hartree-Fock and post-Hartree-Fock theory studies (2003) J. Biomol. Struct, and Dyn, 20 D, pp. 935-936.
[14] Danilov, V.J., Anisimov, V.M. The geometry of canonical Watson-Crick DNA base pairs: Ab initio post-Hartree-Fock theory studies (2003) J. Biomol. Struct, and Dyn, 20, pp. 937-938.
[15] Moller, Chr., Plesset, M.S. Note on an approximation treatment for many-electron systems (1934) Physical Review, 46 (7), pp. 618-622.
[16] Hehre, W., Radom, L., Schleyer, P.V.R., Pople, J.A. (1986) Ab Initio Molecular Orbital Theory. New York: J. Wiley
[17] Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., (...), Montgomery, J.A. General atomic and molecular electronic structure system (1993) J. Comput. Chem, 14, pp. 1347-1363.
[18] Morokuma, K., Kitaura, K. (1981) Energy Decomposition Analysis Chemical Applications of Atomic and Molecular Electrostatic Potentials, pp. 215-242. Eds P. Politzer, D. G. Truhlar. New York: Plenum press
[19] Gordon, M.S., Jensen, J.U. Wavefunctions and chemical bonding: Interpretation (1998) Encyclopedia of Computational Chemistry, pp. 3198-3214. New York: J. Wiley
[20] Chalasinski, G., Szczesniak, M.M. On the connection between the supermolecular Moller-Plesset treatment of the interaction energy and the perturbation theory of intermolecular forces (1988) Mol. Phys, 63, pp. 205-224.
[21] Langlei, J., Claverie, P., Caron, F., Boeuve, J.C. Interactions between nucleic acid bases in hydrogen bonded and stacked configurations: The role of the molecular charge distribution (1981) Int. J. Quant. Chem, 20, pp. 299-338.
[22] Sponer, J., Leszczynski, J., Hobza, P. Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation (1996) Journal of Physical Chemistry, 100 (5), pp. 1965-1974.
[23] Shishkin, O.V., Elstner, M., Frauenheim, T., Suhai, S. Structure of stacked dimers of N-methylated Watson-Crick adenine-thymine base pairs (2003) International Journal of Molecular Sciences, 4 (10), pp. 537-547.
[24] Gould, I.R., Kollman, P.A. Theoretical investigation of the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs (1994) Journal of the American Chemical Society, 116 (6), pp. 2493-2499.
[25] Sponer, J., Mokdad, A., ?poner, J.E., ?pa?kov?, N., Leszczynski, J., Leontis, N.B. Unique tertiary and neighbor interactions determine conservation patterns of cis Watson-Crick A/G base-pairs (2003) Journal of Molecular Biology, 330 (5), pp. 967-978.
[26] El Hassan, M.A., Calladine, C.R. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA (1996) Journal of Molecular Biology, 259 (1), pp. 95-103.