Biopolym. Cell. 2003; 19(4):382-385.
Molecular Biophysics
Is the complementarity of canonical nucleotide bases in DNA their inherent physical-chemical characteristics? Results of the non-empirical quantum-chemical investigation
1Krechkivska O. M., 1Kosach D. A., 2Sudakov O. O., 1, 2, 3Hovorun D. M.
  1. National University of Kyiv-Mohyla Academy
    2, Skovorody Str., Kyiv, Ukraine, 04655
  2. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01033
  3. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680


Using ab initio Quantum-chemical calculation at the B3LYP/6-31++G(d, p) level in t/ie framework of «hydrophobic scenarios, authors arrived at the conclusion that complementarity of nucleotide hoses in DNA is not their intrinsic property, and their prototropir tautomerism – transition of Gua from keto to enolic form and Cyt – from amino to imino form – is a source of point mutations during the DNA biosynthesis. The obtained sequence of thermo-dynamic stability of quasi-isomorphous pairs GuccCyt > Thy:Gua (enolic) > Ade:Cyt(imino) > Ade:Thy enables us to explain the so-called asymmetry of point mutations in the course of the DNA biosynthesis. This, in its turn, evidences the adequacy of assumptions and conclusions made in this work.


[1] Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171(4356):737-8.
[2] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[3] Dolinnaya NG, Gryaznova OI. Complexes of oligo(poly)nucleotides with structural anomalies. Russ Chem Rev. 1989; 58 (8):758-77.
[4] Watson JD, Crick FHC. Genetic implication of the structure of desoxyribonucleic acid. Nature. 1953; 171(4361):964-7.
[5] Leszczynski J. Isolated, solvated and complexed nucleic acid bases: structures and properties. Adv Mol Struct Res. 2000; 6:209-65.
[6] Danilov VI, Kventsel GF. Electronic submission to the theory of point mutations. Kiev: Naukova Dumka, 1971; 84 p.
[7] Rein R. Biomolecular interactions. Structure-function of nucleic acids based on the interaction of their components. In : Intermolecular interactions: from diatomics to biopolymers. Ed Pullman B. (Perspectives in Quantum Chemistry & Biochemistry). John Wiley & Sons Ltd. 1978. 447 p.
[8] Goodman MF. DNA models. Mutations caught in the act. Nature. 1995;378(6554):237-8.
[9] Goldovsky AM. Is water implied in the construction of life-capable structure? Biofizika. 1979;24(4):755-6.
[10] Reddy CK, Das A, Jayaram B. Do water molecules mediate protein-DNA recognition? J Mol Biol. 2001;314(3):619-32.
[11] Petruska J, Sowers LC, Goodman MF. Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc Natl Acad Sci U S A. 1986;83(6):1559-62.
[12] Kiefer JR, Mao C, Braman JC, Beese LS. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 1998;391(6664):304-7.
[13] Doubli? S, Tabor S, Long AM, Richardson CC, Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 1998;391(6664):251-8.
[14] Simonson T, Brooks CL. Charge screening and the dielectric constant of proteins: insights from molecular dynamics. J Am Chem Soc. 1996;118(35):8452–8. :
[15] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga A, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery J. General atomic and molecular electronic structure system. J Comp Chem. 1993;14(11):1347–63.
[16] Boys SF, Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys. 1970;19(4):553–66.
[17] Krechkivs'ka OM, Kosach DA, Hovorun DM. How DNA-polymerase minimizes the level of spontaneous mistakes in the synthesis of DNA caused by prototropic tautomerism of nucleotide bases: a possible physico-chemical mechanism and its quantum-mechanical justification. Dopovidi Nats Akad Nauk Ukrainy. 2002; (11):155-9.
[18] Krechkivska OM, Kosach DA, Hovorun DM. How does DNA-polimerase keep nucleotide basis in canonical tautomeric form: a simple physical mechanism. Nauk Zapysky NAUKMA. 2002; 20(2):517-20.
[19] Ahn J, Werneburg BG, Tsai MD. DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant. Biochemistry. 1997;36(5):1100-7.