Biopolym. Cell. 2010; 26(5):398-405.
Molecular Biophysics
Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation
1, 2Brovarets' O. O., 1Zhurakivsky R. O., 1, 2Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Institute of High Technologies,
    Taras Shevchenko National University of Kyiv
    2, korp.5, Pr. Akademika Hlushkova, Kyiv, Ukraine, 03022

Abstract

Aim. To investigate theoretically the adequacy of the ionization mechanism of the spontaneous transitions appearance, using simple molecular models – DNA base pairs, one of which is ionized, and electroneutral and ionized DNA-like conformers of canonical nucleosides. Methods. Non-empirical quantum chemistry, physicochemical kinetics and analysis of the electron density by means of Bader’s atoms in molecules (AIM) theory were used. Results. It is established at base pairs that the ionization mechanism of transitions origin doesn’t imply any advantages in comparison with other mechanisms described in literature. However, the protonation/deprotonation of base in any canonical nucleoside significantly perturbs DNA-like conformations of the latter. Conclusions. The ionization mechanism can’t explain entirely the nature of the spontaneous transitions.
Keywords: spontaneous transitions, ionization mechanism, mismatched DNA base pairs, hydrogen bonds, quantum-chemical calculations.

References

[1] Echols H., Goodman M. F. Fidelity mechanisms in DNA replication Annu. Rev. Biochem 1991 60:477–511.
[2] Goodman M. F., Creighton S., Bloom L. B., Petrushka J. Biochemical basis of DNA replication fidelity Crit. Rev. Biochem. Mol. Biol 1993 28, N 2:83–126.
[3] Watson J. D., Crick F. H. C. The structure of DNA Cold Spring Harbor Symp. Quant. Biol 1953 18:123–131.
[4] Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations Nature 1976 263, N 5575:285–289.
[5] Sinha N. K., Haimes M. D. Molecular mechanisms of substitution mutagenesis. An experimental test of the WatsonCrick and Topal-Fresco models of base mispairings J. Biol. Chem 1981 256, N 20:10671–10683.
[6] Sowers L. C., Shaw B. R., Veigl M. L., Sedwick W. D. DNA base modification: ionized base pairs and mutagenesis Mutat. Res 1987 177, N 2:201–218.
[7] Lawley P. D., Brookes P. Ionization of DNA bases or base analogues as a possible explanation of mutagenesis, with special reference to 5-bromodeoxyuridine J. Mol. Biol 1962 4, N 3:216–219.
[8] Brovarets' O. O., Hovorun D. M. The novel physico-chemical mechanism of the Watson-Crick base pair Ade Thy transformation to the mispairs involving rare tautomers Ade* Thy and Ade Thy*. Ukr. Bioorg. Acta. 2010; 9, N 1:3–9.
[9] Brovarets' O. O., Hovorun D. M. Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guaninecytosine. Ukr Biokhim Zh. 2010; 82, N 3 P. 55–60.
[10] Brovarets' O. O., Hovorun D. M. Physicochemical mechanism of the wobble DNA base pairs Gua Thy and Ade Cyt transition into the mismatched base pairs Gua* Thy and Ade Cyt* formed by the mutagenic tautomers Ukr. Bioorg. Acta 2009 8, N 2:12–18.
[11] Brovarets' O. O., Hovorun D. M. Quantum chemical investigation of the basic molecular mechanisms of the pyrimidinepyrine transversions. Ukr Biokhim Zh. 2010; (in press).
[12] Brovarets' O. O., Hovorun D. M. How stable are the mutagenic tautomers of DNA bases? Biopolym. Cell. 2010 26, N 1:72–76.
[13] Brovarets' O. O., Hovorun D. M. Stability of mutagenic tautomers of uracil and its halogen derivatives: the results of quantum-mechanical investigation Biopolym. Cell 2010 26, N 4:295–298.
[14] Nedderman A. N. R., Stone M. J., Williams D. H., Lin P. K. Th., Brown D. M. Molecular basis for methoxyamineinitiated mutagenesis: 1H nuclear magnetic resonance studies of oligonucleotide duplexes containing base-modified cytosine residues J. Mol. Biol 1993 230, N 3:1068– 1076.
[15] Fazakerley G. V., Gdaniec Z., Sowers L. C. Base-pair induced shifts in the tautomeric equilibrium of a modified DNA base J. Mol. Biol 1993 230, N 1:6–10.
[16] Dewar M. J. S., Storch D. M. Alternative view of enzyme reactions Proc. Nat. Acad. Sci. USA 1985 82, N 8 P. 2225–2229.
[17] Petrushka J., Sowers L. C., Goodman M. F. Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity Proc. Nat. Acad. Sci. USA 1986 83, N 6:1559–1562.
[18] Peng C., Schlegel H. B. Combining synchronous transit and quasi-newton methods to find transition states Israel J. Chem 1993 33, N 4:449–454.
[19] Peng C., Ayala P. Y., Schlegel H. B., Frisch M. J. Using redundant internal coordinates to optimize equilibrium geometries and transition states J. Comput. Chem 1996 17, N 1:49–56.
[20] Boys S. F., Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors Mol. Phys 1970 19, N 4:553–566.
[21] Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Montgomery Jr., J. A., Vreven T., Kudin K. N., Burant J. C., Millam J. M., Iyengar S. S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G. A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J. E., Hratchian, H. P., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Ayala P. Y., Morokuma K., Voth G. A., Salvador P., Dannenberg J. J., Zakrzewski V. G., Dapprich S., Daniels A. D., Strain M. C., Farkas O., Malick D. K., Rabuck A. D., Raghavachari K., Foresman J. B., Ortiz J. V., Cui Q., Baboul A. G., Clifford S., Cioslowski J., Stefanov B. B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R. L., Fox D. J., Keith T., Al-Laham M. A., Peng C. Y., Nanayakkara A., Challacombe M., Gill P. M. W., Johnson B., Chen W., Wong M. W., Gonzalez C., Pople J. A. Gaussian 03, Revision C.02 Wallingford CT: Gaussian Inc., 2004.
[22] Bader R. W. F. Atoms in molecules. A quantum theory Oxford: Clarendon press, 1990 436 p.
[23] Hydrogen bond. Ed ND Sokolov, VM. Chulanovsky. M.: Nauka, 1964; 340 p.
[24] Biegler-Konig F., Schonbohm J., Bayles D. Software news and updates. AIM2000 – a program to analyze and visualize atoms in molecules. J. Comput. Chem. 2001; 22, N 5 P. 545–559.
[25] Danilov V. I., van Mourik T., Kurita N., Wakabayashi H., Tsukamoto T., Hovorun D. M. On the mechanism of the mutagenic action of 5-bromouracil: a DFT study of uracil and 5bromouracil in a water cluster J. Phys. Chem. A 2009 113, N 11:2233–2235.
[26] Espinosa E., Molins E., Lecomte C. Hydrogen bond strengths revealed by topological analyses of experimentally observed electron densities Chem. Phys. Lett 1998 285, N 3–4 P. 170–173.
[27] Iogansen A. V. Direct proportionality on the hydrogen bonding energy and the intensification of the stretching (XH) vibration in infrared spectra Spectrochim. Acta., Part A 1999 55, N 7–8:1585–1612.
[28] Tang M., Shen X., Frank E. G., O'Donnell M., Woodgate R., Goodman M. F. UmuD2' C is an error-prone DNA polymerase, Escherichia coli pol V Proc. Nat. Acad. Sci. USA 1999 96, N 16:8919–8924.
[29] Kornberg A., Baker T. DNA replication. Eds W. H. Freeman New York: Acad. press, 1992 871 p.
[30] Beard W. A., Wilson S. Structural insights into DNA polymerase fidelity: hold tight if you want it right Chem. Biol 1998 5, N 1:R7–R13.
[31] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.