Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation

Biopolymers and Cell

Volumn 26, Issue 5, 2010, Pages 398-405

  Brovarets, O O ^a,b   Zhurakivsky, R O ^a   Hovorun, D M ^a,b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND GENETICS   (Ukraine)

^b TARAS SHEVCHENKO NATIONAL UNIVERSITY OF KYIV   (Ukraine)

Author keywords

Hydrogen bonds; Ionization mechanism; Mismat ched DNA base pairs; Quantum chemical calculations; Spontaneous transitions

Indexed keywords

NUCLEOSIDE;

ARTICLE; BASE PAIRING; IONIZATION; KINETICS; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PROTON TRANSPORT; QUANTUM CHEMISTRY;

EID: 78349236562     PISSN: 02337657     EISSN: 19936842     Source Type: Journal    
DOI: 10.7124/bc.00016F     Document Type: Article

References (31)

1. Echols H., Goodman M. F. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 1991. 60. P. 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. P. 83-126.
3. Watson J. D., Crick F. H. C. The structure of DNA. Cold Spring Harbor Symp. Quant. Biol. 1953. 18. P. 123-131.
4. Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations. Nature. 1976. 263, N 5575. P. 285-289.
5. Sinha N. K., Haimes M. D. Molecular mechanisms of substitution mutagenesis. An experimental test of the Watson-Crick and Topal-Fresco models of base mispairings. J. Biol. Chem. 1981. 256, N 20. P. 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. P. 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. P. 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. P. 3-9.
9. Brovarets’ O. O., Hovorun D. M. Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine×cytosine. Ukr. Biochem. J. 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. P. 12-18.
11. Brovarets’ O. O., Hovorun D. M. Quantum chemical investigation of the basic molecular mechanisms of the pyrimidine-pyrine transversions. Ukr. Biochem. J. 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. P. 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. P. 295-298.
14. Nedderman A. N. R., Stone M. J., Williams D. H., Lin P. K. Th., Brown D. M. Molecular basis for methoxyamine-initiated mutagenesis: 1H nuclear magnetic resonance studies of oligonucleotide duplexes containing base-modified cytosine residues. J. Mol. Biol. 1993. 230, N 3. P. 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. P. 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. P. 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. P. 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. P. 49-56.
20. Boys S. F., Bernardi F. The calculation of small molecular interactions by the differences of separate total energies. So me procedures with reduced errors. Mol. Phys. 1970. 19, N 4. P. 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. Vodorodnaya svyaz’. Red. N. D. Sokolov, V. M. Chulanovskiy, M. Nauka, 1964. 340 s.
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 5- bromouracil in a water cluster. J. Phys. Chem. A. 2009. 113, N 11. P. 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 n(XH) vibration in infrared spectra. Spectrochim. Acta., Part A. 1999. 55, N 7-8. P. 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. P. 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 b fidelity: hold tight if you want it right. Chem. And Biol. 1998. 5, N 1. P. R7-R13.
31. Saenger W. Principles of nucleic acid structure. New York: Springer, 1988. 584 p.