Biopolym. Cell. 1997; 13(1):39-45.
http://dx.doi.org/10.7124/bc.000465
Structure and Function of Biopolymers
A structural-dynamic model on spontaneous semiopen states in DNA
1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

In this work there is suggested a structural-dynamic model on semiopen states in a two-strand DNA based on the semiempirical quantum-mechanical MNDO/H investigation of topologic properties of potential energy hyperfurface of free Watson-Crick Ade:Thy and Gua:Cyt pairs. In the frame of this model semiopen methastable states of Ade:Thy rich DNA sites are related to the spontaneous methastable state of Ade:Thy Watson-Crick pair, which is stabilized by two intrapair N3H...N1 and C2H...O2 hydrogen bonds, the Ade amino group being released from an H-bond. Therewith virtual semiopen states of the Gua:Cyt pair which are formed as a result of the turn of Gua and Cyt amino groups to cis- and trans-position with respect to the adjacent C2N3 bonds are believed to be a predecessors of methastable semiopen DNA states, arising in the Gua:Cyt rich sites at much higher temperature. The author is opinion that the virtual semiopen states favour to the formation of induced (for examle by interactions with ligands of various nature) semiopen states. A number of experimental facts explained in the frame of the proposed model confirm its adequacy.
Full text: (PDF, in Ukrainian)

References

[1] Volkov SN. [A cracked state of the double-helical DNA]. Mol Biol (Mosk). 1995;29(5):1086-94.
[2] Frank-Kamenetski? MD. [Fluctuational mobility of DNA]. Mol Biol (Mosk). 1983;17(3):639-52.
[3] Reiss C. Selected topics in molecular biology, in need of «hard» science. Nonlinear excitations in biomolecules (Les Houches School (May 30 to June 4, 1994). Ed. M. Peyrard. Amster­dam: Springer, 1994: 35-60.
[4] Danilov VI, Kventsel GF. Electronic submission to the theory of point mutations. Kiev: Naukova Dumka, 1971; 83 p.
[5] Grebneva EA. [Irradiation of DNA with ultraviolet light: potential changes and mutations]. Mol Biol (Mosk). 1994;28(4):805-12.
[6] Grebneva EA. Heat electronic desexitation as a mechanism of twoproton transitions in DNA. Dopovidi Akad Nauk Ukrainy. 1994;(2):73-5.
[7] Florian J, Hrouda V, Hobza P. Proton transfer in the adenine-thymine base pair. J Am Chem Soc. 1994; 116,(4):1457-60.
[8] Longo RL, Freitas LCG. Adenine-Thymine proton relay: Electric field and environmental effects on point mutation DNA. Int J Quant Chem. 1990;38(S17):35–44.
[9] Kwiatkowski JS, Person WB. The tautomerism of the nucleic acid bases revisited: from non-interacting to interacting bases. Theor Biochem Mol Biophys. Eds D. L. Beveridge, R. Lavery. New York: Adenine press, 1990: 153-71.
[10] Nowak MJ, Les A, Adamowicz L. Application of ab-initio quantum mechanical calculations to assign matrix-isolation IR spectra of oxopyrimidines. Trends Phys Chem. 1994; 4: 137-68.
[11] Govorun DM, Kondratyuk IV, Zheltovsky NV. Nucleotide bases as CH-Acids. Biopolym Cell. 1995; 11(5):15-20.
[12] Govorun DM, Kondratyuk IV. Anisotropic rotation of amino groups in canonical nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1996:(10):151-4.
[13] Hovorun DM, Mishchuk YaR, Kondratyuk IV. Topological features of potential energy hypersurface of canonical nucleotide bases. Biopolym Cell. 1996; 12(5):13-7.
[14] Williams NG, Williams LD, Shaw BR. Dimers, trimers, and tetramers of cytosine with guanine. J Am Chem Soc. 1989;111(18):7205-9.
[15] Maleev VIa, Semenov MA, Gasan AI, Kashpur VA. [Physical properties of the DNA-water system]. Biofizika. 1993;38(5):768-90.
[16] Zhurkin VB. [Local mobility of the DNA double helix. Comparison of conformational analysis with experiments]. Mol Biol (Mosk). 1983;17(3):622-38.
[17] Kochoyan M, Leroy JL, Gu?ron M. Processes of base-pair opening and proton exchange in Z-DNA. Biochemistry. 1990;29(20):4799-805.
[18] Pippard A. Physics of oscillations. Quantum-mechanical systems. M.: Vyshchaya Shkova, 1989. 263 p.
[19] Engel JD, von Hippel PH. Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. J Biol Chem. 1978;253(3):927-34.
[20] Grimm H, Rupprecht A. Inelastic neutron scattering studies of oriented DNA. Nonlinear excitations in biomolecules (Les Houches School (May 30 to June 4, 1994). Ed. M. Peyrard. Amsterdam: Springer, 1994: 101-15.
[21] Moe JG, Russu IM. Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers. Nucleic Acids Res. 1990;18(4):821-7.
[22] McAteer K, Ellis PD, Kennedy MA. The effects of sequence context on base dynamics at TpA steps in DNA studied by NMR. Nucleic Acids Res. 1995;23(19):3962-6.
[23] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p. 23. Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[24] Collins MA, Zang F. Model simulation of base pair motion in B-DNA. Nonlinear excitations in biomolecules (Les Houches School, May 30 to June 4, 1994). Ed. M. Peyrard, Amsterdam: Springer, 1994: 117-125.
[25] Volkov SN. The mechanism of long-range DNA. Dopovidi akad nauk UkrSSR. 1988;(?):48-52
[26] Iakushevich LV. [Dynamics of DNA]. Mol Biol (Mosk). 1989;23(3):652-62.
[27] Manevich LI, Savin AV, Smirnov VV, Volkov SN. Solitons in non-degenarated bistable systems. Uspekhi Fizicheskih Nauk. 1994. 164(9):937-58.
[28] Burd JF, Wartell RM, Dodgson JB, Wells RD. Transmission of stability (telestability) in deoxyribonucleic acid. Physical and enzymatic studies on the duplex block polymer d(C15A15) - d(T15G15). J Biol Chem. 1975;250(13):5109-13.
[29] Lyubchenko YuA. Intramolecular melting of DNA: Auth Thesis. dr biol. nauk. M, Inst mol. genet AN SSSR. 1988. 52 p.
[30] Lando DIu, Fridman AS. [Theory of melting of chemically modified DNA containing a cross-link between chains]. Mol Biol (Mosk). 1995;29(5):1064-75.
[31] Auffinger P, Westhof E. H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys J. 1996;71(2):940-54.
[32] Govorun DM, Mischuk YaR, Kondratyuk IV, Zheltovs'kyi MV. Dynamic stereo isomerism of Watson-Crick nucleotide base pairs. Dopovidi Nats Akad Nauk Ukrainy. 1995;(11):121-3.