Biopolym. Cell. 1994; 10(2):79-85.
http://dx.doi.org/10.7124/bc.0003A9
Numerical simulation of local base pairs opening in DNA molecule
1Yegorenkov A. I.
  1. Ukrainian O.O. Bogomolets state medical university
    Blvd. Shevchenko, 13, Kyiv, Ukraine, 01601

Abstract

The method of atom-atomic potentials has permitted to realize the numerical simulation of local base pairs opening in a trinucleotide model of B-form DNA molecule. Having used molecular dynamics calculation and also data concerning potential energy surfase topology adequate to a type of conformation flexibility studied here, the author has determined correlation degree for some types of DNA bases movements in any opening DNA bases pair and has shown the dependence of opening processes in a central nucleotide pair on nucleotide content of DNA duplex being studied.
Full text: (PDF, in Russian)

References

[1] Iakushevich LV. Dynamics of DNA. Mol Biol (Mosk). 1989;23(3):652-62.
[2] Egorenkov AI. The package of teaching programs for studing in biophysic foundations of molecular genetics. Biopolym Cell. 1993; 9(6):96-8.
[3] Volkov SN. Conformational stimulation in DNA type macromolecules. Mol Biol (Mosk). 1992;26(4):835-46.
[4] Englander SW, Kallenbach NR, Heeger AJ, Krumhansl JA, Litwin S. Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. Proc Natl Acad Sci U S A. 1980;77(12):7222-6.
[5] Pechenaia VI, Volkov SN. Mechanism of hydrogen exchange in DNA. Mol Biol (Mosk). 1984;18(4):1134-40.
[6] Ramstein J, Lavery R. Base pair opening pathways in B-DNA. J Biomol Struct Dyn. 1990;7(4):915-33.
[7] Briki F, Ramstein J, Lavery R, Genest D. Evidence for the stochastic nature of base pair opening in DNA: a Brownian dynamics simulation. J Am Chem Soc. 1991;113(7):2490–3.
[8] Keepers JW, Kollman PA, Weiner PK, James TL. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings. Proc Natl Acad Sci U S A. 1982;79(18):5537-41.
[9] Chen YZ, Feng Y, Prohofsky EW. Premelting thermal fluctuational base pair opening probability of poly(dA).poly(dT) as predicted by the modified self-consistent phonon theory. Biopolymers. 1991;31(2):139-48.
[10] von Hippel PH, Berg OG. On the specificity of DNA-protein interactions. Proc Natl Acad Sci U S A. 1986;83(6):1608-12.
[11] Holbrook SR, Kim SH. Local mobility of nucleic acids as determined from crystallographic data. I. RNA and B form DNA. J Mol Biol. 1984;173(3):361-88.
[12] Frank-KamenetskiÄ­ MD. Fluctuational mobility of DNA. Mol Biol (Mosk). 1983;17(3):639-52.
[13] Polozov PV. Semiempirical method of force field in conformational analysis of biopolymers. M.: Nauka, 1981. 120 p.
[14] Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc. 1984;106(3):765–84.
[15] Vedani A, Dunitz JD. Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides. J Am Chem Soc. 1985;107(25):7653–8.
[16] Arnott S, Smith PJ, Chandrasekaran R. Handbook of biochem and mol biol. Ed. G. D. Fasman. New. York: CRC press, 1976. V. 2: 411-22.
[17] Komarov VM, Polozov RV, Konoplev GG. Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs. J Theor Biol. 1992;155(3):281-94.
[18] Govorun DM, Mishchuk YAR, Kondratyuk IV, Zheltovs'kiy MV. About nonplanarity hydrogenbinded complementary pairs of DNA bases: Proc. I Ukrainian-Polish symposium on hydrogen bonding. Odessa, 1992: 26.
[19] Mishchuk YaR. Study of physical and chemical nature of the elementary acts of protein-nucleic acid and nucleic-nucleic acid recognition in low-model systems: Author. Thesis. ... Kand biol nauk. Kyiv: IMBG NAS Ukraine, 1993 21 p.
[20] Egorenkov AI, Korol VV. The package of applied the programs for the studying of the potential energy surface topology corresponding to the conformation dynamics of DNA molecule. Biopolym Cell. 1993; 9(5):66-72.
[21] Gotlib YuYa, Darinskiy AA, Svetlov YuE. Physical Kinetics macromolecules. L. : Khimiya, 1986. 272 p.