Biopolym. Cell. 1997; 13(1):46-54.
http://dx.doi.org/10.7124/bc.000466
Structure and Function of Biopolymers
The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by Monte Carlo method
1Danilov V. I., 1Zheltovsky N. V., 1Slyusarchuk O. N., 2Alderfer J. L.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Roswell Park Cancer Institute
    Elm and Carlton Str., Buffalo, New-York, USA, 14263

Abstract

Extensive computer simulation of nucleic acids bases and Watson-Crick base pairs in water and DMSO by Monte Carlo method was conducted. It was detected that the energetic unfavorability of pairs formation in water is determined by significant destabilizing contribution of solvent to the enthalpy of complex formation. It was shown that the formation of coplanar base pairs in DMSO is favorable. This solvent stabilizes A-U and A-T base pairs and the insignificant destabilization of G-C base pair by it is much less than the stabilization due to the bases attraction.
Full text: (PDF, in Russian)

References

[1] Danilov VI, Zakshevskaya KM, Zheltovskiy IV. The problem of DNA stability: the contribution bases. Itogi nauki i tekhniki. (Ser Mol Biol). 1979; 15: 74-124.
[2] Cantor CR, Schimmel PR. Biophysical Chemistry. Ed. W. H. Freeman. San Fransisco, 1980; Pt 1:311-41.
[3] Ts'o POP. Bases, nucleosides and nucleotides. In: Basic principles in nucleic acid chemistry. Ed. P. O. P. Ts'o. New. York; London: Acad press, 1974; Vol. 1:453-584.
[4] Pullman B, Claverie P, Caillet J. Van der Waals-London interactions and the configuration of hydrogen-bonded purine and pyrimidine pairs. Proc Natl Acad Sci U S A. 1966;55(4):904-12.
[5] Pullman B, Clavarie P, Caillet J. On the exclusivity of hydrogen-bonded pairing between the Watson-Crick complementary bases. J Mol Biol. 1966;22(2):373-5.
[6] Yanson IK, Teplitsky AB, Sukhodub LF. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers. 1979;18(5):1149-70.
[7] Rein R, Coeckelenbergh Y, Egan JT. Elaboration of the principle of base complementarity and the elements of a theory of point mutations. Int J Quant Chem 1975;9(S2):145–53.
[8] P?rschke D, Eggers F. Thermodynamics and kinetics of base-stacking interactions. Eur J Biochem. 1972;26(4):490-8.
[9] Marenchic MG, Sturtevant JM. Calorimetric investigation of the association of various purine bases in aqueous media. J Phys Chem. 1973;77(4):544-8.
[10] Plesiewicz E, Stepie? E, Bolewska K, Wierzchowski KL. Osmometric studies on self-association of pyrimidines in aqueous solutions: evidence for involvement of hydrophobic interactions. Biophys Chem. 1976;4(2):131-41.
[11] Plesiewicz E, Stepie? E, Bolewska K, Wierzchowski KL. Stacking self-association of pyrimidine nucleosides and of cytosines: effects of methylation and thiolation. Nucleic Acids Res. 1976;3(5):1295-306.
[12] Danilov VI, Tolokh IS, Poltev VI, Malenkov GG. Nature of the stacking interaction of nucleotide bases in water: a Monte Carlo study of the hydration of uracil molecule associates. FEBS Lett. 1984;167(2):245–8.
[13] Danilov VI, Tolokh IS. Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation. J Biomol Struct Dyn. 1984;2(1):119-30.
[14] Danilov VI, Tolokh IS. On the role of hydrophobic groups in nucleotide base stacking. FEBS Lett. 1984;173(2):347–50.
[15] Danilov VI, Tolokh IS. Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation. J Biomol Struct Dyn. 1984;2(1):119-30.
[16] Danilov VI. Application of the Monte Carlo method for studying the hydration of molecules: base stacking. Mathe­ matics and computational concepts in chemistry. Ed. N. Trinajstic. Chichester: Ellis Horwood Limited, 1986: 48-59.
[17] Pohorille A, Pratt LR, Burt SK, MacElroy RD. Solution influence on biomolecular equilibria: nucleic acid base associations. J Biomol Struct Dyn. 1984;1(5):1257-80.
[18] Pohorille A, Burt SK, MacElroy RD. Monte Carlo simulation of the influence of solvent on nucleic acid base associations. J Am Chem Soc. 1984;106(2):402–9.
[19] Schweighardt FK, Moll C, Li NC. Nuclear magnetic resonance study of guanosine-cytidine pairing in mixed solvents. J Magn Reson. 1970;2(1):35–41.
[20] Binford JS Jr, Holloway DM. Heats of base pair formation with adenine and uracil analogs. J Mol Biol. 1968;31(1):91-9.
[21] Hruska FE, Bell CL, Victor TA, Danyluk SS. Medium effects on the nuclear magnetic resonance spectra of purines. Biochemistry. 1968;7(10):3721-7.
[22] Kyogoku Y, Lord RC, Rich A. An infrared study of hydrogen bonding between adenine and uracil derivatives in chloroform solution. J Am Chem Soc. 1967;89(3):496-504.
[23] Kyogoku Y, Lord RC, Rich A. An infrared study of the hydrogen-bonding specificity of hypoxanthine and other nucleic acid derivatives. Biochim Biophys Acta. 1969;179(1):10-7.
[24] Newmark RA, Cantor CR. Nuclear magnetic resonance study of the interactions of guanosine and cytidine in dimethyl sulfoxide. J Am Chem Soc. 1968;90(18):5010-7.
[25] Petersen SB, Led JJ. Watson-Crick base pairing between guanosine and cytidine studied by carbon-13 nuclear magnetic resonance spectroscopy. J Am Chem Soc. 1981;103(18):5308–13.
[26] Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys. 1953;21(6):1087-92.
[27] Mruzik MR, Abraham FF, Schreiber DE, Pound GM. A Monte Carlo study of ion-water clusters. J Chem Phys. 1976; 64(2):481-91.
[28] Dyakonova LP, Malenkov GG. Modeling of the structure of liquid water by the Monte Carlo method. Zh strukt khim. 1979; 20(5):854-61.
[29] Zhurkin VB, Poltev VI, Florent'ev VL. [Atom--atomic potential functions for conformational calculations of nucleic acids]. Mol Biol (Mosk). 1980;14(5):1116-30.
[30] Poltev VI, Danilov VI, Sharafutdinov MR et al. Simulation of the interaction of nucleic acid fragments with solvent using atom-aiom Potential function. Stud biophys. 1982; 91(1):37-43.
[31] Danilov VI. On the nature of stability of the nucleotide base associates in water solution. Mol Biol Rep. 1975;2(3):263-6.
[32] Kudritskaya ZG, Danilov VI. Quantum mechanical study of bases interactions in various associates in atomic dipole approximation. J Theor Biol. 1976;59(2):303–18.
[33] Goldblum A, Perahia D, Pullman A. Hydration scheme of the complementary base-pairs of DNA. FEBS Lett. 1978;91(2):213-5.
[34] Pullman B, Miertus S, Perahia D. Hydration scheme of the purine and pyrimidine bases and base-pairs of the nucleic acids. Theoret Chim Acta. 1979;50(4):317–25.
[35] Danilov VI, Sharafutdinov MR, Tolokh IS. Theoretical study of the nucleotide base associates. Stud biophys. 1982; 93:193-6.
[36] Shoup RR, Miles HT, Becker ED. NMR evidence of specific base-pairing between purines and pyrimidines. Biochem Biophys Res Commun. 1966;23(2):194-201.
[37] Katz L, Penman S. Association by hydrogen bonding of free nucleosides in non-aqueous solution. J Mol Biol. 1966;15(1):220-31.
[38] Wang SM, Li NC. Proton magnetic resonance studies of self-association and metal complexation of nucleosides in dimethyl sulfoxide. J Am Chem Soc. 1968;90(19):5069-74.