Biopolym. Cell. 1985; 1(2):59-69.
Structure and Function of Biopolymers
Nature of nucleotide base associations in water: the Monte Carlo simulation of the hydration of pyrimidine bases and their molecular associates
1Danilov V. I., 1Tolokh I. S.
  1. Institute of Molecular Biology and Genetics, Academy of Sciences of the Ukrainian SSR
    Kiev, USSR


Results of the Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It is shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It is found that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the slack. The simulation of the hydration of different stacked thymine dimers has shown that the most favourable of them is the one for which base methyl groups are close to each other.


[1] 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.
[2] Pullman A, Pullman B. Aspects of the electronic structure of purine and pyrimidine bases of the nucleic acids and their interactions. In book: Adv. Quantum Chem., 1968, 4:267-325.
[3] Danilov VI, Zheltovsky NV, Kudritskaya ZG. Quantum mechanical study of interactions between the nucleic acid bases. Stud. biophys. 1974; 43(3):201-216.
[4] Danilov VI. On the nature of stability of the nucleotide base associates in water solution. Mol Biol Rep. 1975;2(3):263-6.
[5] Sinanoglu O, Abdulnur S. Effect of water and other solvents on the structure of biopolymers. Fed Proc. 1965;24:S12-23.
[6] Sinanoglu O. Solvent effects on molecular associations. In: Molecular Associations in Biology. Ed. B. Pullman. New York: Acad, press, 1968:427-445.
[7] Sapper H, Lohmann W. Stacking interaction of nucleobases: NMR investigations. III. Molecular aspects of the solvent dependence. Biophys Struct Mech. 1978;4(4):327-35.
[8] 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.
[9] 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.
[10] Mruzik MR, Abraham FF, Schreiber DE, Pound GM. A Monte Carlo study of ion-water clusters. J Chem Phys. 1976; 64(2):481-91.
[11] Dyakonova LP, Malenkov GG. Modeling of the structure of liquid water by the Monte Carlo. Zh. Strukt. Khim, 1979; 20(5): 854-861
[12] 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.
[13] 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.
[14] Danilov VI, Tolokh IS. Nature of the stacking interactions of nucleic acid bases in water: a study using the Monte Carlo method. Dokl Akad Nauk SSSR. 1984;274(4):968-72.
[15] Teplitsky AB, Yanson IK, Glukhova OT, Zielenkiwicz A, Zielenkiewicz W, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases. III. Enthalpies of hydration of uracil, thymine and their derivatives. Biophys Chem. 1980;11(1):17-21.
[16] Danilov VL, Sharafutdinov MR, Tolokh IS. Theoretical study of the stability of nucleotide base associates. Stud biophys. 1983; 93(3):193-196.
[17] 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):245-248.
[18] Danilov VI, Tolokh IS, Poltev VI. Nature of the stacking interactions of nucleotide bases in water: a Monte Carlo study of the hydration of thymine moleculeassociates. FEBS Lett. 1984; 171(2):325-328.
[19] Poltev VI, Shulga SM. Semiempirical calculations of stacking interactions. Selfassociations of nucleic acid bases. Stud biophys. 1978; 70(1):51-61.
[20] Pohorille A1, Pratt LR, Burt SK, MacElroy RD. Solution influence on biomolecular equilibria: nucleic acid base associations. J Biomol Struct Dyn. 1984;1(5):1257-80.