Biopolym. Cell. 1989; 5(5):19-31.
http://dx.doi.org/10.7124/bc.0000E0
Structure and Function of Biopolymers
Hydration of uracil and thymine metliylderivatives: Monte Carlo simulation
1Danilov V. I., 1Tolokh I. S.
  1. Institute of Molecular Biology and Genetics, Academy of Sciences of the Ukrainian SSR
    Kiev, USSR

Abstract

The performed simulation has shown that under methylation of uractl and thymine NH-groups the interaction energy between base and water (Uwb) increases. It has also been detected that this energy increase is observed in the 1st and 3-rd sectors. These conclusions do not confirm the assumption made in literature about the character of interaction between methylated bases and water. According to this assumption, when the NH-group is methylated, the energy of UWb in this sector decreases at the expense of the van der Waals interactions between the methyl group and water, whose energy compensates the Uwb energy increase due to the break of the H-bond. Regulation of water molecules near hydrophobic group under the hydration of polar molecules is detected for the first time.
Full text: (PDF, in Russian)

References

[1] 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.
[2] Sukhodub LF, Glukhova OT, Teplitskv AB et al. Hydration heats of nucleic acid bases: contribution of sPecific interactions. Int symp. biochem. Tbilisi,,1981 :65.
[3] Glukhova OT, Kiselev VD, Teplitskii AB, Ustiugov AN, Ianson IK. Hydration of nucleic acid bases. Cytosine and its methyl-derivatives. Biofizika. 1981;26(2):351-2.
[4] Teplitsky AB, Glukhova OT, Sukhodub LF, Yanson IK, Zielenkiewicz A, Zielenkiewicz W, Kosinski J, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases. IV. Enthalpies of hydration of 5-alkyluracils. Biophys Chem. 1982;15(2):139-47.
[5] Glukhova OT, Teplitsky AB, Sukhodub LF et al. Thermodynamics of hydration of nucleic acid bases. I All-Union biophys. Meet.: Thes. of reports. Moscow, 1982; 56.
[6] Glukhova OT, Teplitsky AB, Sukhodub LF et al. Hydration heats of nitrogen bases on nucleic acids in aqueous solutions. 3rd Int. conf. on water and ions in biol. systems. Bucharest, 1984:108.
[7] Zielenkiewicz A, Zielenkiewicz W, Sukhodub LF, Glukhova OT, Teplitsky AB, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases V. Enthalpies of hydration of N-methylated adenines. J Solution Chem. 1984;13(11):757-65.
[8] Glukhova OT. EnthalPy of hydration of nucleobases and their alkyl derivatives: Dis. ... Kand. Phys-math. nauk. Kharkiv, 1985. 118 p.
[9] Sukhodub LF. Experimental studies of intermolecular interactions and hydration of nucleobases, their methyl derivatives in various states of aggregation: Author. dis. ... Dr. Phys-math. nauk. Moscow, 1985; 37 p.
[10] Sukhodub LF. Interaction and hydration of nucleotide bases in a vacuum. ExPerimental studies. II. Autoassosiates of water and hydrates bases. Kharkov, 1987; 37 P. (PrePrint Ukrainian Academy of Sciences. Phys.-Tech. Inst. low temPeratures; ILTPE-38-87).
[11] Sukhodub LF. Interactions and hydration of nucleic acid bases in a vacuum. Experimental study. Chem Rev. 1987;87(3):589-606.
[12] Sinanoglu O, Abdulnur S. Effect of water and other solvents on the structure of biopolymers. Fed Proc. 1965;24:S12-23.
[13] Sinanoglu O. Solvent effects on molecular associations. Mol. assoc. in biology Ed B Pullman. New York: Acad, Press, 1968:427-445.
[14] Sinanoglu O, Abdulnur S. Hydrophobic stacking of bases and the solvent denaturation of DNA. Photochem Photobiol. 1964;3(4):333-42.
[15] 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.
[16] 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.
[17] 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.
[18] Dyakonova LP, Malenkov GG. Modeling of the structure of liquid water by the Monte Carlo method. Zh strukt khim. 1979; 20(5):854-861.
[19] Danilov VI, Sharafutdinov MR, Tolokh I. S. Theoretical study of the stability of nucleotide base associates. Stud biophys. 1983. 93(3):193-6.
[20] Danilov V. I. Nature of the stacking interactions of nucleic acid bases and their derivatives: theory and experiment. Steric aspects of biomolecular interactions Eds G. Naray-Szabo, K. Simon - Boca Raton: CRC Press, 1987:235-242.