Biopolym. Cell. 1997; 13(1):46-54.
Структура та функції біополімерів
Вивчення стабільності уотсон-криківських пар основ
нуклеїнових кислот у воді та диметилсульфоксиді: комп'ютерне
моделювання методом Монте-Карло
1Данілов В. І., 1Желтовський М. В., 1Слюсарчук О. М., 2Альдерфер Дж. Л.
- Інститут молекулярної біології і генетики НАН України
Вул. Академіка Заболотного, 150, Київ, Україна, 03680 - Раковий інститут ім. Розвелл Парк
вул. Елм і Карлтон, Баффало, Нью-Йорк, США, 14 263
Abstract
Проведено екстенсивне комп'ютерне моделювання основ нуклеїнових кислот і уотсон-криківських пар у воді та ДМСО
методом Монте-Карло. Виявлено, що енергетична невигідність утворення пар у воді зумовлена значним дестабілізуючим внеском розчинника в ентальпію утворення комплексів. Показано, що у ДМСО утворення копланарних пар
вигідно. Цей розчинник стабілізує пари A-U і А-Т, а незначна дестабілізація цим розчинником пари G-C значно менша, ніж
стабілізація, пов'язана з притягненням між основами.
Повний текст: (PDF, російською)
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.
