Biopolym. Cell. 1988; 4(2):85-90.
Структура и функции биополимеров
Влияние объемных эффектов на топологические свойства кольцевых ДНК
1Кленин К. В., 1Вологодский А. В., 1Аншелевич В. В., 2Дыхне А. М., 1Франк-Каменецкий М. Д.
  1. Институт молекулярной генетики АН СССР
    Москва, СССР
  2. Институт атомной энергии им. И. В. Курчатова
    Москва, СССР

Abstract

Методом Монте-Карло рассчитана зависимость вероятности образования узлов при случайной циклизации молекулы ДНК, дисперсии райзинга и коэффициента набухания кольцевых ДНК от эффективного диаметра молекулы. Очень резкий характер этих зависимостей открывает путь для надежного экспериментального определения эффективного диаметра ДНК как функции ионной силы раствора.

References

[1] Brian AA, Frisch HL, Lerman LS. Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers. 1981;20(6):1305-28.
[2] Yarmola EG, Zarudnaya MI, Lazurkin YuS. Osmotic pressure of DNA solutions and effective diameter of the double helix. J Biomol Struct Dyn. 1985;2(5):981-93.
[3] Stigter D. Interactions of highly charged colloidal cylinders with applications to double-stranded. Biopolymers. 1977;16(7):1435-48.
[4] Hagerman PJ. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 1981;20(7):1503-35.
[5] Kirste RG. Radius of gyration of stiff chain molecules as a function of the chain length and the interactions with the solvent. Discuss Faraday Soc. 1970; 49:51-59.
[6] Yamakawa H, Stockmayer WH. Statistical Mechanics of Wormlike Chains. II. Excluded Volume Effects. J Chem Phys. 1972; 57(7):2843-2854.
[7] Webman I, Lebowitz JL, Kalos MH. Excluded-volume expansion of polymer chains: a Monte Carlo study of the scaling properties. Phys Rev B Solid State. 1980. 21(12):5540-5543.
[8] Slonitskii SV, Frisman EV, Valeev AD, El'iashevich AM. Calculation of the intrinsic viscosity of synthetic and biological polyelectrolytes of various rigidity. Mol Biol (Mosk). 1980;14(3):484-95.
[9] Manning GS. A procedure for extracting persistence lengths from light-scattering data on intermediate molecular weight DNA. Biopolymers. 1981; 20(8):1751-5.
[10] Post CB. Excluded volume of an intermediate-molecular-weight DNA. A Monte Carlo analysis. Biopolymers. 1983;22(4):1087-96.
[11] Vologodskii AV, Anshelevich VV, Lukashin AV, Frank-Kamenetskii MD. Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix. Nature. 1979;280(5720):294-8.
[12] Le Bret M. Monte Carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA. Biopolymers. 1980;19(3):619-37.
[13] Shimada J, Yamakawa H. Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules. 1984; 17(4):689-698.
[14] Shimada J, Yamakawa H. DNA-topoisomer analysis on the basis of the helical wormlike chain. Biopolymers. 1984;23(5):853-7.
[15] Frank-Kamenetskii MD, Lukashin AV, Anshelevich VV, Vologodskii AV. Torsional and bending rigidity of the double helix from data on small DNA rings. J Biomol Struct Dyn. 1985;2(5):1005-12.
[16] Depew DE, Wang JC. Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975;72(11):4275-9.
[17] Pulleyblank DE, Shure M, Tang D, Vinograd J, Vosberg HP. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci U S A. 1975;72(11):4280-4.
[18] Shore D, Baldwin RL. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol. 1983;170(4):957-81.
[19] Shore D, Baldwin RL. Energetics of DNA twisting. II. Topoisomer analysis. J Mol Biol. 1983;170(4):983-1007.
[20] Horowitz DS, Wang JC. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol. 1984;173(1):75-91.
[21] Frank-Kamenetskii MD, Vologodskii AV. Topological aspects of the physics of polymers: theory and its biophysical applications. Usp fiz nauk. 1981; 134(4):641-73.
[22] Vologodskii AV, Lukashin AV, Frank-Kamenetskii MD, Anshelevich VV. Problem nodes in statistical mechanics of polymer chains. Zh Eksp i Teor. Fiziki. 1974; 66(6):2153-2163.
[23] des Cloizeaux J, Mehta M. L.Topological constraints on polymer rings and critical indices. J Phys Lett. 1979; 40(7):665-70.
[24] Chen Y-D. Monte Carlo study of freely jointed ring polymers. II. The writhing number. J Chem Phys. 1981; 75(5):2447-53.
[25] Michels JPJ, Wiegel FW. Probability of knots in a polymers ring. Phys Lett A. 1982; 90(7):381-384.
[26] White JH. Self-Linking and the Gauss Integral in Higher Dimensions. Amer J Math. 196; 91(5):693-728.
[27] Fuller FB. The writhing number of a space curve. Proc Natl Acad Sci U S A. 1971;68(4):815-9.
[28] Spengler SJ, Stasiak A, Cozzarelli NR. The stereostructure of knots and catenanes produced by phage lambda integrative recombination: implications for mechanism and DNA structure. Cell. 1985;42(1):325-34.
[29] Vologodskii AV, Frank-Kamenetskii MD. Theoretical study of cruciform states in superhelical DNAs. FEBS Lett. 1982;143(2):257-60.
[30] Frank-Kamenetskii MD, Vologodskii AV. Thermodynamics of the B-Z transition in superhelical DNA. Nature. 1984 Feb 2-8;307(5950):481-2.
[31] Peck LJ, Wang JC. Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci U S A. 1983;80(20):6206-10.
[32] Singleton CK, Klysik J, Stirdivant SM, Wells RD. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982;299(5881):312-6.
[33] Singleton CK. Effects of salts, temperature, and stem length on supercoil-induced formation of cruciforms. J Biol Chem. 1983;258(12):7661-8.
[34] Nordheim A, Rich A. The sequence (dC-dA)n X (dG-dT)n forms left-handed Z-DNA in negatively supercoiled plasmids. Proc Natl Acad Sci U S A. 1983;80(7):1821-5.