Biopolym. Cell. 1990; 6(4):21-31.
Огляди
Розвиток нелінійної конформаційної динаміки ДНК
- Інститут теоретичної фізики АН УРСР
Київ, СРСР
Abstract
Представлено критичний огляд основних напрямків розвитку теоретичних досліджень нелінійної конформаційної динаміки ДНК. Показано недоліки використовуваних моделей конформаційної рухливості макромолекули і неадекватність більшості з них фізиці ДНК. Сформульовано принципові моменти коректної побудови моделей для вивчення нелінійної динаміки макромолекул типу ДНК. Зазначено умови виникнення солітонного режиму і зроблено оцінки можливості його реалізації для природних ДНК.
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References
[1]
Hogan M, Dattagupta N, Crothers DM. Transmission of allosteric effects in DNA. Nature. 1979;278(5704):521-4.
[2]
Mandal C, Kallenbach NR, Englander SW. Base-pair opening and closing reactions in the double helix. A stopped-flow hydrogen exchange study in poly(rA).poly(rU). J Mol Biol. 1979;135(2):391-411.
[4]
Banerjee A, Sobell HM. Presence of nonlinear excitations in DNA structure and their relationship to DNA premelting and to drug intercalation. J Biomol Struct Dyn. 1983;1(1):253-62.
[5]
Crothers DM, Fried M. Transmission of long-range effects in DNA. Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:263-9.
[6]
Rich A. Right-handed and left-handed DNA: conformational information in genetic material. Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:1-12.
[7]
Edwards G, Davis C, Saffer J, Swicord M. Resonant Microwave Absorption of Selected DNA Molecules. Phys Rev Lett. 1984;53(13):1284–7.
[8]
Luchnik AN. Long-distance signal transfer in transcriptionally active chromatin--how does it occur? Bioessays. 1985;3(6):249-52.
[9]
Levitt M. Computer simulation of DNA double-helix dynamics. Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:251-62.
[10]
Englander SW, Kallenbach NR, Heeger AJ, Krumhansl JA, Litwin S. Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. Proc Natl Acad Sci U S A. 1980;77(12):7222-6.
[11]
Yomosa S. Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys Rev A. 1983;27(4):2120–5.
[12]
Takeno S, Homma S. Topological Solitons and Modulated Structure of Bases in DNA Double Helices: A Dynamic Plane Base-Rotator Model. Progr Theor Phys. 1983;70(1):308–11.
[13]
Toyoki H, Yomosa S, Takeno S, Homma S. Commensurate, incommensurate and chaotic phase in DNA double helices. Physics Letters A. 1983;97(1-2):70–2.
[14]
Homma S, Takeno S. A Coupled base-rotator model for structure and dynamics of DNA: local fluctuations in helical twist angles and topological solitons. Prog Theor Phys. 1984;72(4):679–93.
[15]
Yomosa S. Solitary excitations in deoxyribonuclei acid (DNA) double helices. Phys Rev A. 1984;30(1):474–80.
[16]
Fedyanin VK, Gochev I, Lisy V. Nonlinear dynamics of bases in a continual model of DNA double helices. Stud biophys. 1986; 116(1):59-64.
[17]
Fedyanin VK, Lisy V. Soliton conformational excitations in DNA. Stud biophys. 1986; 116:65-71.
[18]
Zhang CT. Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys Rev A. 1987;35(2):886-891.
[19]
Yakushevich LV. Nonlinear DNA dynamics: A new model. Phys Lett A 1989;136(7-8):413–7.
[20]
Yakushevich LV, Fedyanin VK. Scattering of neutrons and light by DNA solitons. Stud biophys. 1984; 103(3):171-8.
[21]
Balanovski E, Beaconsfield P. The role of nonlinear electric field effects and soliton formation and propagation in DNA function. Phys Lett A. 1982;93(1):52–4.
[22]
Beaconsfield P, Balanovski E. Energy transfer in B-DNA: Mechanism and effects. Phys Lett A.1983;95(8):454–6.
[23]
Giudice ED, Doglia S, Milani M. A collective dynamics in metabolically active cells. Phys Scr. 1982;26(3):232–8.
[24]
Prohofsky EW. Solitons hiding in DNA and their possible significance in RNA transcription. Phys Rev A. 1988;38(3):1538-1541.
[25]
Scott AC. Soliton oscillations in DNA. Phys Rev A. 1985;31(5):3518-3519.
[26]
Scott AC. Anharmonic analysis of resonant microwave absorption in DNA. Phys Scr. 1985;32(6):617–23.
[27]
Muto V, Halding J, Christiansen PL, Scott AC. Solitons in DNA. J Biomol Struct Dyn. 1988;5(4):873-94.
[28]
Muto V, Scott AC, Christiansen PL. Thermally generated solitons in a toda lattice model of DNA. Phys Lett A. 1989;136(1-2):33–6.
[29]
Krumhansl JA, Alexander DM. Nonlinear dynamics and conformational excitations in biomolecular materials. Structure and dynamics: nucleic acids and proteins. Eds. E. Clementi, R. H. Sarma. New York : Adenine press, 1983:61-80.
[30]
Volkov SN. Nonlinear waves and conformational flexibility DNA. (Preprint Ukrainian Academy of Sciences. Inst theor. Physics; N 52R). Kyiv, 1984; 36 p.
[31]
Sarai A. Stress-induced nonlinear structural transition in DNA. Phys Lett A. 1984;103(8):397–401.
[32]
Volkov SN. On the possibility of propagation of nonlinear waves in DNA. Problems of Nonlinear and turbulent processes in physics. Kyiv, Naukova Dumka, 1985; Ch. 1:161-4.
[33]
Volkov SN. On the dynamics of local conformational transitions in quasi-one-dimensional molecular systems. Kyiv, 1987; 27 p. (Preprint Ukrainian Academy of Sciences. Inst theor. Physics; N 76R).
[34]
Arnott S, Hukins DW. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972;47(6):1504-9.
[35]
Pardi A, Tinoco I Jr. Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices. Biochemistry. 1982;21(19):4686-93.
[36]
Guéron M, Kochoyan M, Leroy JL. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 1987 Jul 2-8;328(6125):89-92.
[37]
Preisler RS, Mandal Ch, Englander SW. et al. Equilibrium and kinetic characteristics of the low temperature open state in polynucleotide duplexes. Biomolecular sterodynamics. Ed. R. Sarma-New York: Adenine press, 1981:405-415.
[38]
Davydov AS. Solitons in quasi-one-dimensional molecular structures. Usp fiz nauk. 1982; 138(4):603-43.
[39]
Tsuboi M. Application of Infrared Spectroscopy to Structure Studies of Nucleic Acids. Applied Spectroscopy Reviews. 1970;3(1):45–90.
[40]
Sukhorukov BI, Montrel MM. IR spectroscopic manifestation of crystallinity of DNA in films: Proc. of reports V Conf. spectroscopy for biopolymers. Kharkiv, 1984:227-228.
[41]
Maleev VYa, Kashpur VA, Glibitsky GM, Krasnitskaya AA, Veretelnik YeV. Absorption of DNA solutions in the 9-12 GHz frequency range. Biopolym Cell. 1986; 2(1):35-8.
[42]
Foster KR, Epstein BR, Gealt MA. "Resonances" in the dielectric absorption of DNA? Biophys J. 1987;52(3):421-5.
[43]
Gabriel C, Grant EH, Tata R, Brown PR, Gestblom B, Noreland E. Microwave absorption in aqueous solutions of DNA. Nature. 1987 Jul 9-15;328(6126):145-6.
[44]
Volkov SN, Kosevich AM. Conformation oscillations of DNA. Mol Biol (Mosk). 1987;21(3):797-806.
[45]
Ivanov VI. Double helix DNA. Mol Biol (Mosk). 1983;17(3):616-21.
[46]
Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[47]
Ivanov VI. B–A transition in DNA and transcription. Biopolym. Cell. 1985; 1(1):5-13.
[48]
Bruce AD, Cowley RA. Structural phase transitions. London, Teylor & Francis, 1981; 326 p.
[49]
Volkov SN. The mechanism of long-range DNA. Dopovidi akad nauk UkrSSR. 1988;(?):48-52.
[50]
Dickson RC, Abelson J, Barnes WM, Reznikoff WS. Genetic regulation: the Lac control region. Science. 1975;187(4171):27-35.
[51]
Ivanov VI, Zhurkin VB, Zavriev SK, Lysov YP, Minchenkova LE, Minyat EE, et al. Conformational possibilities of double-helical nucleic acids: Theory and experiment. Int J Quantum Chem. 1979;16(1):189–201.
[52]
Volkov SN. Conformational transitions and the mechanism of transmission of long-range effects in DNA. Kiev (Preprint Acad. iSei. USSR. Inst. Theor. Phys.) 1988. 21 p.
[53]
Volkov SN. Propagation of local conformational transitions in molecular chains. Phys Lett A. 1989;136(1-2):41–4.
[54]
Krumhansl J, Schrieffer J. Dynamics and statistical mechanics of a one-dimensional model Hamiltonian for structural phase transitions. Phys Rev B. 1975;11(9):3535–45.
[55]
Martel P, Powell BM. Measurement of acoustic modes of vibration in 1-methylthymine by neutron scattering. Chem Phys Lett. 1976;39(2):339–41.
[56]
Frank-Kamenetskiĭ MD. Fluctuational mobility of DNA. Mol Biol (Mosk). 1983;17(3):639-52.
[57]
Maret G, Oldenbourg R, Winterling G, Dransfeld K, Rupprecht A. Velocity of high frequency sound waves in oriented DNA fibres and films determined by Brillouin scattering. Colloid Polym Sci. 1979;257(10):1017–20.
[58]
Voet D, Rich A. The crystal structures of purines, pyrimidines and their intermolecular complexes. Prog Nucleic Acid Res Mol Biol. 1970;10:183-265.
[59]
Lazurkin YuS. DNA: supercoiling and alternative structures. Biopolym. Cell. 1986; 2(6):283-92.