Biopolym. Cell. 1992; 8(1):89-100.
Структура та функції біополімерів
Флуоресцентна спектроскопія у дослідженні білково-нуклеїнових взаємодій у хроматині
1Сиволоб А. В., 1Храпунов С. М.
  1. Київський національний університет імені Тараса Шевченка
    вул. Володимирська 64, Київ, Україна, 01033

Abstract

Короткий огляд, присвячений вивченню молекулярної організації хроматину флюоресцентними методами. Викладено результати досліджень хроматину та нуклеосоми за допомогою специфічних для ДНК та білків флюоресцентних зондів і міток, а також дані власної білкової флюоресценції, головним чином одержані авторами огляду. Продемонстровано і обговорено можливості різних підходів флюоресцентної спектроскопії при вивченні білково-нуклеїнової взаємодії, що дозволяють одержувати унікальну інформацію щодо структури та динаміки нуклеопротеїдних комплексів.

References

[1] McGhee JD, Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115-56.
[2] Mirzabekov AD. Nucleosomes structure and its dynamic transitions. Q Rev Biophys. 1980;13(2):255-95.
[3] Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 1984 Oct 11-17;311(5986):532-7.
[4] Thoma F, Koller T. Unravelled nucleosomes, nucleosome beads and higher order structures of chromatin: influence of non-histone components and histone H1. J Mol Biol. 1981;149(4):709-33.
[5] Karnaukhov VN. Luminescent spectral analysis of cells. Moscow: Nauka, 1978; 207 p.
[6] LePecq JB, Paoletti C. A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization. J Mol Biol. 1967;27(1):87-106.
[7] Schmitz KS. A model for the association of intercalating ligands with mononucleosomes and chromatin. J Theor Biol. 1982;98(1):29-43.
[8] Wang J, Hogan M, Austin RH. DNA motions in the nucleosome core particle. Proc Natl Acad Sci U S A. 1982;79(19):5896-900.
[9] Ashikawa I, Kinosita K Jr, Ikegami A, Nishimura Y, Tsuboi M, Watanabe K, Iso K, Nakano T. Internal motion of deoxyribonucleic acid in chromatin. Nanosecond fluorescence studies of intercalated ethidium. Biochemistry. 1983;22(25):6018-26.
[10] Sivolob AV, Khrapunov SN. The effect of DNA supercoiling DNA on nucleosome structure. Mol Biol (Mosk). 1991;25(1):144-52.
[11] Millar DP, Robbins RJ, Zewail AH. Torsion and bending of nucleic acids studied by subnanosecond time?resolved fluorescence depolarization of intercalated dyes. J Chem Phys. 1982;76(4):2080–94.
[12] Shimada J, Yamakawa H. Statistical mechanics of DNA topoisomers. The helical worm-like chain. J Mol Biol. 1985;184(2):319-29.
[13] Levene SD, Crothers DM. Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles. J Mol Biol. 1986;189(1):73-83.
[14] Hancock R. Topological organization of interphase DNA: the nuclear matrix and other skeletal structures. Biol Cell. 1982; 46(2): 105-22.
[15] Cook PR. The nucleoskeleton and the topology of transcription. Eur J Biochem. 1989;185(3):487-501.
[16] Bauer WR. Structure and reactions of closed duplex DNA. Annu Rev Biophys Bioeng. 1978;7:287-313.
[17] Shurdov MA, Svinarchuk FP, Gruzdev AD. Torsional stress in the DNA of polytene chromosomes. Mol Biol (Mosk). 1989; 23(1):204-14.
[18] Watanabe F. Cooperative interaction of histone H1 with DNA. Nucleic Acids Res. 1986;14(8):3573-85.
[19] Sivolob AV, Khrapunov SN. A theoretical model of the mechanism of DNA compactization by polycations. Biofizika. 1989;34(1):28-33.
[20] Hartman PG, Chapman GE, Moss T, Bradbury EM. Studies on the role and mode of operation of the very-lysine-rich histone H1 in eukaryote chromatin. The three structural regions of the histone H1 molecule. Eur J Biochem. 1977;77(1):45-51.
[21] Bradbury EM, Chapman GE, Danby SE, Hartman PG, Riches PL. Studies on the role and mode of operation of the very-lysine-rich histone H1 (F1) in eukaryote chromatin. The properties of the N-terminal and C-terminal halves of histone H1. Eur J Biochem. 1975;57(2):521-8.
[22] Bode J. On the reactions of fluorescamine with chromosomal proteins. Anal Biochem. 1979;99(2):274-80.
[23] Dieterich AE, Axel R, Cantor CR. Salt-induced structural changes of nucleosome core particles. J Mol Biol. 1979;129(4):587-602.
[24] Daban JR, Cantor CR. Structural and kinetic study of the self-assembly of nucleosome core particles. J Mol Biol. 1982;156(4):749-69.
[25] Daban JR, Cantor CR. Role of histone pairs H2A,H2B and H3,H4 in the self-assembly of nucleosome core particles. J Mol Biol. 1982;156(4):771-89.
[26] Isenberg I. Histones. Annu Rev Biochem. 1979;48:159-91.
[27] Dragan AI, Khrapunou SN. The red shift of tyrosine fluorescence spectrum in polyethylenglyeol and urea solutions. Stud biophys. 1983; 96(2):127-32.
[28] Khrapunov SN, Dragan AI, Protas AF, Berdyshev GD. Structure of the histone tetramer (H3-H4)2: 2. Position of ?max in the tyrosyl fluorescence spectra and tyrosyl accessibility to quenchers. Int J Biol Macromol. 1984;6(1):31–4.
[29] Khrapunov SN, Dragan AI, Protas AF, Berdyshev GD. Spatial organization of the histone dimer H2A-H2B in solutions of different ionic strengths. Mol Biol (Mosk). 1983;17(5):992-1000.
[30] Khrapunov SN, Dragan AI, Protas AF, Berdyshev GD. The structure of the histone dimer H2A-H2B studied by spectroscopy. Biochim Biophys Acta. 1984;787(1):97-104.
[31] Khrapunov SN, Dragan AI, Protas AF, Berdyshev GD. Spatial organization of the (H3-H4-H2A-H2B)2 histone octamer. Mol Biol (Mosk). 1985;19(4):1011-20.
[32] Dragan AI, Khrapunov SN. Spectroscopic studies of molecular interactions of tyrosine chromophore. I. Analysis of absorption and fluorescence. Biofizika. 1989; 34(1):7-13.
[33] Dragan AI, Khrapunov SN. Absorbtion and luminescent studies of molecular interactions of tyrosine chromophore. II. Effect of solvent polarity on chromophore fluorescence spectra. Biofizika. 1989;34(2):187-94.
[34] Krapunov SN, Dragan AI. Spectroscopy of intermolecular interactions of a tyrosine chromophore. III. Classification of the state of tyrosine residues in proteins based on their electron spectra. Biofizika. 1989;34(3):357-63.
[35] Khrapunov SN, Protas AF, Sivolob AV, Dragan AI, Berdyshev GD. Intrinsic fluorescence, difference spectrophotometry and theoretical studies on tertiary structure of calf thymus histone H1. Int J Biochem. 1985;17(2):217-22.
[36] Thomas GJ Jr, Prescott B, Olins DE. Secondary structure of histones and DNA in chromatin. Science. 1977;197(4301):385-8.
[37] Eickbush TH, Moudrianakis EN. The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry. 1978;17(23):4955-64.
[38] Helene C, Dimicoli JL. Interaction of oligopeptides containing aromatic amino acids with nucleic acids. Fluorescence and proton magnetic resonance studies. FEBS Lett. 1972;26(1):6-10.
[39] Mayer R, Toulme F, Montenay-Garestier T, Helene C. The role of tyrosine in the association of proteins and nucleic acids. Specific recognition of single-stranded nucleic acids by tyrosine-containing peptides. J Biol Chem. 1979;254(1):75-82.
[40] H?l?ne C, Lancelot G. Interactions between functional groups in protein-nucleic acid associations. Prog Biophys Mol Biol. 1982;39(1):1-68.
[41] Shiffman ML, Maciewicz RA, Hu AW, Howard JC, Li HJ. Protein dissociation from DNA in model systems and chromatin. Nucleic Acids Res. 1978;5(9):3409-26.
[42] Khrapunov SN, Sivolob AV, Kucherenko NE. Fluorescence study of the interaction of calf thymus histone H1 with DNA. Int J Biol Macromol 1984;6(4):199–202.
[43] Khrapunov SN, Sivolob AV, Kucherenko NE. The peculiarities of the H1 histone-DNA interaction. Biopolym Cell. 1986; 2(1):39-44.
[44] Khrapunov SN, Sivolob AV, Dragan AI, Berdyshev GD. Structure of histone octamers in reconstituted polynucleosomes. Mol Biol (Mosk). 1985;19(6):1553-61.
[45] Sivolob AV, Khrapunov SN. The structure of histone octamer in the composition of reconstituted polynucleosomes in presence of H1 histone and divalent cations. Biopolym Cell. 1987; 3(4):192-201.
[46] Libertini LJ, Small EW. Effects of pH on low-salt transition of chromatin core particles. Biochemistry. 1982;21(14):3327-34.
[47] Libertini LJ, Small EW. Effects of pH on the stability of chromatin core particles. Nucleic Acids Res. 1984;12(10):4351-9.
[48] Quadrifoglio F, Giancotti V, Crescenzi V. On the interaction of oligopeptides containing aromatic amino acids with DNA in aqueous solution. FEBS Lett. 1976;65(3):345-7.
[49] Lakowicz JR, Principles of Fluorescence Spectroscopy. Plenum Press, New York, London, 1983.
[50] Konev SV. Excited electronically states of biopolymers. Minsk: Nauka i tekhnika, 1965; 184 p.
[51] Gordon VC, Knobler CM, Olins DE, Schumaker VN. Conformational changes of the chromatin subunit. Proc Natl Acad Sci U S A. 1978;75(2):660-3.
[52] Wu HM, Dattagupta N, Hogan M, Crothers DM. Structural changes of nucleosomes in low-salt concentrations. Biochemistry. 1979;18(18):3960-5.
[53] Uberbacher EC, Ramakrishnan V, Olins DE, Bunick GJ. Neutron scattering studies of nucleosome structure at low ionic strength. Biochemistry. 1983;22(21):4916-23.
[54] Martinson HG, True RJ, Burch JB. Specific histone-histone contacts are ruptured when nucleosomes unfold at low ionic strength. Biochemistry. 1979;18(6):1082-9.
[55] Burton DR, Butler MJ, Hyde JE, Phillips D, Skidmore CJ, Walker IO. The interaction of core histones with DNA: equilibrium binding studies. Nucleic Acids Res. 1978;5(10):3643-63.
[56] Fulmer AW, Fasman GD. Ionic strength-dependent conformational transitions of chromatin. Circular dichroism and thermal denaturation studies. Biopolymers. 1979;18(11):2875-91.
[57] Sivolob AV, Dragan AI, Khrapunov SN. Theoretical study of structural transition in a nucleosome at low ionic strength. Mol Biol (Mosk). 1987;21(3):714-23.
[58] Cary PD, Moss T, Bradbury EM. High-resolution proton-magnetic-resonance studies of chromatin core particles. Eur J Biochem. 1978;89(2):475-82.
[59] Walker IO. Differential dissociation of histone tails from core chromatin. Biochemistry. 1984;23(23):5622-8.
[60] Oohara I, Wada A. Spectroscopic studies on histone-DNA interactions. I. The interaction of histone (H2A, H2B) dimer with DNA: DNA sequence dependence. J Mol Biol. 1987;196(2):389-97.
[61] Dragan AI, Sivolob AV, Khrapunov SN. The nature of forces stabilizing nucleosome structure. Dissociation of histone octamers from DNA. Mol Biol (Mosk). 1987;21(3):724-36.
[62] Ichimura S, Mita K, Zama M. Essential role of arginine residues in the folding of deoxyribonucleic acid into nucleosome cores. Biochemistry. 1982;21(21):5329-34.