Abstract
Initiation of transcription in eukaryotes requires a multitude of transcription factors (TFS) that interact with the transcription complex (TC), with DNA, and among themselves. One important step in the assembly of the active transcription complex at the promoter is the interaction of transcription factors bound to distant enhancer sites with the proteins already present on the promoter. The simultaneous binding of a TF to a DNA binding site and to the TC on the promoter implies that the DNA between TF and promoter must have some higher order structure — in the simplest case, the DNA forms a loop (Fig. 1). The probability that the TF interacts with the TC will then depend on the probability that the two ends of a stretch of DNA meet within a given distance.
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References
Allison SA (1986) Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering. Maeromolecules 19:118–124
Allison SA, McCammon J A (1984) Transport properties of rigid and flexible macro-molecules by Brownian dynamics simulation. Biopolymers 23:167–187
Allison SA, Austin R, Hogan M (1989) Bending and twisting dynamics of short linear DNAs — analysis of the triplet anisotropy decay of a 209-base pair fragment by Brownian dynamics simulation. J Chem Phys 90:3843–3854
Barkley MD, Zimm BH (1979) Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA. J Chem Phys 70:2991–3007
Bednar J, Furrer P, Stasiak A, Dubochet J, Egelman EH, Bates AD (1994) The twist, writhe and overall shape of superhelical DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J Mol Biol 235:825–847
Bednar J, Furrer P, Katritch V, Stasiak AZ, Dubochet J, Stasiak A (1995) Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J Mol Biol 254:579–594
Bloomfield VA, Crothers DM, Tinoco JI (1974) Physical chemistry of nucleic acids. Harper & Row, New York
Chirico G, Langowski J (1992) Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm. Macromolecules 25:769–775
Chirico G, Langowski J (1994) Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers 34:415–433
Chirico G, Langowski J (1996) Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys J 71:955–971
Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, et al. (1996) DNA: an extensible molecule. Science 271:792–794
Crothers DM, Drak J, Kahn JD, Levene SD (1992) DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol 212:3–29
Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69:1352–1359
Flory PJ (1969) Statistical mechanics of chain molecules. Wiley, New York
Fujimoto BS, Schurr JM (1990) Dependence of the torsional rigidity of DNA on basecomposition. Nature 344:175–178
Garcia de la Torre, J (1994) Hydrodynamics of segmentally flexible macromolecules -invited review. Eur Biophys J 23:307–322
Gebe JA, Allison SA, Clendenning JB, Schurr JM (1995) Monte-Carlo simulations of supercoiling free-energies for unknotted and trefoil knotted DNAs. Biophys J 68:619–633
Hagerman PJ (1988) Flexibility of DNA. Annu Rev Biophys Biophys Chem 17:265–286
Hagerman PJ, Ramadevi VA (1990) Application of the method of phage T4 DNA ligase catalyzed ring-closure to the study of DNA structure. I. Computational analysis. J Mol Biol 212:351–362
Horowitz DS, Wang JC (1984) Torsonal rigidity of DNA and length dependence of the free energy of DNA supercoiling. J Mol Biol 173:75–91
Jacobson H, Stockmayer WH (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 18:1600–1606
Kim JL, Nikolov DB, Burley SK (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:521–527
Klenin KV, Vologodskii AV, Anshelevich VV, Klishko VY, Dykhne AM, Frank-Kamenetskii MD (1991) Computer simulation of DNA supercoiling. J Mol Biol 217:413–419
Klenin K, Frank-Kamenetskii MD, Langowski J (1995) Modulation of intramolecular interactions in superhelical DNA by curved sequences. A Monte-Carlo simulation study. Biophys J 68:81–88
Kratky O, Porod G (1949) Röntgenuntersuchung gelöster Fadenmoleküle. Ree Trav Chim 68:1106–1113
Kremer W, Klenin K, Diekmann S, Langowski J (1993) DNA curvature influences the internal motion of superhelical DNA. EMBO J 12:4407–4412
Langowski J, Olson WK, Pedersen SC, Tobias I, Westcott TP, Yang Y (1996) DNA supercoiling, localized bending and thermal fluctuations. Trends Biochem Sci 21:50
Laundon CH, Griffith JD (1988) Curved helix segments can uniquely orient the topology of supertwisted DNA. Cell 52:545–549
Levene SD, Crothers DM (1986) Ring closure probabilities for DNA fragments by Monte-Carlo simulation. J Mol Biol 189:61–72
Liu LF, Wang JC (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84:7024–7027
Malhotra A, Gabb HA, Harvey SC (1993) Modeling large nucleic acids. Curr Opin Struct Biol 3:241–246
Manning GS (1970) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys 11:179–246
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092
Olson WK (1996) Simulating DNA at low resolution. Curr Opin Struct Biol 6:242–256
Rippe K, von Hippel PH, Langowski J (1995) Action at a distance: DNA-looping and initiation of transcription. Trends Biochem Sci 20:500–506
Rybenkov VV, Cozzarelli NR, Vologodskii AV (1993) Probability of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sci USA 90:5307–5311
Schlick T (1995) Modeling superhelical DNA: recent analytical and dynamic approaches. Curr Opin Struct Biol 5:245–262
Schurr JM, Fujimoto BS, Wu P, Song L (1992) Fluorescence studies of nucleic acids: dynamics, rigidities and structures. In: Lakowicz JR (ed) Topics in fluorescence spectroscopy vol 3. Plenum Press, New York, pp 137–229
Shaw SY, Wang JC (1993) Knotting of a DNA chain during ring closure. Science 260:533–536
Shimada J, Yamakawa H (1984) Ring-closure probabilities of twisted wormlike chains. Application to DNA. Macromolecules 17:689–698
Shore D, Baldwin RL (1983) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol 179:957–981
Shore D, Langowski J, Baldwin RL (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78:4833–4837
Smith S, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271:795–799
Song L, Schurr JM (1990) Dynamic bending rigidity of DNA. Biopolymers 30:229–237
Sprous D, Harvey SC (1996) Action at a distance in supercoiled DNA: effects of sequence on slither, branching and intramolecular concentration. Biophys J 70:1893–1908
Tan RK-Z, Harvey SC (1989) Molecular mechanics model of supercoiled DNA. J Mol Biol 205:573–591
Taylor WH, Hagerman PJ (1990) Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. NaCl-dependence of DNA flexibility and helical repeat. J Mol Biol 212:363–376
Trifonov EN, Tan RK-Z, Harvey SC (1988) Static persistence length of DNA. In: Olson WK, Sarma MH, Sundaralingam M (eds) DNA bending and curvature. Structure and expression. Adenine Press, Albang, pp 243–254
Vologodskii AV, Levene SD, Klenin KV, Frank-Kamenetskii MD, Cozzarelli NR (1992) Conformational and thermodynamic properties of supercoiled DNA. J Mol Biol 227:1224–1243
White JH (1989) An introduction to the geometry and topology of DNA structure. In: Waterman MS (ed) Mathematical methods for DNA sequences. CRC Press, Boca Raton
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© 1997 Springer-Verlag Berlin Heidelberg
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Langowski, J. (1997). Modeling Large DNA Molecules: Long-Range Interactions and Regulation of Transcription. In: Eckstein, F., Lilley, D.M.J. (eds) Mechanisms of Transcription. Nucleic Acids and Molecular Biology, vol 11. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-60691-5_14
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DOI: https://doi.org/10.1007/978-3-642-60691-5_14
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