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2009 | 56 | 4 | 695-702
Article title

Evaluation of mixed-salt effects on thermodynamic and kinetic parameters of RNA polymerase-promoter DNA complexes in terms of equivalent salt concentrations. General applicability to DNA complexes

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EN
Abstracts
EN
Facile evaluation of mixed-salt effect on the strongly salt-dependent thermodynamic and kinetic parameters of protein-DNA complexes is of importance for relevant biochemical and biophysical studies. In pursuit of this aim, binding isotherms for open transcription complex (RPo) of Escherichia coli RNA polymerase (R) at λPR promoter DNA (P) were determined as a function of salt concentration in pure NaCl and Tris/HCl solutions, and as a function of [NaCl] in the presence of fixed concentrations of MgCl2 and Tris/HCl. A concept of equivalent salt concentrations, i.e. concentrations at which the binding equilibrium constant is the same, was introduced and applied for prediction of binding isotherms in mixed salt solutions. Full coincidence between the experimental and predicted isotherms indicated that individual contributions of salts to the global salt-effect are additive in a broad range of salt concentrations. A generalized formula for calculation of salt equivalents characteristic for any of the thermodynamic or kinetic parameters of a complex (e.g., free energy, binding equilibrium and association/dissociation kinetic rate constants) is presented and its applicability to a number of protein-DNA complexes and dsDNA melting demonstrated using authors' own and literature data.
Year
Volume
56
Issue
4
Pages
695-702
Physical description
Dates
published
2009
received
2009-07-21
revised
2009-10-08
accepted
2009-10-27
(unknown)
2009-11-05
References
  • Burgess RR, Jendrisek JJ (1975) A procedure for the rapid, large scale purification of Escherichia coli DNA-dependent RNA polymerase involving polyamine P precipitation and DNA-cellulose chromatography. Biochemistry 14: 4634-4638.
  • Capp MW, Cayley DS, Zhang W, Guttman HJ, Melcher SE, Saecker RM, Anderson CF, Record MT Jr (1996) Compensation effects of opposing changes in putrescine (2+) and K+ concentrations on lac repressor-lac operator binding: in vitro thermodynamic analysis and in vivo relevance. J Mol Biol 258: 25-36.
  • Chamberlin M, Kingstone R, Gilman M, Wiggs J, DeVera A (1983) Isolation of bacterial and bacteriophage RNA polymerases and their use in synthesis of RNA in vitro. Methods Enzymol 101: 540-568.
  • Chen SW, Honig B (1997) Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: application to DNA binding reactions. J Phys Chem B 101: 9113-9118.
  • Cuauhtemoc G-G, Draper DE (2003) Electrostatic interactions in a peptide-RNA complex. J Mol Biol 331: 75-88.
  • deHaseth PL, Lohman TM, Record MT Jr (1977) Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry 16: 4783-4790.
  • Gavryushov S, Zielenkiewicz P (1998) Electrostatic potential of B-DNA: effect of interionic correlations. Biophys J 75: 2732-2742.
  • Kolasa IK, Łoziński T, Wierzchowski KL (2001) Mg2+ does not induce isomerization of the open transcription complex of Escherichia coli RNA polymerase at the model Pa promoter bearing consensus −10 and −35 hexamers. Acta Biochim Polon 48: 985-994.
  • Leirmo S, Harrison C, Cayley DS, Burgess RR, Record MT Jr (1987) Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro. Biochemistry 26: 2095-2101.
  • Leirmo S, Record MT Jr (1990) Structural, thermodynamic and kinetic studies of the interaction of Eσ70 RNA polymerase with promoter DNA. In Nucleic acids and molecular biology. Eckstein F, Lilley DMJ, eds. vol 4, pp 123-151. Springer-Verlag, Berlin, Heidelberg.
  • Lohman TM, deHaseth PL, Record Jr MT (1980) Pentalysine-deoxyribonucleic acid interaction. A model for the general effects of ion concentrations on the interaction of proteins with nucleic acids. Biochemistry 19: 3522-3530.
  • Łoziński T, Wierzchowski KL (2005) Mg2+ modulated KMnO4 reactivity of thymines in the open transcription complex reflects variation in the negative electrostatic potential along the separated DNA strands. Footprinting of Escherichia coli RNA polymerase complex at the λPR promoter revisited. FEBS J 272: 2838-2853.
  • Łoziński T, Markiewicz WT, Wyrzykiewicz TK, Wierzchowski KL (1989) Effect of the sequence-dependent structure of the 17 bp AT spacer on the strength of consensus-like E.coli promoters in vivo. Nucleic Acids Res 17: 3855-3863.
  • Łoziński T, Bolewska K, Wierzchowski KL (2009) Equivalence of Mg2+ and Na+ ions in salt dependence of the equilibrium binding and dissociation rate constants of Escherichia coli RNA polymerase open complex. Biophys Chem 142: 65-75.
  • Mascotti DP, Lohman TM (1993) Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition. Biochemistry 32: 10568-10579.
  • Mascotti DP, Lohman TM (1997) Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry 36: 7272-7279.
  • Misra VK, Draper DE (1999) The interpretation of Mg(2+) binding isotherms for nucleic acids using Poisson-Boltzman theory. J Mol Biol 294: 1135-1147.
  • Misra VK, Sharp KA, Friedman RA, Honig B (1994a) Salt effects on ligand-DNA binding; Minor groove binding antibiotics. J Mol Biol 238: 245-263.
  • Misra VK, Hecht J, Sharp K, Friedman RA, Honig B (1994b) Salt effects on protein-DNA interactions. The lambda cI repressor and EcoR1 endonuclease. J Mol Biol 238: 264-280.
  • Nakano S, Fujimoto M, Hara H, Sugimoto N (1999) Nucleic acid duplex stability: influence of base composition on cation effects. Nucleic Acids Res 27: 2957-2965.
  • Overman LB, Bujalowski W, Lohman TM (1988) Equilibrium binding of Escherichia coli single-strand binding protein to single-stranded nucleic acids in the (SSB)65 binding mode. Cation and anion effects and polynucleotide specificity. Biochemistry 27: 456-471.
  • Record Jr MT, deHaseth PL, Lohman TM (1977) Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry 16: 4791-4796.
  • Record Jr MT, Ha J-H, Fisher MA (1991) Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol 208: 291-343.
  • Record Jr MT, Reznikoff WS, Craig ML, McQuade KL, Schlaz PJ (1996) Escherichia coli RNA polymerase (Eσ70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella: cellular and molecular biology. Neidhardt FC, ed, pp 792-820. ASM Press, Washington D.C.
  • Roe J-H, Record Jr MT (1985) Regulation of the kinetics of the interaction of Escherichia coli RNA polymerase with the λPR promoter by salt concentration. Biochemistry 24: 4721-4726.
  • Rouzina I, Pant K, Karpel RL, Williams MC (2005) Theory of electrostatically regulated binding of T4 gene 32 protein to single- and double-stranded DNA. Biophys J 89: 1941-1956.
  • Shokri L, Marintcheva B, Richardson CC, Rouzina I, Williams MC (2006) Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA. J Biol Chem 281: 38689-38696.
  • Shokri L, Marintcheva B, Eldib M, Hanke A, Rouzina I, Williams MC (2008) Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA. Nucleic Acids Res 36: 5668-5677.
  • Sosunov V, Sosunova E, Mustaev A, Bass I, Nikiforov V, Goldfarb A (2003) Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J 22: 2234-2244.
  • Suh WC, Leirmo S, Record Jr MT (1992) Roles of Mg2+ in the mechanisms of formation and dissociation of open complex between Escherichia coli RNA polymerase and the λPR promoter; kinetic evidence for a second open complex requiring Mg2+. Biochemistry 31: 7815-7825.
  • Yarborough LR, Schlageck JG, Baughman M (1979) Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J Biol Chem 254: 12069-12073.
Document Type
Publication order reference
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv56p695kz
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