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Chaires JB. Thermodynamics of the daunomycin-DNA interaction: ionic strength dependence of the enthalpy and entropy. Biopolymers 1985; 24:403-19. [PMID: 3978225 DOI: 10.1002/bip.360240208] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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102
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Abstract
The kinetics of the interaction of daunomycin with calf thymus DNA are described. Stopped-flow and temperature-jump relaxation methods, using absorption detection, were used to study the binding reaction. Three relaxation times were observed, all of which are concentration dependent, although the two slower relaxations approach constant values at high reactant concentrations. Relaxation times over a wide range of concentrations were gathered, and the data were fit by a minimal mechanism in which a rapid bimolecular association step is followed by two sequential isomerization steps. The six rate constants for this mechanism were extracted from our data by relaxation analysis. The values determined for the six rate constants may be combined to calculate an overall equilibrium constant that is in excellent agreement with that obtained by independent equilibrium measurements. Additional stopped-flow experiments, using first sodium dodecyl sulfate to dissociate bound drug and second pseudo-first-order conditions to study the fast bimolecular step, provide independent verification of three of the six rate constants. The temperature dependence of four of the six rate constants was measured, allowing estimates of the activation energy of some of the steps to be made. We speculate that the three steps in the proposed mechanism may correspond to a rapid "outside" binding of daunomycin to DNA, followed by intercalation of the drug, followed by either conformational adjustment of the drug or DNA binding site or redistribution of bound drug to preferred sites.
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103
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Palumbo M, Capasso L, Palù G, Marciani Magno S. DNA-binding of water-soluble furocoumarins: a thermodynamic and conformational approach to understanding different biological effects. Nucleic Acids Res 1984; 12:8567-78. [PMID: 6504703 PMCID: PMC320399 DOI: 10.1093/nar/12.22.8567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The interaction of two water-soluble furocoumarins, 8-(omega-diethyl aminopropyloxy)psoralen hydrochloride (I) and its 5-isomer (II), with DNA has been investigated by spectroscopic, equilibrium dialysis, hydrodynamic and chiroptical techniques. Both compounds intercalate into the polynucleotide double helix. From the dependence of the binding on ionic strength, ion release and binding free energy corrected for counterion release have been quantitatively estimated. It is shown that the differences in DNA-affinity observed for compounds I and II arise primarily from non electrostatic contributions. The binding process is exothermic, with slightly different van't Hoff enthalpies for the examined furocoumarins. Helix lengthening and dichroic effects indicate different intercalation geometries for the isomeric compounds. These studies allow a possible explanation for the finding that isomer I exhibits largely better DNA-photobinding properties, while isomer II is by far more effective as an antiviral agent.
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104
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Kim R, Modrich P, Kim SH. 'Interactive' recognition in EcoRI restriction enzyme-DNA complex. Nucleic Acids Res 1984; 12:7285-92. [PMID: 6093038 PMCID: PMC320161 DOI: 10.1093/nar/12.19.7285] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A solution study of interaction between DNA and EcoRI restriction enzyme shows that there is a definite distortion of DNA in the specific recognition complexes but no measurable DNA distortion in the non-specific interaction.
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105
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Berg OG. Diffusion-controlled protein-DNA association: influence of segmental diffusion of the DNA. Biopolymers 1984; 23:1869-89. [PMID: 6498284 DOI: 10.1002/bip.360231005] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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106
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Vincent WR, Rosenberg LS, Schulman SG. Microcalorimetric investigation of the binding of some chemotherapeutic agents and related molecules to calf thymus DNA. J Pharm Sci 1984; 73:1279-84. [PMID: 6491951 DOI: 10.1002/jps.2600730923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Batch microcalorimetry was used to estimate directly the standard enthalpies of the binding of small molecules to DNA. These values were compared with those obtained from spectrophotometric binding constants and van't Hoff plots. The close agreement between the independently obtained enthalpies indicates that the appropriate (best) binding model has four phosphates per binding site. Thermodynamic binding constants were obtained from apparent binding constants measured at different ionic strengths. From these and the measured standard enthalpies, standard free energies and standard entropies of binding were calculated. The weak, presumably external, binding alleged to occur at high formal molar concentration ratios of ligand to DNA bases could not be detected by a measurable heat of binding.
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107
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108
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Hertzberg RP, Dervan PB. Cleavage of DNA with methidiumpropyl-EDTA-iron(II): reaction conditions and product analyses. Biochemistry 1984; 23:3934-45. [PMID: 6435669 DOI: 10.1021/bi00312a022] [Citation(s) in RCA: 381] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The synthesis of methidiumpropyl-EDTA (MPE) is described. The binding affinities of MPE, MPE.Ni(II), and MPE.Mg(II) to calf thymus DNA are 2.4 X 10(4) M-1, 1.5 X 10(5) M-1, and 1.2 X 10(5) M-1, respectively, in 50 mM NaCl, pH 7.4. The binding site size is two base pairs. MPE.Mg(II) unwinds PM2 DNA 11 +/- 3 degrees per bound molecule. MPE.Fe(II) in the presence of O2 efficiently cleaves DNA and with low sequence specificity. Reducing agents significantly enhance the efficiency of the cleavage reaction in the order sodium ascorbate greater than dithiothreitol greater than NADPH. At concentrations of 0.1-0.01 microM in MPE.Fe(II) and 10 microM in DNA base pairs, optimum ascorbate and dithiothreitol concentrations for DNA cleavage are 1-5 mM. Efficient cleavage of DNA (10 microM in base pairs) with MPE.Fe(II) (0.1-0.01 microM) occurs over a pH range of 7-10 with the optimum at 7.4 (Tris-HCl buffer). The optimum cleavage time is 3.5 h (22 degrees C). DNA cleavage is efficient in a Na+ ion concentration range of 5 mM to 1 M, with the optimum at 5 mM NaCl. The number of single-strand scissions on supercoiled DNA per MPE.Fe(II) under optimum conditions is 1.4. Metals such as Co(II), Mg(II), Ni(II), and Zn(II) inhibit strand scission by MPE. The released products from DNA cleavage by MPE.Fe(II) are the four nucleotide bases. The DNA termini at the cleavage site are 5'-phosphate and roughly equal proportions of 3'-phosphate and 3'-(phosphoglycolic acid). The products are consistent with the oxidative degradation of the deoxyribose ring of the DNA backbone, most likely by hydroxy radical.
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109
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110
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Palumbo M, Antonello S, Bonali F, Marciani Magno S. Interaction of deoxyribonucleic acid with potential photobiological agents: a physicochemical investigation. Int J Biol Macromol 1984. [DOI: 10.1016/0141-8130(84)90032-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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111
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Chandrasekaran S, Krishnamoorthy CR, Jones RL, Smith JC, Wilson WD. Stopped-flow kinetic, 1H, and 31P NMR analysis of the intercalation of ethidium with poly d(G-C) X d(G-C). Biochem Biophys Res Commun 1984; 122:804-9. [PMID: 6466339 DOI: 10.1016/s0006-291x(84)80105-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In a low salt buffer (0.011 M Na+) stopped-flow kinetic results for the SDS driven dissociation of an ethidium-Poly d(G-C) X d(G-C) complex are 8.7, 23, and 58.5 s-1 at 20, 30, and 40 degrees C, respectively. These results predict that in NMR experiments at high field strengths, ethidium should be in slow exchange among polymer binding sites. This has been found to be the case for both 31P (109 MHz) and 1H (imino proton spectra in H2O at 270 MHz) experiments. At higher salt, and/or higher temperature, and/or lower field, the bound and free peaks are no longer resolved in the NMR spectra. Good agreement is obtained between the stopped-flow kinetic results and the coalescence temperature observed in NMR experiments. Imino protons in base pairs on both sides of the intercalated ethidium are shifted approximately one ppm upfield while only the phosphate groups at the intercalation site experience large chemical shifts.
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112
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Fox KR, Waring MJ. Stopped-flow kinetic studies on the interaction between echinomycin and DNA. Biochemistry 1984; 23:2627-33. [PMID: 6466601 DOI: 10.1021/bi00307a014] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The kinetics of association between the quinoxaline antitumor antibiotic echinomycin and DNA have been studied by stopped-flow methods. With natural DNAs, the reaction profile is completely described by a single exponential, the time constant for which varies linearly with the DNA concentration. This bimolecular rate constant is similar for both calf thymus and Micrococcus lysodeikticus DNA (k = 6 X 10(4) M-1 s-1 at 25 degrees C, I = 0.01) and is probably dominated by interaction with relatively weak but abundant binding sites from which the antibiotic dissociates fairly quickly. The observed single exponential suggests a molecular mechanism of binding in which both chromophores of the antibiotic become intercalated simultaneously rather than sequentially; no transition from a mono-intercalated state to a bis-intercalated state could be detected. The reaction is slowed by a factor of about 3 on raising the salt concentration from I = 0.01 to I = 0.5. Binding to poly(dA-dT) is also described by a single exponential, the time constant for which is about 3 times faster than that seen with natural DNAs. By contrast, the interaction with poly-(dG-dC) requires two exponentials for a proper description, the faster of which is similar to that seen with natural DNAs. This may reflect the initial interaction of the antibiotic with two types of sequences, tentatively identified as GpC and CpG, from which it dissociates at very different rates. The differences in kinetic behavior may be explicable on the basis of an alternating B structure for poly(dA-dT) and a more classical B form for poly(dG-dC).
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113
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Interaction of anthracycline antibiotics with biopolymers: 9. Comparative study of the interaction kinetics of daunomycin, adriamycin and iremycin with DNA. Int J Biol Macromol 1984. [DOI: 10.1016/0141-8130(84)90051-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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114
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115
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116
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Abstract
The binding of the Escherichia coli cyclic AMP receptor protein (CAP) to restriction fragments containing the lac promoter-operator region has been investigated as a function of cAMP concentration, using a sensitive gel electrophoresis assay. Under standard conditions (13 mM ionic strength), the equilibrium constant for CAP binding to its primary site on a 203 base-pair lac promoter fragment is 6.3 X 10(8) M-1 at 0.2 microM-cAMP, and increases to 8.4 X 10(10) M-1 at 5.0 microM-cAMP. The latter is about 10(5) times larger than the equilibrium constant for binding to an isolated, non-specific site. The L8 mutation, which renders the lac promoter unresponsive to CAP in vivo, lowers this binding affinity by five- to tenfold. Analysis of the cAMP dependency of binding over the concentration range of 0.2 microM to 10 microM reveals that uptake of a single equivalent of cAMP is required for site-specific binding. Similarly, the transfer of CAP from a non-specific DNA site to a specific site requires the net uptake of a single molecule of cAMP. In contrast, co-operative non-specific binding to DNA was found to be independent of cAMP concentration with an equilibrium binding constant of 6 X 10(6) M-1. We conclude that the cAMP affinity of the two CAP subunits in the specific promoter complex is not equal, and that the complex structure therefore deviates significantly from twofold symmetry. A model for the regulation of the lac promoter by the intracellular cAMP concentration is proposed on the basis of the equilibrium binding results.
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117
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Dougherty G, Pilbrow JR. Physico-chemical probes of intercalation. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1984; 16:1179-92. [PMID: 6397369 DOI: 10.1016/0020-711x(84)90215-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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118
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Neidle S, Abraham Z. Structural and sequence-dependent aspects of drug intercalation into nucleic acids. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1984; 17:73-121. [PMID: 6094101 DOI: 10.3109/10409238409110270] [Citation(s) in RCA: 139] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Information gained from X-ray crystallographic studies on drug-nucleic acid complexes is described, with emphasis on the intercalation process. Relevant data from NMR experiments are examined in order to highlight similarities and differences between solution and solid-state structures. Theoretical analyses of intercalation complexes are also discussed and evaluated, with respect to the structural methods, with special reference being made to nucleic acid conformation and positions of drug molecules in the binding sites.
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119
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Palumbo M, Marciani Magno S. Interaction of deoxyribonucleic acid with anthracenedione derivatives. Int J Biol Macromol 1983. [DOI: 10.1016/0141-8130(83)90046-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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120
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Icenogle RD, Elson EL. Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. I. Theory and FCS measurements. Biopolymers 1983; 22:1919-48. [PMID: 6616014 DOI: 10.1002/bip.360220808] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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121
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Icenogle RD, Elson EL. Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. II. FPR and FCS measurements at low and high DNA concentrations. Biopolymers 1983; 22:1949-66. [PMID: 6616015 DOI: 10.1002/bip.360220809] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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122
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Delbarre A, Gourevitch MI, Gaugain B, Le Pecq JB, Roques BP. 1H NMR study of an ethidium dimer poly(dA-dT) complex: evidence of a transition between bis and monointercalation. Nucleic Acids Res 1983; 11:4467-82. [PMID: 6866771 PMCID: PMC326059 DOI: 10.1093/nar/11.13.4467] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Comparative 1H NMR and optical studies of the interaction between poly(dA-dT), ethidium bromide (Et) and ethidium dimer (Et2) in 0.7 M NaCl are reported as a function of the temperature. Denaturation of the complexes followed at both polynucleotide and drug levels leads to a biphasic melting process for poly(dA-dT) complexed with ethidium dimer (t1/2 = 75 degrees C; 93 degrees C) but a monophasic one in poly(dA-dT): ethidium bromide complex (t1/2 = 74 degrees C). In both cases drug signals exhibit monophasic thermal dependence (Et = 81 degrees C; Et2 = 95 degrees C). Evidence is presented showing that the ethidium dimer bisintercalates into poly(dA-dT) in high salt, based on the observation that i) dimer and monomer ring protons exhibit similar upfield shifts upon DNA binding, ii) upfield shifts of DNA sugar protons are twice as large with the dimer than with ethidium bromide. Comparison between native DNA fraction and bound drug fraction indicates that ethidium covers, n = 2.5-3 base pairs. The dimer bisintercalates and covers, n = 5.7 base pairs when the helix fraction is high but as the number of available sites decreases the binding mode changes and the drug monointercalates (n = 2.9).
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123
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Doglia S, Gräslund A, Ehrenberg A. Binding of ethidium bromide to self-complementary deoxydinucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 133:179-84. [PMID: 6852024 DOI: 10.1111/j.1432-1033.1983.tb07445.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Optical spectra titrations were performed with ethidium bromide and the self-complementary deoxydinucleotides pdCpdG, pdGpdC, pdTpdA, and pdApdT. The titrations were performed in 7.5 mM phosphate buffer, pH 7.0, at 7 degrees C, and with varying dinucleotide concentrations always in large excess of the dye concentration. Well-defined isosbestic points were present in each titration after correction for dinucleotide light absorption. The binding curves were evaluated in terms of simple bimolecular or termolecular reaction models. The bimolecular reaction model gave a significantly better fit to the experimental data, judging from a computerized nonlinear least-squares fitting procedure. The following equilibrium constants were obtained: KC-G = 2000 M-1; KG-C = 950 M-1; KT-A = 370 M-1; KA-T = 350 M-1. From these data the absorption spectra of the completely bound dye were evaluated. These spectra showed bathchromic shifts of their maxima, increasing with the magnitude of K. Fluorescence spectra of ethidium bromide/dinucleotide mixtures were recorded under conditions similar to those for absorption spectra. From the known equilibrium constants the contributions of the bound dye could be estimated. The following fluorescence enhancements Ib/If were found: IC-Gb/If = 6.5; IG-Cb/If = 3.0; IT-Ab/If = 2.0; IA-bT/If = 2.0. From our results, in relation to other theoretical and experimental studies, we conclude that electrostatic phosphate-dye interactions give rise to a major part of the binding energy, which varies with dinucleotide geometry. The more strongly bound complexes exhibit less exposure of the dye to the solvent.
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124
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Dougherty G. The unwinding of circular DNA by intercalating agents as determined by gel electrophoresis. Biosci Rep 1983; 3:453-60. [PMID: 6688368 DOI: 10.1007/bf01121956] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The conventional counting of electrophoretically resolvable topoisomers is an attractive technique for determining the number of superhelical turns in a closed circular DNA molecule. The method can be extended in order to determine the unwinding produced by a drug, if its binding constants are known under similar environmental conditions. Ethidium bromide was found to unwind a DNA molecule derived from the plasmid pBR322 by 26.0 degrees in a magnesium-containing buffer. The method is convenient for investigating the possible effects of different environmental changes (such as ionic strength, ionic species, or temperature) on the unwinding angle produced by a particular drug. It can also give an early indication of multiple modes of binding.
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125
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Mirau PA, Kearns DR. The effect of intercalating drugs on the kinetics of the B to Z transition of poly(dG-dC). Nucleic Acids Res 1983; 11:1931-41. [PMID: 6835844 PMCID: PMC325847 DOI: 10.1093/nar/11.6.1931] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We have measured the ability of the intercalating drugs proflavine, ethidium bromide, actinomycin D, and bismethidiumspermine to inhibit the salt induced transition of poly(dG-dC) from the B to the Z form. While all of the drugs studied slowed the B to Z transition, the effectiveness of the drugs correlates much better with their DNA binding kinetics than their DNA binding constants. In studies where the binding densities of ethidium and actinomycin were varied we have found that high levels of ethidium, more than 1 per 20 base pairs, were required to inhibit the B to Z transition while low levels of actinomycin, less than 1 per 450 base pairs, reduced the transition rate. Studies of the B to Z transition in the presence of both actinomycin and ethidium suggest that the drugs inhibit the transition by different mechanisms. The results are interpreted in terms of a modification of the kinetic model proposed by Pohl and Jovin in which, depending on the DNA binding kinetics of the drug, the drug may inhibit nucleation and/or propagation of the B to Z transition.
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126
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Fried MG, Crothers DM. CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Res 1983; 11:141-58. [PMID: 6306561 PMCID: PMC325695 DOI: 10.1093/nar/11.1.141] [Citation(s) in RCA: 135] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The binding stoichiometries of the complexes formed when the E. coli cyclic AMP receptor protein (CAP) binds to 203 bp lac promoter-operator restriction fragments have been determined. Under quantitative binding conditions, a single dimer of CAP occupies each of two sites in the promoter. Different electrophoretic mobilities are observed for 1:1 complexes formed with L8-UV5 mutant, L305 mutant, and wild type promoter fragments, indicating sequence-specific structural differences between the complexes. The differences in gel mobility between L8-UV5 and wild type complexes disappear when the promoter fragments are cleaved with Hpa II restriction endonuclease. Models in which CAP alters DNA conformation or in which CAP forms a transient intramolecular bridge between two domains of a DNA molecule could account for these observations. The selective binding of RNA polymerase to CAP-promoter complexes is demonstrated: the binding of a single CAP dimer to the promoter is sufficient to stimulate subsequent polymerase binding. Functional CAP molecules are not released from the promoter on polymerase binding.
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127
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Hall SB, Schellman JA. Flow dichroism of capsid DNA phages. II. Effect of DNA deletions and intercalating dyes. Biopolymers 1982; 21:2011-31. [PMID: 6216924 DOI: 10.1002/bip.360211007] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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128
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Wu CW, Tweedy N. Mechanistic aspects of promoter binding and chain initiation by RNA polymerase. Mol Cell Biochem 1982; 47:129-49. [PMID: 6755217 DOI: 10.1007/bf00229597] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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129
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Schmitz KS. A model for the association of intercalating ligands with mononucleosomes and chromatin. J Theor Biol 1982; 98:29-43. [PMID: 7176667 DOI: 10.1016/0022-5193(82)90056-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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130
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Sturm J. Binding of ligands to a one-dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides. Biopolymers 1982; 21:1189-206. [PMID: 7093435 DOI: 10.1002/bip.360210613] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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131
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Mirau PA, Shafer RH. Role of actinomycin pentapeptides in actinomycin-deoxyribonucleic acid binding and kinetics. Biochemistry 1982; 21:2626-31. [PMID: 7093211 DOI: 10.1021/bi00540a008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Results are reported on equilibrium and kinetic experiments probing the DNA binding properties of a series of actinomycin analogues differing at the 3'-amino acid position. While the parent compound, actinomycin D, contains proline at this position on both pentapeptide lactone rings, the analogues under consideration here contain either azetidine-2-carboxylic acid, pipecolic acid, or 4-ketoproline on one or both pentapeptide rings. This study extends our earlier results on doubly substituted analogues [Shafer, R.H., Burnett, R. R., & Mirau, P.A. (1980) Nucleic Acids Res. 8, 1121]. DNA binding constants were determined from Scatchard plots constructed from visible absorption data and covered the range of (0.3-9) X 10(6) M-1 for the whole series of analogues. The thermal denaturation temperature of calf-thymus DNA was increased by 3-17 degrees C. DNA dissociation kinetics, along with enthalpies and entropies of activation, were also determined. The time constant for the slowest dissociation process ranged from 278 to 10 900 s. The strongest DNA binding analogue, in terms of the largest binding constant, the largest increase in DNA thermal denaturation temperature, and the slowest DNA dissociation rate, was actinomycin V, which has 4-ketoproline in the beta peptide ring, while the weakest DNA binding analogue has pipecolic acid on both peptide rings. Evidence is presented for one peptide ring exerting a greater influence than the other in the interaction with DNA. Also, the possible role of cis-trans isomerization about one or two peptide bonds in determining the slow DNA binding kinetics is discussed.
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132
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Abstract
The interactions in solution and in the fibre state of the trypanocidal drug, prothidium dibromide, with DNA have been investigated using a number of biophysical techniques. The binding parameters at 0.11 ionic strength were determined by spectroscopic means. Sedimentation studies show that the drug is able to unwind closed circular DNA in solution, but X-ray diffraction and linear dichroism experiments indicate that it is uncertain whether this unwinding can be attributed to intercalation in the classical sense. On the basis of our results, we propose that the primary mode of binding is "sideways" intercalation, supplemented by electrostatic binding along the sugar-phosphate chains and interstrand binding involving hydrogen bonding.
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133
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Fox KR, Olsen RK, Waring MJ. Equilibrium and kinetic studies on the binding of des-N-tetramethyltriostin A to DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 696:315-22. [PMID: 7066328 DOI: 10.1016/0167-4781(82)90063-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The interaction between TANDEM (a des-methyl analogue of triostin A) and poly(dA-dT) results in extension of the helix by 6.8 A for each ligand molecule bound, exactly as predicted for a bis-intercalation reaction. Cooperativity is evident in Scatchard plots for the interaction at ionic strengths of 0.2 and 1.0, where the binding constant is diminished compared to that which pertains at low salt concentrations. Binding to a natural DNA (calf thymus), already considerably weaker than binding to poly(dA-dT), is also sensitive to increased ionic strength. With a self-complementary octanucleotide d(G-G-T-A-T-A-C-C) the binding curve indicates the presence of a single des-N-tetramethyltriostin A binding site per helical fragment with a non-cooperative association constant about 6 . 10(6) M-1. Detergent-induced dissociation of des-N-tetramethyltriostin A-poly(dA-dT) complexes results in a simple exponential decay at all levels of binding, but the time constant of decay is dependent upon the initial binding ratio. This behavior cannot directly explain the cooperativity of equilibrium binding isotherms but suggests the occurrence of relatively long-lived perturbations of the helical structure by binding of the ligand. [Ala3, Ala7]des-N-tetramethyltriostin A, which has a more flexible octapeptide ring lacking the disulphide cross-bridge, dissociates from poly(dA-dT) much faster than des-N-tetramethyltriostin A. Dissociation of des-N-tetramethyltriostin A from calf thymus DNA is more rapid than dissociation of triostin A or other quinoxaline antibiotics, which may account for its low antimicrobial activity.
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134
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Wilson WD, Jones RL. Interaction of actinomycin D, ethidium, quinacrine, daunorubicin, and tetralysine with DNA: 31P NMR chemical shift and relaxation investigation. Nucleic Acids Res 1982; 10:1399-410. [PMID: 7071016 PMCID: PMC320534 DOI: 10.1093/nar/10.4.1399] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The binding of actinomycin D, ethidium, quinacrine, daunorubicin, and tetralysine to DNA has been investigated using 31P NMR. Titration of DNA with actinomycin yields a new downfield peak or overlapping peaks as would be expected from the slow dissociation kinetics of this compound. The other intercalators shift the DNA 31P signal downfield as a single exchange averaged peak. Tetralysine causes a slight upfield shift. The chemical shift titration curves for the intercalators are sigmoid curves suggesting that cooperative processes or competing effects on the chemical shift are being observed. The magnitude of the chemical shift change at saturation of DNA with the compounds is found to vary significantly and to be linearly related to the DNA base pair unwinding angle for the compounds. Analysis of 31P spin lattice relaxation times (T1) and linewidths as a function of temperature (below Tm) and titration with the above compounds indicates that T1 does not change significantly while linewidth increases with decreasing temperature and increasing bound intercalator. One interpretation of these results is that in both cases the overall motion of DNA becomes slower while the internal motion is not greatly affected.
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135
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Dougherty G, Pigram WJ. Spectroscopic analysis of drug-nucleic acid interactions. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1982; 12:103-32. [PMID: 6175481 DOI: 10.3109/10409238209108704] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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136
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Feigon J, Leupin W, Denny WA, Kearns DR. Binding of ethidium derivatives to natural DNA: a 300 MHz 1H NMR study. Nucleic Acids Res 1982; 10:749-62. [PMID: 7063414 PMCID: PMC326183 DOI: 10.1093/nar/10.2.749] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The binding of three ethidium derivatives, ethidium (1), des-3-amino ethidium (2) and des-8-amino ethidium (3), to short (approximately 35 base pairs), random sequence DNA has been investigated using 300 MHz proton NMR. At 35 degrees C all three drugs cause upfield shifts of the resonances from the exchangeable imino protons, as expected for intercalative binding to DNA. However, the lineshapes vary significantly with the nature of the drug. The temperature dependence of the spectra of the DNA shows that differences between spectra observed at 35 degrees C with ethidium and with des-3-amino ethidium are primarily due to differences in the drug binding kinetics rather than to differences in mode of binding. Removal of the amino group at position 3, but not at position 8, on the parent ethidium shortens the lifetime of the intercalative state; this implies that the 3-NH2 group is involved in stabilization of the drug-DNA complex. Analysis of the drug-DNA spectra indicates that there is a preference for binding of the drugs adjacent to G.C base pairs.
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137
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Dougherty G. A comparison of the base-pair specificities of three phenanthridine drugs using solution spectroscopy. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1982; 14:493-504. [PMID: 7106349 DOI: 10.1016/0020-711x(82)90117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. The absorption spectrum of three phenanthridine drugs (ethidium, dimidium and prothidium bromide) bound to natural DNAs of differing G-C content were obtained using a novel mixing scheme and analysed according to the excluded site binding model. 2. Ethidium bromide shows a strong G-C specificity at low binding ratios. especially at low ionic concentration. 3. Dimidium bromide shows a less strong G-C specificity. 4. For both drugs, the binding site size reflects a situation close to nearest-neighbour exclusion. 5. Prothidium shows no specificity in its binding. The binding modes are different than for the other two phenanthridines, and it is suggested that the primary mode is "sideways" intercalation.
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138
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Fried M, Crothers DM. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 1981; 9:6505-25. [PMID: 6275366 PMCID: PMC327619 DOI: 10.1093/nar/9.23.6505] [Citation(s) in RCA: 2380] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We describe the use of gel electrophoresis in studies of equilibrium binding, site distribution, and kinetics of protein-DNA interactions. The method, which we call protein distribution analysis, is simple, sensitive and yields thermodynamically rigorous results. It is particularly well suited to studies of simultaneous binding of several proteins to a single nucleic acid. In studies of the lac repressor-operator interaction, we found that binding to the so-called third operator site (03) is 15-18 fold weaker than operator binding, and that the binding reactions with the first and third operators are uncoupled, implying that there is no communication between the sites. Pseudo-first order dissociation kinetics of the repressor-203 bp operator complex were found to be temperature sensitive, with delta E of 80 kcal mol-1 above 29 degrees C and 26 kcal mol-1 below. The half life of the complex (5 min at 21 degrees C) is shorter than that reported for very high molecular weight operator-containing DNAs, but longer than values reported for much shorter fragments. The binding of lac repressor core to DNA could not be detected by this technique: the maximum binding constant consistent with this finding is 10(5) M-1.
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139
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Aktipis S, Panayotatos N. A kinetic study on the mechanism of inhibition of RNA synthesis catalyzed by DNA-dependent RNA polymerase. Differences in inhibition by ethidium bromide, 3,8-diamino-6-ethylphenanthridinium bromide and actinomycin d. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 655:278-90. [PMID: 7025910 DOI: 10.1016/0005-2787(81)90038-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The mechanism of inhibition of RNA polymerase-catalyzed synthesis of RNA by actinomycin D and the phenan-thridinium derivatives ethidium bromide and 3,8-diamino-6-ethylphenanthridinium bromide (DEMB) is examined. A general kinetic equation describing the dependence of RNA synthesis on DNA template concentration is derived and distinct expressions corresponding to various possible mechanisms of inhibition are subsequently obtained by introducing into the equations assumptions as appropriate for the individual mechanisms. The fitting of the experimental results of inhibition into the resulting equations suggested that the ethidium bromide and DEMB inhibit RNA polymerase by forming an inhibitor-template complex which interferes with enzyme recognition of, and binding to, appropriate sites on the template (binding inhibition). The fitting of the dependence of the rate of RNA synthesis on the bound-inhibitor to DNA ratios to the derived kinetic expressions also allows a tentative distinction to be made as to whether ethidium bromide and DEMB interfere with RNA synthesis by a mechanism of 'partial' or 'complete' inhibition.
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140
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Lohman TM, Kowalczykowski SC. Kinetics and mechanism of the association of the bacteriophage T4 gene 32 (helix destabilizing) protein with single-stranded nucleic acids. Evidence for protein translocation. J Mol Biol 1981; 152:67-109. [PMID: 6279865 DOI: 10.1016/0022-2836(81)90096-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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141
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Fox KR, Wakelin LP, Waring MJ. Kinetics of the interaction between echinomycin and deoxyribonucleic acid. Biochemistry 1981; 20:5768-79. [PMID: 7295702 DOI: 10.1021/bi00523a020] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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142
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Busby S, Spassky A, Buc H. On the binding of tRNA to Escherichia coli RNA polymerase. Interactions between the core enzyme, DNA and tRNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 118:443-51. [PMID: 6170513 DOI: 10.1111/j.1432-1033.1981.tb05540.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We have investigated the interplay between the binding of tRNA and DNA to core RNA polymerase. We show that the monomer core enzyme can bind stably to either DNA or tRNA, whereas the dimer core can fix both DNA and tRNA in a stable ternary complex. We have examined the kinetics of the exchange between DNA and tRNA bound to the core enzyme. DNA bound to monomer core can be rapidly displaced by tRNA without prior dissociation of the core from the DNA. Similarly tRNA bound to the core can be displaced by DNA without prior dissociation of the tRNA. We confirm the result of Hinkle and Chamberlin [J. Mol. Biol. 70, 157-185 (1972)] that, in contrast, the core enzyme must first dissociate from one DNA molecule before it can transfer to another DNA. As this dissociation is very slow we suggest that, in vivo, the tRNA can act as a 'porter' providing the core enzyme with a more kinetically favourable path to transfer from one DNA site to another.
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143
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Weisehahn G, Varga JM, Hearst JE. Interactions of daunomycin and melanotropin-daunomycin with DNA. Nature 1981; 292:467-9. [PMID: 7254342 DOI: 10.1038/292467a0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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144
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Fox KR, Waring MJ. Kinetics of dissociation of quinoxaline antibiotics from DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 654:279-86. [PMID: 7284382 DOI: 10.1016/0005-2787(81)90182-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The kinetics of detergent-induced dissociation of triostins A and C and quinomycin C from DNA have been investigated. All three antibiotics dissociate from poly(dA-dT) and poly(dG-dC) in a simple first-order fashion whereas their dissociation from a natural DNA (calf thymus) is complex, requiring three exponential terms for its complete description. This behaviour is attributed to sequence-selectivity on the part of the drugs and seems to represent dissociation from different classes of intercalative binding site. The time constants of dissociation are better resolved for quinomycins than for triostins, consistent with the view that quinomycins are more sequence-specific in their interaction with DNA, but it is not possible to identify any class of binding site with the alternating purine-pyrimidine sequences of the synthetic polydeoxynucleotides. In general, the triostins dissociate an order of magnitude faster than the corresponding quinomycins. This is attributable to a larger entropy of activation, presumably reflecting greater flexibility of the octapeptide ring when the cross-bridge is a disulphide as opposed to the slightly shorter thioacetal found in quinomycins. The longest time constant in the dissociation of each of the four quinoxaline antibiotics from calf thymus DNA correlates well with its antibacterial potency, in agreement with the conclusion that the biological effects result from impairment of the role of DNA as a template for polymerase activity.
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145
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Abstract
We report equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.U (or T) and I.C base pairs. The results are interpreted in terms of the neighbor exclusion model of drug binding, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively. Both DNA and the alternating copolymers examined [poly[d(A-T)] and poly[d(I-C)]] showed high affinity (10(4)--10(5) M-1) in 1 M salt. Homopolynucleotides showed a more complicated pattern of affinities: poly(rA).poly(rU), poly(rA).poly(dT), and poly(dA).poly(rU) showed high affinity, whereas poly(dA).poly(dT), poly(rI).poly(rC), and poly(dI).poly(dC) showed low affinity (less than or equal to 10(3) M-1). The neighbor exclusion range was inferred to be two base pairs for DNA or B family helices and three for RNA or A family helices. Generally, polynucleotides showed some cooperativity in their ethidium binding. The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively.
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146
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Lye DJ, Birge EA. The use of nitrocellulose filters to study DNA binding proteins in crude cell lysates: Effect of competing DNA. Curr Microbiol 1981. [DOI: 10.1007/bf01642387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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147
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Graves DE, Watkins CL, Yielding LW. Ethidium bromide and its photoreactive analogues: spectroscopic analysis of deoxyribonucleic acid binding properties. Biochemistry 1981; 20:1887-92. [PMID: 7225364 DOI: 10.1021/bi00510a026] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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148
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Finkentey JH, Zimmermann HW. 8-Amino-5-ethyl-3-oxido-6-phenylphenanthridinium-betain, eine neue solvatochrome Verbindung. ACTA ACUST UNITED AC 1981. [DOI: 10.1002/jlac.198119810102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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149
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Wilson WD, Jones RL. Intercalating drugs: DNA binding and molecular pharmacology. ADVANCES IN PHARMACOLOGY AND CHEMOTHERAPY 1981; 18:177-222. [PMID: 6172965 DOI: 10.1016/s1054-3589(08)60255-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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150
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Wakelin LP, Waring MJ. Kinetics of drug-DNA interaction. Dependence of the binding mechanism on structure of the ligand. J Mol Biol 1980; 144:183-214. [PMID: 6785442 DOI: 10.1016/0022-2836(80)90032-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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