Interaction of netropsin and distamycin with deoxyribonucleic acid: electric dichroism study

Kinetics of the daunomycin--DNA interaction

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.

Interaction of diamidino-2-phenylindole (DAPI) with natural and synthetic nucleic acids

The interaction of DAPI with natural and synthetic polydeoxynucleotides of different base content and sequences was studied with circular dichroism, ultracentrifugation, viscosity and calorimetry. All the polymers show two types of binding. The strength of the interaction and its resistance to ionic strength are related to the content of AT clusters in the chain. On the other hand, sedimentation measurements rule out an intercalation mechanism. A model of DAPI interaction with DNA, similar to that displayed by distamycin and netropsin, is proposed.

Daunomycin inhibits the B leads to Z transition in poly d(G-C)

The cancer drug daunomycin is an effective inhibitor of the B leads to Z transition in poly d(G-C) in 4 M NaCl. Both the rate and extent of the B leads to Z transition are decreased by the drug, as judged by equilibrium and kinetic studies. Daunomycin can, under some conditions, convert Z form DNA back to B form. Drug binding to poly d(G-C) in 4 M NaCl is slow and highly cooperative, consistent with a role for daunomycin as an allosteric effector on the B leads to Z equilibrium. Since daunomycin binds preferentially to alternating purine-pyrimidine sequences, which are the very sequences capable of undergoing the B leads to Z transition, these effects may be an important part of the mechanism by which the drug inhibits transcription and replication.

Thermodynamics of drug-DNA interactions

Batch calorimetry, differential scanning calorimetry (DSC), uv/vis absorption spectroscopy, fluorescence spectroscopy, and circular dichroism (CD), have been used to detect, monitor, and thermodynamically characterize the binding of daunomycin, dipyrandenium, dipyrandium, and netropsin to poly d(AT) and actinomycin D to salmon testes (ST) DNA. The following thermodynamic binding profiles have been obtained. (table; see text) All the poly d(AT) binding studies were done at 25 degrees C while actinomycin binding to ST DNA was performed at 1 degree C to enhance drug solubility. These thermodynamic parameters are interpreted in terms of specific interactions that have been proposed as part of models for the binding of each drug.

Single-cell partition analysis--a direct fluorescence technique for examining ligand-macromolecule interactions

Single-cell partition analysis is described as a novel technique for examining ligand-macromolecule interactions. This procedure is a combination of the classical fluorescence titration technique and phase-partition techniques and allows three separate methods for calculating and comparing both free and bound drug concentrations. The value of this technique is demonstrated by the comparison of the binding properties of the potent antitumor antibiotic adriamycin and ethidium bromide to nucleic acids. Binding isotherms of both drugs were obtained at low r (concentration of bound drug per base pair) values, showing strikingly different results, thus allowing insight to be gained into the cooperative binding of these drugs to DNA.

Equilibrium studies on the interaction of daunomycin with deoxypolynucleotides

Fluorescence and absorbance methods were used to study the interaction of daunomycin with four deoxypolynucleotides. The binding may be described by the neighbor-exclusion model for binding ratios greater than 0.05, with intrinsic binding constants decreasing in the order poly[d(A-T)] X poly[d(A-T)] greater than poly[d(G-C)] X poly[d(G-C)] greater than poly(dG) X poly(dC) greater than poly(dA) X poly(dT). The exclusion parameter was found to be approximately 2 for the A-T-containing polynucleotides, 4 for the alternating G-C polymer, and nearly 10 for poly(dG) X poly(dC). Poly(dA) X poly(dT) showed positive cooperativity at low binding ratios. Thermal denaturation studies provided quantitative support for the measured binding parameters; the delta Tm values measured may be correlated primarily with the differences seen in the exclusion parameter. Sedimentation velocity experiments on daunomycin-deoxypolynucleotide complexes show an unusual nonlinear dependence of Sapp on the binding ratio for poly[d(A-T)] X poly[d(A-T)], poly[d(G-C)] X poly[d(G-C)], and poly(dA) X poly(dT), indicative of either a nonstandard conformational change accompanying intercalation or cooperative drug binding.

Production of positively supercoiled DNA by netropsin

The antibiotic netropsin binds to DNA by a non-intercalative mechanism. It increases the linking number of DNA so that in the presence of topoisomerase I, positively supercoiled molecules are produced.

The use of radiolabelled triostin antibiotics to measure low levels of binding to deoxyribonucleic acid

Triostin antibiotics, which contain a cyclic peptide with a disulphide bridge, have been prepared by growing Streptomyces triostinicus in the presence of inorganic [35S]-sulphate. The labelled triostin A has been shown to behave in all respects similarly to the authentic natural product and to enable a much more sensitive radiochemical adaptation of the solvent-partition method for determining antibiotic binding to DNA. By this means, binding isotherms at low, biologically relevant levels (down to one antibiotic molecule per gene) have been measured. The results indicate the existence of some tight binding sites in natural DNA species that are preferentially occupied at low concentrations. No evidence has been found for any allosteric transitions provoked by interaction between these antibiotics and natural DNA species, though there is evidence for co-operativity in the binding of triostin A to poly(dA-dT). For the first time accurate isotherms have been determined for the binding of triostin C to DNA; its binding constants for a variety of polydeoxynucleotides are uniformly tighter than those of triostin A but fall into the same ranking order when different species of natural DNA are compared.

Calorimetric and spectroscopic investigation of drug-DNA interactions. I. The binding of netropsin to poly d(AT)

We report the first calorimetric investigation of netropsin binding to poly d(AT). Temperature-dependent uv absorption, circular dichroism (CD), batch calorimetry, and differential scanning calorimetry (DSC) were used to detect, monitor, and thermodynamically characterize the binding process. The following results have been obtained: 1) Netropsin groove binding is accompanied by a large exothermic enthalpy of 9.2 kcal/mol of drug bound at 25 degrees C. This indicates that a large negative binding enthalpy may be a necessary but not a sufficient criterion for drug intercalation. We suggest that the exothermic binding might be correlated with specific H-bonding interactions. 2) From the difference in DSC transition enthalpies in the presence and absence of netropsin, we calculate a binding enthalpy of -10.7 kcal/mol of netropsin at 88 degrees C. 3) We calculate a positive delta S for netropsin binding to poly d(AT) at 25 degrees C. This positive entropy change may reflect netropsin-induced release of condensed cations and/or bound water. 4) The netropsin-saturated duplex monophasically melts 46 degrees C higher than the free duplex. The unsaturated duplex melts through two thermally-resolved transitions that correspond to netropsin-free and netropsin-bound regions. These two regions interact dynamically with no substantial influence on the thermal stabilities of the separate domains. 5) Netropsin binding decreases the cooperativity of the duplex to single strand transition.

On the cooperative and noncooperative binding of ethidium to DNA

The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other hand, no evidence of cooperative binding was observed in the binding isotherms obtained with calf thymus, C. perfringens, M. lysodeikticus, or poly(dG-dC) X (dG-dC) under the experimental conditions used (0.1 M NaCl).

DNA conformation, dynamics, and interactions in solution

The conformation and dynamics of the d(CGCGAATTCGCG) duplex, its analogs containing mismatched base pairs and helix interruptions, and its complexes with actinomycin and Netropsin, bound separately and simultaneously, have been investigated by nuclear magnetic resonance spectroscopy in aqueous solution. Structural information has been deduced from chemical shift and nuclear Overhauser effect parameters, while the kinetics have been probed from line width and saturation recovery experiments on proton and phosphorus markers at the individual base pair level. These studies lead to an improved understanding of the role of nucleic acid sequence on the structure, flexibility, and conformational interconversions in the duplex state. The nuclear magnetic resonance measurements readily identify helix modification and antibiotic binding sites on the nucleic acid and estimate the extent to which the observed conformational and dynamic perturbations are transmitted to adjacent base pair regions.

Two identical subunits of the EcoRI restriction endonuclease Co-operate in the binding and cleavage of the palindromic substrate

The cleavage of radioactively labelled double-stranded d(G-G-A-A-T-T-C-C) was studied in single turnover experiments with substrate and enzyme both being in the micromolar range. The reaction rate was found to increase with enzyme concentration until a ratio of one tetrameric enzyme to two double-stranded substrates was reached, further increase of the enzyme concentration then leads to a sharp decline of the reaction rate. These findings are interpreted in the following manner. (a) Two subunits of the EcoRI endonuclease co-operate in binding and possibly also in cleaving the palindromic substrate. (b) The enzymatic action of the EcoRI endonuclease is inhibited by excess enzyme, possibly due to unspecific binding of the enzyme-substrate complex. The self-inhibition of EcoRI endonuclease has also been observed with macromolecular substrates.

Interaction of actinomycin D, ethidium, quinacrine, daunorubicin, and tetralysine with DNA: 31P NMR chemical shift and relaxation investigation

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.

The effect of several nucleic acid binding drugs on the cleavage of d(GGAATTCC) and pBR 322 by the Eco RI restriction endonuclease

The endonucleolytic action of the EcoRI restriction enzyme on the double-stranded oligonucleotide d(GGAATTCC) and the supercoiled plasmid DNA pBR 233 is inhibited by actinomycin D, ethidium bromide, proflavin, distamycin A and netropsin. Half-maximal inhibition is observed at around 100 microM concentrations for the intercalating drugs, and around 0.1 to 1 microM concentrations for netropsin and distamycin A. The inhibitory activity of these drugs can be correlated with their affinity to the oligonucleotide and the plasmid DNA. Since at high concentrations of the drugs a complete inhibition is observed, it is concluded that the effect of the drugs on the stereochemistry of the EcoRI site is such that recognition is excluded.

Equilibrium binding of carcinogens and antitumor antibiotics to DNA: site selectivity, cooperativity, allosterism

The equilibrium binding of the carcinogens N-hydroxy-N-acetyl-2-amino-fluorene (HAAF) and 4-nitroquinoline-1-oxide (NQO) to phi X174RF DNA have been studied by phase partition techniques. Both molecules bind in a cooperative manner with only a few carcinogen molecules binding to each phi X174RF DNA molecule. The binding data for both HAAF and NQO fit a model in which two carcinogens cluster into a small number of sites--four sites for HAAF and twelve sites for NQO. Phase partition techniques were also used to study the binding of actinomycin D to both calf thymus DNA and poly (dG-dC) . poly (dG-dC) at much lower r values than had been previously reported. These data exhibit humped Scatchard plots which are indicative of cooperative binding; the overall shape of the Scatchard plots are consistent with a model for drug induced allosteric transitions in the DNA structure. The cooperativity in the actinomycin D binding to calf thymus DNA increases with decreasing sodium chloride concentration, suggesting a role for DNA flexibility in allosteric binding.

Solution structural studies of the Ag(I)-DNA complex

We report equilibrium dialysis and electric dichroism studies of the two strong complexes (I and II) of silver ion with DNA. Cooperative conversion of DNA to the stronger type I complex results in a 9% length decrease, and a structure in which intercalated ethidium is perpendicular to the helix axis. Upon addition of more Ag+ to form the type II complex, the DNA length reverts to its original value and bound ethidium once again becomes tilted from the plane perpendicular to the helix axis. In both type I and type II Ag (I) - DNA complexes, ethidium binding is mildly cooperative. We interpret the results in terms of a sequence of silver-induced cooperative switches of DNA from its B-form structure with propeller twisted base pairs to a structure with flat base pairs in the type I complex, and back again to propellered base pairs in the type II complex.