Altered physiochemical properties of the deoxyribonucleic acid-mitomycin C complex. Evidence for the conformational change in deoxyribonucleic acid

Binding of the antibiotic mitomycin C to sonicated calf thymus DNA results in increased viscosity and an unaltered sedimentation constant of DNA. Flow dichroism measurements of the mitomycin C-DNA complex indicate that the 310-nm absorbance vector of the chromophore of the bound drug is oriented at approximately 57.2 degrees relative to the helix axis. A conclusion drawn from these results is that mitomycin C does not intercalate between base pairs, but rather, it is bound in one of the grooves. Binding of mitomycin C causes a number of changes which are DNA size dependent: (1) increased viscosity of sonicated, decreased viscosity of nonsonicate DNA; (2) unaltered sedimentation rate of sonicated, increased rate of nonsonicated DNA; (3) reduced electrophoretic mobility of nonsonicated DNA; (4) electron microscopic appearance of sonicated DNA-mitomycin complexes which is similar to that of control, while nonsonicated DNA complexes which display highly coiled, looped structures not seen in control nonsonicated DNA. These size-dependent effects are interpreted as indicative of conformational distortion of DNA at rare intervals, caused by a minor fraction of total bound mitomycin. The parallel used of sonicated and nonsonicated DNA as probes for certain effects of drug binding may be useful for detecting this type of phenomenon in general.     

Calcium and cadmium binding to troponin C. Evidence for cooperativity

Proton NMR is used to compare the structural changes induced in bovine cardiac troponin C on binding of cadmium and calcium ions. The same spectral changes are observed for both ion species. The rate of the conformational changes associated with cadmium binding to the two high-affinity sites is slow, that associated with cadmium ions binding to the low-affinity site is high. 113Cd-NMR spectra of cardiac troponin C feature two signals interpreted as due to cadmium ions bound to the strong sites. Strong arguments are given in favour of cooperativity in binding of the first two cadmium or calcium ions to cardiac and skeletal muscle troponin C.     

Evidence for the reversible binding of paraquat to deoxyribonucleic acid

Evidence for the reversible binding of paraquat to calf thymus DNA has been obtained using equilibrium dialysis and thermal melting point determinations. The data indicated the presence of at least two populations of binding site with affinity constants of 6.2 X 10(4) and 7.1 X 10(3) M-1, respectively. The binding capacities of DNA for paraquat were 66 and 480 nmol/mumol DNA nucleotide, respectively, and were equivalent to one ligand bound per 2 DNA phosphate groups. Putrescine inhibited paraquat binding to the low affinity sites without altering binding to the high affinity sites. Scatchard plots of paraquat binding characteristics indicated the presence of positive cooperativity between the compound and DNA. Thermal melting curves of DNA in the presence of paraquat and the endogenous amines putrescine, spermidine and spermine, provided evidence that paraquat cross-linked to DNA with a similar affinity as spermidine. The thermal melting point data also suggested the presence of positive cooperativity between ligand and macromolecule that possibly resulted from a conformation change in the structure of the DNA molecule. Paraquat competitively inhibited the binding of ethidium bromide to DNA and this effect was reversed by Na+. From the data, it is suggested that paraquat binds primarily to the negatively charged phosphates on the DNA backbone but is displaced into the interbase region occupied by the intercalator ethidium bromide. DNA binding of paraquat may, in part, account for its weak mutagenic activity.     

Cobalt-bleomycin-deoxyribonucleic acid system. Evidence of deoxyribonucleic acid bound superoxo and mu-peroxo cobalt-bleomycin complexes

Co(II) interacts with bleomycin in aqueous solution, in the presence of air, to give a short-lived mononuclear superoxo Co(III) complex (I). Then, two molecules of complex I react together, with the loss of oxygen, to yield the dinuclear mu-peroxo Co(III) complex (II); the dimerization follows a second-order rate law with k2 = 200 +/- 50 M-1 s-1 at 25 degrees C. The rate of dimerization is lowered by a factor of 2000 when DNA is present at a molar ratio of [nucleotide]/[Co] higher than 16. These results and studies of circular dichroism and electron paramagnetic resonance spectra of complexes strongly suggest the binding of the superoxo complex to DNA (I') as well as that of the mu-peroxo complex (II'); the binding of 1 molecule of complex II for every 2.9 base pairs in DNA has been determined with an apparent equilibrium constant of 8.4 x 10(4) M-1.     

Accelerated dissociation of estrogen receptor--ligand complexes by estradiol. Evidence for negative cooperativity of binding

The rate of dissociation of 17β-[³H]estradiol that had been previously equilibrated to a low degree of saturation of immature rat uterine cytoplasmic estrogen receptor was shown to increase over 40-fold in the presence of additional ligand. This effect was specific for either labeled or unlabeled estradiol, was observed under conditions in which the rebinding of dissociated ligand was shown not to occur, was distinguishable from the activation of cytoplasmic receptor, and was dependent upon the degree of saturation of the receptor by ligand. It occurred under conditions in which the receptor population was apparently uniform and stable and utilized an assay method that is particularly sensitive to low concentrations of cytosol protein. Once saturation of the receptor attained 15% of the available ligand binding sites, further increases of the dissociation rate of receptor-ligand complex could not be produced by the inclusion of additional estradiol. It was shown that exchange of ligand molecules in given binding sites was unlikely. Rather, support was given to the hypothesis that interactions were occurring between separate binding sites in the receptor population. The decrease of the apparent affinity of receptor for ligand when the fractional saturation of receptor increases has been defined as negative cooperativity. It is proposed that this phenomenon may be significant in the regulation of the response of target cells to estrogens.     

The binding of echinomycin to deoxyribonucleic acid.

Echinomycin is a peptide antibiotic which binds strongly to double-helical DNA up to a limit of approximately one molecule per five base-pairs. There is no detectable interaction with rRNA and only extremely feeble non-specific interaction with poly(rA)-poly(rU). Heat denaturation of DNA greatly decreases the binding, and similarly limited interaction is observed with naturally occurring single-stranded DNA. Association constants for binding to nine double-helical DNA species from different sources are presented; they vary by a factor of approximately 10, but are not simply related to the gross base composition. The interaction with DNA is ionic-strength-dependent, the binding constant falling by a factor of 4 when the ionic strength is raised from 0.01 to 0.10mol/litre. From the effect of temperature on the association constant for calf thymus DNA, the enthalpy of interaction is calculated to be about -13kJ/mol (-3kcal/mol). Binding of echinomycin persists in CsCl gradients and the buoyant density of nicked bacteriophage PM2 DNA is decreased by 25 mg/ml. Echinomycin interacts strongly with certain synthetic poly-deoxynucleotides, the binding constant decreasing in the order poly(dG)-poly(dC) greater than poly(dG-dC) greater than poly(dA-dT). For the latter two polymers the number of base-pairs occluded per bound antibiotic molecule is calculated to be three, whereas for poly(dG)-poly(dC) it is estimated to be four to five. Poly(dA)-poly(dT) and poly(dI)-poly(dC) interact only very weakly with the antibiotic. Poly(dI-dC) interacts to a slightly greater extent, but the binding curve is quite unlike that seen with the three strongly binding synthetic polynucleotides. Echinomycin affects the supercoiling of closed circular duplex bacteriophage PM2 DNA in the characteristic fashion of intercalating drugs. At low ionic strength the unwinding angle is almost twice that of ethidium. Likewise the extension of the helix, determined from changes in the viscosity of rod-like sonicated DNA fragments, is nearly double that expected for a simple (monofunctional) intercalation process. On this basis the interaction process is characterized as bifunctional intercalation. At higher ionic strength the unwinding angle relative to that of ethidium and the helix extension per bound echinomycin molecule fall, indicating a smooth progression towards more nearly monofunctional intercalation. Two simpler compounds which act as analogues of the quinoxaline chromophores of echinomycin, quinoxaline-2-carboxamide and the trypanocidal drug Bayer 7602, interact with DNA very much more weakly than does echinomycin, showing that the peptide portion of the antibiotic plays an essential role in determining the strength and specificity of the interaction.     

10-Formyltetrahydrofolate synthetase. Evidence for a conformational change in the enzyme upon binding of tetrahydropteroylpolyglutamates

The 10-formyltetrahydrofolate synthetase domain of the trifunctional enzyme C1-tetrahydrofolate synthase appears to undergo a conformational change in the presence of tetrahydropteroylpolyglutamates, MgATP, and ammonium ion. The binding of these ligands increases the denaturation temperature of the enzyme by 12 degrees C, abolishes the cold lability of the enzyme, and alters its susceptibility to digestion by chymotrypsin. The results suggest that a conformational change is dependent upon binding of the third glutamate residue of tetrahydropteroylpolyglutamates and the beta-phosphoryl group of MgATP. The Km values for MgATP and formate are lowered 3.6- and 520-fold, respectively, when tetrahydropteroyltriglutamate is used as the substrate in place of tetrahydropteroylmonoglutamate. A sensitive coupled assay involving C1-tetrahydrofolate synthase and serine hydroxymethyltransferase was developed to determine the activity of 10-formyltetrahydrofolate synthetase. The assay gives linear rates with the tetrahydropteroylpolyglutamates as substrates but not with the monoglutamate form.     

The binding of o-aminoazotoluene to deoxyribonucleic acid, ribonucleic acid and protein in the C57 mouse

1. (3)H-labelled o-aminoazotoluene was synthesized from [G-(3)H]o-toluidine on a semi-micro scale. 2. An association of (3)H with DNA, RNA and protein from the liver, kidney and spleen of female C57b mice was demonstrated after the administration of a single dose of [(3)H]o-aminoazotoluene. 3. This association is judged to represent covalent binding as a result of experiments involving solvent extraction, examination of the acid hydrolysates of the DNA and RNA and administration of [(3)H]water with unlabelled o-aminoazotoluene. 4. Examination of the extents of binding at various times after the administration of a single dose of [(3)H]o-aminoazotoluene showed that there was a peak of binding to liver DNA in the female mice at about 16hr. that was not present in the male mice. 5. The extent of binding to DNA, RNA and protein at 16hr. in the female C57b mouse liver was greater than that in the spleen and kidney.     

Platinum-pyrimidine complexes for electron microscopic cytochemistry of deoxyribonucleic acid.

Platinum-pyrimidine complexes that are amorphous and highly soluble in water when used as sole electron-dense stains show high selectivity for nucleic acid-rich areas like chromatin, nucleolus and ribosomes. A method is presented for the selective staining of deoxyribonucleic acid. Glutaraldehyde-fixed tissue are exposed to 3 N HCL hydrolysis for an optimum time of 1 hr at room temperature before being embedded in Epon. Thin sections are then exposed to Schiff's reagent for 30 min and treated with 1% platinum-pyrimidine complex. The results inselective staining of structures containing deoxyribonucleic acid.     

Variation in the inhibition of restriction enzyme cleavage of lambda phage DNA produced by two covalent binding antitumor agents: Anthramycin and mitomycin C

DNA-drug complexes containing various levels of covalently bound mitomycin C (MC) or anthramycin were subjected to the actions of a number of restriction enzymes. While MC presented only a partial block to the actions of a number of these enzymes, anthramycin, at high binding ratios, blocked enzymatic activity very well. The contrast seen in the restriction cleavage of these DNA-drug complexes may be related to the different points of attachment in DNA (minor groove vs. major groove) for these drugs. Although similarities in electrophoretic band patterns exist for both drug complexes, certain differences are indicative of preferences in binding sequences that these drugs may have for DNA. The results show that these sequences do not necessarily lie immediately within the restriction cut sites but may effect the cutting of these sites from a distance. The results also further support anthramycin's potential usage as a selective/reversible blocking agent for recombinant research.     

The compatibility of netropsin and actinomycin binding to natural deoxyribonucleic acid.

The simultaneous binding of netropsin and actinomycin to four natural DNAs was studied to determine the influence of one ligand on the binding of the other. Actinomycin binds specifically to GC sites, whereas netropsin binds specifically to AT sites. Spectral titrations, thermal denaturation, and analytical buoyant density centrifugation were employed to measure the binding interference of these drugs. The binding of actinomycin to DNA was decreased by the presence of netropsin. Increasing the GC content of the DNA resulted in a decreased effect of netropsin on actinomycin binding. Quantitative analysis of the binding parameters indicated that netropsin and actinomycin can bind in close proximity along the DNA chain. Supercoiled DNA gave the same result as linear DNA. These results imply that DNA can absorb alterations in conformation within a short distance.