Kinetic studies of drug-dinucleotide complexes

Photoaffinity approaches to determining the sequence selectivities of DNA-small molecule interactions: actinomycin D and ethidium

The DNA photoaffinity ligands, 7-azidoactinomycin D and 8-azidoethidium, form DNA adducts that cause chain cleavage upon treatment with piperidine. Chemical DNA sequencing techniques were used to detect covalent binding. The relative preferences for modifications of all possible sites defined by a base pair step (e.g. GC) were determined within all quartet contexts such as (IGCJ). These preferences are described in terms of 'effective site occupations', which express the ability of a ligand to covalently modify some base in the binding site. Ideally, the effective site occupations measured for photoaffinity agents can also be related to site-specific, non-covalent association constants of the ligand. The sites most reactive with 7-azidoactinomycin D were those preferred for non-covalent binding of unsubstituted actinomycin D. GC sites were most reactive, but next-nearest neighbors exerted significant influences on reactivity. GC sites in 5'-(pyrimidine)GC(purine)-3' contexts, particularly TGCA, were most reactive, while reactivity was strongly suppressed for GC sites with a 5'-flanking G, or a 3'-flanking C. High reactivities were also observed for bases in the first (5') GG steps in TGGT, TGGG and TGGGT sequences recently shown to bind actinomycin D with high affinity. Pyrimidine-3',5'-purine steps and GG steps flanked by a T were most preferred by 8-azidoethidium, in agreement with the behavior of unsubstituted ethidium. The good correspondence between expected and observed covalent binding preferences of these two azide analogs demonstrates that photoaffinity labeling can identify highly preferred sites of non-covalent DNA binding by small molecules.

Cooperative interactions in the binding of ethidium ion to the self-complementary ribodinucleoside monophosphates CpG and GpC

Complexes exhibiting the characteristics of cooperative interactions are formed by ethidium ion and the self-complementary dinucleoside monophosphates CpG and GpC. Complex formation, observed with an ethidium ion selective electrode, can be described by an equilibrium binding model in which complexes are formed with dinucleoside:ethidium combining ratios of 2:1, 2:2, and 2:3. The total amount of ethidium bound in 2:2 and 2:3 complexes, as calculated from the model, is proportional to a circular dichroism band in CpG-ethidium spectra near 305 nm. Van't Hoff analysis of the model equilibrium constants reveals that the addition of ethidium ion to the 2:1 and 2:2 species is exothermic and that the corresponding entropy changes are large and negative. Cooperative interactions in the binding of ethidium ion and of other ligands to some natural and synthetic polymeric nucleic acids have now been observed in several laboratories, but the present work shows that the effect can arise even with nucleic acid fragments as small as dinucleosides. Apparently, a macromolecular nucleic acid is not essential for cooperative interactions.

Ethidium cooperativity in the formation of complexes with CpG

The formation of complexes between the self-complementary ribo-dinucleoside monophosphate CpG and ethidium ion is observed by use of an ethidium ion selective electrode. The ratio of total CpG to total ethidium was varied from 50:1 to .4:1, with CpG concentrations ranging from 0.2 to 1.1 mM. Scatchard plots show that the system is strongly cooperative with respect to ethidium ion; cooperativity with respect to dinucleoside has been previously reported (Krugh, T.R., Wittlin, F.N., and Cramer, S.P. (1975) Biopolymers 14,197-210). Cooperative behavior with respect to ethidium ion implies the existence of complexes containing at least two molecules of ethidium ion in combination with one or more CpG molecules.

Microcalorimetric investigation of the binding of some chemotherapeutic agents and related molecules to calf thymus DNA

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.

Aqueous solution structure of an intercalated actinomycin D-dATGCAT complex by two-dimensional and one-dimensional proton NMR

Two-dimensional NOESY and COSY 1H NMR techniques have been employed to determine the conformation of the complex formed by actinomycin D and the hexanucleoside pentaphosphate dATGCAT. One-dimensional NOE experiments in H2O confirmed the intact nature of the oligonucleotide double helix within the complex. The drug chromophore was intercalated between the GC base pairs, with the pentapeptide lactones nestled in the minor groove. No significant conformational change of the pentapeptide lactones between bound and free drug was observed.

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.

Calorimetric and spectroscopic investigation of drug--DNA interactions: II. Dipyrandium binding to poly d(AT)

We report the first calorimetric investigation of steroid diamine binding to a DNA duplex. Absorption spectroscopy, batch calorimetry, and differential scanning calorimetry (DSC) have been used to detect, monitor, and thermodynamically characterize the binding of the steroid diamine, dipyrandium, to poly d(AT). The following thermodynamic data for the binding in 16 mM Na+ at 25 degrees C have been obtained: delta G degree = -6.5 kcal/mol, delta H degree = +4.2 kcal/mol, and delta S = +36 e.u. We interpret the endothermic binding enthalpy in terms of steroid-induced conformational changes in the duplex (e.g. "kinking"). The large positive entropy is interpreted in terms of binding-induced release of bound water and condensed sodium ions. The salt-dependence of the binding constant is interpreted in terms of dipyrandium site-binding involving only one of the two charged ends of the steroid. The optical and DSC curves for the unsaturated steroid-poly d(AT) complexes exhibit biphasic behavior. A comparison of the van't Hoff and the calorimetric transition enthalpies reveals that steroid binding reduces the cooperativity of the transition.

Comparative binding of ethidium and three azido analogs to dinucleotides: affinity and intercalation geometry. A 1H NMR and visible spectroscopy study

Geometrical and thermodynamic information has been obtained from theoretical analysis of both visible and 1H-NMR spectroscopic binding isotherms of ethidium and three photoactivable derivatives (8-azido-ethidium, 3-azido-ethidium and 3,8-diazido-ethidium) to self-complementary ribodinucleosides. The following results have been obtained. 1. Interaction with pyrimidine(3-5')purine sequences is well accounted for by multicomponent equilibria involving self-association of the dyes in oligomers, formation of 1:1 and 2:1 (nucleoside:dye) complexes. This model provided evidence for intercalation of all dyes, though with weaker affinity in the case of diazido-ethidium (2 X 10(6) M-2 vs 6 X 10(7) M-2). Moreover 3-azido-ethidium was shown to intercalate into cytidylyl(3'-5')guanosine (CpG) with its phenyl group lying in the major groove of the minihelix. This geometry is inverted with respect to that of all other compounds. It should be emphasized that visible and 1H-NMR techniques independently provided similar results (intercalation, affinity constants) therefore supporting this stepwise model. 2. Interaction of all dyes with purine(3'-5')pyrimidine sequences is not intercalative, even at low temperature (4 degrees C), but is well described by self-association of the dyes and formation of 1:1 (nucleoside:dye) complexes. Regarding the reversible DNA intercalation process, these studies show that 8-azido-ethidium is the only photoactivatable derivative which behaves exactly as ethidium. Therefore 8-azido-ethidium can be used as a covalent probe to investigate the DNA-related cytotoxic effects of ethidium.

Binding of ethidium bromide to self-complementary deoxydinucleotides

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.

Role of actinomycin pentapeptides in actinomycin-deoxyribonucleic acid binding and kinetics

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.

Competitive binding studies of compounds that interact with DNA utilizing fluorescence polarization

The increase in the fluorescence polarization of acridine orange upon binding to DNA molecules is used as the basis of a competitive method to study the interaction of a variety of fluorescent and non-fluorescent compounds with DNA. Test compounds that interact with DNA inhibit both the binding of acridine orange to DNA and the accompanying increase in fluorescence polarization. Actinomycin D exhibits a dose-dependent inhibition of acridine orange-DNA binding with Micrococcus luteus DNA, calf thymus DNA, and poly(dG-dC); no detectable inhibition of acridine orange intercalation into poly(dA-dT) is observed. In contrast, proflavine shows similar acridine orange inhibition for poly(dA-dT), calf thymus DNA and M. luteus DNA.

Selective repression of transcription by base sequence specific synthetic polymers

We report the effect of novel synthetic polymers on deoxyribonucleic acid (DNA) directed ribonucleic acid (RNA) synthesis in vitro. Polymers contained base-selective monomers, including a GC-specific phenazine derivative and an AT-specific triphenylmethane dye. Radical chain polymerization was carried out in aqueous solution by using monomers bound to a template DNA, which was obtained from either lambda or T7 bacteriophage. Polymers were isolated and reannealed with DNA samples, including competitive mixtures of T7 and lambda DNAs. We measured transcription from DNA-polymer complexes by using Escherichia coli RNA polymerase and determined not only the reduction in total transcription levels but also the relative inhibition of lambda- or T7-specific transcription by using a hybridization assay. The results show that micromolar concentrations of individual dyes are sufficient to cause substantial inhibition of transcription when the dyes are incorporated into polymers. More significantly, a number of the polymers inhibited more strongly transcription from the DNA which had served as template for polymer synthesis than from the DNA present as competitor in the annealing process. We conclude that template synthesis of DNA-binding polymers can lead to preferential inhibition of function of the original template. The apparent relative affinity of polymer for competing DNAs can be altered by at least an order of magnitude depending on which DNA was used as the synthesis template. The results offer a new approach to improving the specificity of DNA-binding drugs.

Structure of mutagen nucleic acid complexes in solution. Proton chemical shifts in 9-aminoacridine complexes with dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT

The influence of self-complementary oligodeoxynucleotides on the chemical shifts of protons of the mutagenic acridine dye 9-aminoacridine has been measured. Upfield shifts indicative of intercalative binding are found in the cases of dG-dC, dC-dG, and dA-dT-dG-dC-dA-dT but not in dA-dT. Geometries for the complexes that are compatibile with the chemical-shift data and the X-ray structure of the complex between ri5C-rG and 9-aminoacridine determined by Sakore et al. [Sakore, T.D., Jain, S.C., Tsai, C., and Sobell, H.M. (1977), Proc. Natl. Acad. Sci. U.S.A. 74, 188--192] can be identified using recent theoretical estimates of shifts induced by nucleotide bases.