Studies of the binding of actinomycin and related compounds to DNA

Transmission of allosteric effects in DNA

Binding of distamycin induces a cooperative transition of calf thymus DNA to a new form with higher affinity for the drug and altered structural properties.

Comparative cytotoxic and antitumoral effects of ellipticine derivatives on mouse L 1210 leukemia

Twelve derivatives of the antitumoral alkaloid ellipticine (E) and ellipticinium were assayed in vitro on cultured L 1210 cells. These drugs possess varying abilities to decrease the cell growth rate in a 1--1000-fold range. Some of them have a highly cytotoxic effect in the 10(-8)--10(-6) M range. Non-specific intracellular damages are produced: multilobation of nuclei, occurrence of numerous lipid granules, diminution of the size and increase in the number of mitochondrial profiles and several modifications of the internal architecture of mitochondria. 2-Methyl-9-hydroxyellipticinium (2-CH3-9-OHE) was submitted to a bioassay; it inactivates the tumorigenic potency of the cells exposed to it, when they are grafted back into mice in the same dose range which reduces in vitro the growth rate of the cells. A fairly good correlation holds between the in vitro and in vivo (antitumor effect) assays, offering a possible prescreening test for a cheaper and rapid evaluation of chemotherapeutic activity of these compounds. The results stress again the importance of the 9-hydroxy substitution in these series for improving the anticancer efficiency. The nature of the biochemical target of E and derivatives is discussed according to our data.

Phenazines with two cationic side chains as potential antimalarials

1,9-Phenazine-bis(dialkylaminocarboxamides) were prepared for screening as potential antimalarials. No significant activity against Plasmodium berghei was observed. The phenazine targets were prepared from 1,9-phenazinedicarboxylic acid by standard methods. The reaction between 1,9-phenazinedicarboxylic acid and thionyl chloride in the presence of dimethylformamide unexpectedly gave 4-chloro-1,9-phenazinedicarbonyl chloride.

Interaction of phenosafranine with nucleic acids and model polyphosphates. III. Heterogeneity in phenosafranine interactions with DNA base pairs

Fluorescence and circular dichroism spectral measurements, thermal denaturation studies and binding competition experiments with netropsin and actinomycin D were carried out in systems containing phenosafranine bound to DNA's differing in base composition. The investigated properties exhibit a heterogeneity related to the content of A.T and G.C pairs in DNA and to the nature of phenosafranine binding modes. At low level of saturation of binding sites (r less than 0.1) phenosafranine does not show strong preference for any of the DNA base pairs in the overall binding. However, the strong monomer non-cooperative binding outside the helix (mode I1) occurs predominantly, even though not exclusively in G.C rich regions. The strong binding modes involving intercalated dye molecules (mode I2 and eventually mode II1) prevail in A.T rich regions. These binding modes become the principal types of strong phenosafranine interaction with DNA when the level of saturation of binding sites increases, i.e. at r greater than 0.1.20

Characterization of ellipticine binding to native calf thymus DNA

The binding of [14C]ellipticine to native calf thymus DNA was studied using equilibrium dialysis. A Scatchard polt revealed the presence of high-and low-affinity binding sites in DNA, the former having a K of 4.0 X 10(7) M(-1) and an n (saturation limiting of binding) of 0.078 (1mol ellipticine/13 mol of DNA nucleotides). The forces involved in stabilizing the high-affinity binding, which has been equated with intercalative binding, were due to a combination of hydrophobic interactions and hydrogen bonding. Difference spectra of ellipticine in the presence of the polydeoxynucleotides, poly d(A-T) or poly d(G-C), showed that there was no base specificity involved in the high-affinity binding. Ellipticine binding to the low-affinity sites, which has been equated with surface binding, was due primarily to the participation of electrostatic interactions of ellipticine with the anionic phosphate groups on the double helical surface of DNA.

The interaction of 7-substituted actinomycin D analogs with DNA

The interaction of actinomycin D and three new 7-substituted analogs with calf thymus DNA has been studied by a number of physical techniques. The methods utilized in this investigation include visible absorption spectrometry and ultrafiltration methodology for the determination of equilibrium binding constants; viscometry; and circular dichroism. The studies show that the 7-substituted actinomycin D analogs retain the G . C base pair specific DNA binding demonstrated by actinomycin D. The mode of binding to native DNA, despite substitution at position 7, is practically unaltered. The retention of this binding specificity by these analogs seems to be unaffected by changes in the electon properties of the chromophore.

Anthracycline antitumor antibiotic nucleic-acid interactions. Structural aspects of the daunomycin poly(dA-dT) complex in solution

The helix-to-coil transition of the synthetic DNA poly(dA-dT) in the presence of the anthracycline antitumor antibiotic daunomycin has been investigated by high-resolution proton nuclear magnetic resonance (NMR) spectrocopy in 1 M salt solution. The dissociation of the complex, containing molar ratios of phosphate to daunomycin (Pi/drug) of 50, 25, 9 and 5, with increasing temperature can be monitored independently at the nucleic acid and the antibiotic resonances under conditions of fast exchange. The antibiotic complex formation shifts suggest that either ring B and/or C of the intercalated anthracycline chromophore of daunomycin overlaps with adjacent nucleic acid base pairs. Ultraviolet/visible melting studies of daunomycin complexes with a series of synthetic DNAs substituted with halogen atoms (Br, I) at position 5 of the pyrimidine ring suggest that intercalation of the antibiotic into poly(dA-dU) is not perturbed by bulky substituents at this position. A comparison of the melting curves for the daunomycin . poly(dA-dT) complex with an analog of the antibiotic where the NH3 + group is replaced by dimethylglycine demonstrates the important contributions of electrostatic interactions between the amino sugar and backbone phosphates to the stability of the complex in low salt solution. The ultraviolet/visible and NMR studies monitor biphasic melting transitions at the nucleic acid markers in the daunomycin . poly(dA-dT) complexes, Pi/drug = 50--9, so that antibiotic-free base-pair regions and those centered about bound daunomycin can be independently studied at the synthetic DNA level in solution.

The use of base pair specific DNA binding agents as affinity labels for the study of mammalian chromosomes

The fluorochromes Hoechst 33258 and olivomycin are base pair specific DNA binding agents. The fluorescence enhancement of Hoechst 33258 and olivomycin in the presence of DNA can be directly related to the A--T and G--C content of the interacting DNA respectively. Cytological observations of metaphase chromosomes treated with these two compounds suggest that the fluorescent banding patterns produced are the reverse of one another.--Non-fluorescent base pair specific DNA binding agents have been used as counterstains in chromosome preparations to enhance the contrast of the banding patterns produced by the base specific fluorochromes. The non-fluorescent G--C specific antibiotic actinomycin-D enhanced the resolution of fluorescent bands produced by the A--T specific fluorochrome Hoechst 33258. Similarly the non-fluorescent A--T specific antibiotic netropsin was found to enhance resolution of the bands produced by the G--C -specific fluorochrome olivomycin. Netropsin was also found to increase the differential fluorescent enhancement of complexes of olivomycin with DNAs of various base composition in solution. These findings suggest that counterstaining agents act through a base sequence dependent inhibition of subsequent binding by base pair specific fluorochromes.--The base specific DNA binding agents have been used to differentiate different types of constitutive heterochromatin in mammalian species, and to facilitate chromosome identification in somatic cell hybrids.

Ultraviolet resonance Raman study of DNA and of its interaction with actinomycin D

The DNA-Actinomycin D interaction has been studied by resonance Raman effect using DNA as chromophore. First, the resonance Raman spectra of DNA obtained with a U.V. excitation at wavelengths of 300 nm and 280 nm are presented. The main Raman hands are assigned to the convenient nucleic bases by comparison with the spectra of mononucleotides obtained under the same experimental conditions. In particular, with a 300 nm excitation, the 1582 cm-1 line is provided by adenine, while the 1492 cm-1 one is almost exclusively due to guanine. Then, the DNA-Actinomycin D complex has been studied: the line enhancements and the specificity of the resonance permits the displaying of the DNA spectrum free of any contribution of Actinomycin. The interaction provides a large intensity decrease of the 1492 cm-1 guanine line: this is a direct consequence of the orbital overlapping of the guanine 2-aminogroup with the ring nitrogen of Actinomycin in the DNA-Actinomycin pi complex.

3h-actinomycin-D binding to mitotic chromosomes of Drosophila melanogaster

The binding of 3H-AMD to the metaphase chromosomes of Drosophila melanogaster has been analyzed after two different periods of exposure to photographic emulsion. The entirely heterochromatic Y chromosome was markedly less labelled than euchromatin and other heterochromatic regions. Moreover, the few grains present on the Y chromosome were clustered in two regions, one localized in the middle Ys and the other in the proximal third of YL. This labelling pattern is not affected by removing histones with a 2-hour treatment with 2N HCl. It is suggested that the specific underlabelling of the Y chromosome reflects a peculiar AT richness.

Binding of 3-aminoacridinium and 7-aminoquinolinium monocations to double-stranded DNA: evidence for nonlinear binding isotherm in intercalative region

The complexations of the singly charged cations of 3-aminoacridine and 7-aminoquinoline by double-stranded, calf thymus DNA were studied by electronic absorption spectrophotometry. At high ratios of total DNA phosphate concentration to total probe concentration (the region associated with intercalative binding), four DNA phosphate units are associated with each bound monocation. However, a binding isotherm based on four DNA phosphate groups in a single binding site does not yield a reproducible equilibrium constant for the binding process. Rather, the sequestration of the monocations by two binding sites, each containing two DNA phosphate units, yields a satisfactory equilibrium expression. This result suggests that the intercalative mode of binding by DNA is not a simple one-step process, which is in agreement with previous kinetic studies. In the region of low DNA phosphate concentration to monocation concentration (the external binding region), the binding is described adequately by a linear isotherm.

Influence of 4'-6'-diamidino-2-phenylindole on the secondary structure and template activities of DNA and polydeoxynucleotides

The interaction between 4'-6-Diamidino-2-Phenylindole-hydrochloride (DAPI) and a variety of DNAs and synthetic polydeoxynucleotides was investigated in order to delineate the nucleic acid structural features necessary for binding. The spectra of DAPI-DNA complexes, measured at various DAPI:DNA molar ratios (r), are hypochromic relative to DNA in the region of its maximum absorption. All the curves pass through an isosbestic point at 268 nm. A new maxima appears in the region of 380-392 nm for DAPI-DNA COMplexes. The magnitude of the peaks in the region are directly proportional to the amount of drug present in the complex. Studies with various DNA types and synthetic polydeoxynucleotides indicate that the drug preferentially binds to dAT-rich regions of DNA. This was also confirmed by enzymatic studies. The inhibition of template action by DAPI in a purified DNA-polymerase reaction was dependent on the dAT-content of the template. The implication of these data to explain a selective binding of DAPI to mitochondrial DNA have been discussed.

Structural transition in chromatin induced by ions in solution

Structural transition in chromatin was measured as a function of counter ions in solution (NaCl or MgCl(2)) and of histones bound on the DNA. The addition of counter ions to aqueous solutions of chromatin, partially dehistonized chromatin, and DNA caused a drastic reduction in viscosity and a significant increase in sedimentation coefficient. Transitions occurred primarily at about 2 x 10(-3) M NaCl and 1 x 10(-5) M MgCl(2) and are interpreted as a change in structure of chromatin induced by tight binding of cations (Na(+) or Mg(++)) to DNA, either free or bound by histones, and is an intrinsic property of DNA rather than of the type of histone bound. At a given ionic condition, removal of histone H1 from chromatin had only a minor effect on the hydrodynamic properties of chromatin while removal of other histones caused a drastic change in these properties. An increase in the sedimentation coefficient of DNA was observed also for protamine. DNA complexes wherein the bound protein contains only unordered coil rather than the alpha-helices found in histones.

Stereochemical model for proflavin intercalation in A-DNA

Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA.

Interactions of some nitro-derivatives of substituted 9-aminoacridine with DNA

The mechanism of the biological activity of the 1-nitro and 2-nitro aminoacridine derivatives containing the dimethylaminopropyl side chain was studied. RNA synthesis in the isolated rat liver nuclei was only slightly influenced by both compounds. They do not differ in their ability to form an intercalative complex with DNA. Only the 1-nitro derivative exhibited strong inhibitory effect on RNA biosynthesis and caused distinct ultrastructural changes (nucleolar segregation, chromatine margination etc.) in a living cell. The 1-nitro derivative binds covalently to DNA in vivo resulting in crosslink formation. It is concluded that the biological activity of 1-nitro acridine derivatives depends more on their crosslinking activity than on their ability to intercalate into DNA.

A mechanism for the entrapment of DNA at an air-water interface

Addition of the intercalating dye quinacrine to a low ionic strength solution of DNA in quantities sufficient to saturate the high affinity sites in the DNA will result in the accumulation of the DNA at the solution interface. This entrapment of DNA at the air-water interface has been assayed by the adsorption of DNA to untreated carbon-coated electron microscope grids touched to the solution surface. Other intercalating dyes can also bring about this entrapment, if they possess a side arm large enough to occupy one of the DNA grooves when the dye is intercalated into the DNA. The extension and unwinding of the DNA helix brought about by the intercalating chromophore of the dye molecules are not requirements for the entrapment process. Spermidine, a simple polyamine that will bind to the DNA minor groove but that has no intercalating chromophore, was found to bring about this entrapment. Even simple mono- and divalent cations in the absence of the above ligands were found to promote a low level of surface entrapment. A model for the entrapment of DNA at the air-water interface is proposed in which one (or both) of the hydrophobic grooves of the DNA becomes a surface-active agent as a consequence of the association of various ligands and charge neutralization.

Interaction of acridines and tetrahydroacridines with DNA at low DNA/dye ratios

This study examines certain aspects of the interaction of acridines with DNA. A comparative study of the methods available for the determination of the association constants (Kap) for compounds which interact with DNA has been pursued. A new equation which permits the spectrophotomeric determination of Kap has been derived. This equation can be applied to compounds which upon interaction with a polymer exhibit discrete absorption changes. Application of this equation to substituted acridines and tetrahydroacridines yields some preliminary information on the effect of ring substituents on the interaction of acridines with DNA. Low levels of DNA/dye ratios have been used in the studies reported herein.

The superhelical density of nuclear DNA from human cells

Structures resembling nuclei may be released by gently lysing human cells in solutions containing non-ionic detergents and high concentrations of salt. These structures, which we call nucleoids, sediment in sucrose gradients containing the intercalating agent, actinomycin D, in the manner characteristic of superhelical DNA. We have determined the concentration of actinomycin that minimises the rate of sedimentation of nucleoids. At this concentration, we have determined the amount of drug bound per base pair of DNA by means of a double-labelling procedure. Assuming that each molecule of actinomycin bound to nucleoid DNA unwinds the double helix by 26 degrees, we calculate that there is one supercoil every 90-180 base pairs in nucleoid DNA. These values lie within the range found for the circular DNA molecules of plasmids and viruses.

Fluorescence of actinomycin D and its DNA complex

In order to show that naturally occurring actinomycin D can be used as a fluorescent cytochemical probe, the fluorescence spectra of 50 micronM solution of actinomycin D in several solvents and in its DNA complex are reported. The excitation spectra of both bands observed are compared to the absorption spectrum, and the fluorescence quantum yields is estimated to be 0.65-10(-4), taking rhodamine B as a reference. Strong solvent-induced spectrum modifications are evidenced, interpreted as a solvent shell reorientation about the molecule chromophore in the excited state. The changes in the fluorescence spectrum of actinomycin due to an interaction with DNA (marked blue shift and decreased quantum yield) cannot be interpreted as a solvent effect; they express the properties of the DNA-chromophore eta-complex involving an orbital overlapping of actinomycin and guanine in DNA.

Kinetic studies of drug-dinucleotide complexes

Three classes of kinetic behavior are observed in the complexes of actinomycin or ethidium with deoxydinucleotides. First, the initial dinucleotide binding to form a 1:1 complex is a rapid bimolecular process, whose rate could be measured for combination of actinomycin with d(pTpG) d(pGpT), d(pGpA), d(pGpG) d(pCpGpG), and d(pCpG) andfor combination of ethidium with d(pGpC). Second, with one exception, all reactions in which a second dinucleotide is added to form a 2:1 dinucleotide-drug complex are limited by a first-order step at high concentration. This class includes the combination of actinomycin with all dinucleotides tested except d(pGpC), and the reaction of ethidium with nucleotides of complementary sequence pyrimidine-purine, such as d(pCpG). The final class is the special case of d(pGpC) interacting to form a 2:1 complex with actinomycin. Third-order kinetics is observed, with no evidence for a first-order, rate-limiting step.

Daunorubicin inhibition of DNA-dependent RNA polymerases from Ehrlich ascites tumor cells

Two different forms of DNA-dependent RNA polymerase have been solubilized and purified from nuclei of Ehrlich ascites tumor cells. The purification procedure involves ammonium sulfate precipitation and gel filtration on Sephadex G-25. The separation of A and B activities is achieved by chromatography on DEAE-cellulose. Nuclei are prepared from cells, sensitive or resistant to daunorubicin. RNA polymerases A and B have an absolute requirement of divalent cations for activity. Native DNAs are better templates than heat-denatured DNAs for RNA polymerase A. On the contrary heat-denatured DNA is more transcribed than the native one by RNA polymerase B. The low level of transcription of total and nucleolar ascites DNAs is due to the DNA, the same results being obtained with ascites and calf thymus RNA polymerases A and B. The inhibitory action of daunorubicin on RNA polymerases A and B from Ehrlich ascites tumor cells has been studied in vitro. The same results are obtained with enzymes extracted from sensitive or resistant cells. Daunorubicin does not inhibit the binding of RNA polymerases to the DNA template, but prevents the transformation of the DNA-daunorubicin-RNA-polymerase unstable complex into the highly stable one. This inactive ternary complex has a dissociation rate faster than the stable complex formed without daunorubicin. The size of the RNA synthesized in the presence or absence of daunorubicin is the same.

Binding isotherms and the interaction between proflavin and a DNA of high G-C content

Binding isotherms corresponding to several situations of ligand binding to a linear polymer are calculated, including cases of cooperativity or anticooperativity between the bound ligand states, multiple binding modes that are competitive or non competitive, and possible exclusive of an arbitrary number of adjacent sites upon occupancy of a site by a single ligand. The sequence generating function method of Lifson and Bradley is used, requiring the assumption that no end effects are involved. The case of strong binding of the dye proflavin to a DNA of high G-C content, that of M. lysodeikticus, is considered in detail, and a single model capable of reconciling the available kinetic and equilibrium data on this system, involving two competing binding modes, is discussed.

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.