Effect of Distamycin A on the template activity of DNA in a DNA polymerase system

Linked lexitropsins and the in vitro inhibition of HIV-1 reverse transcriptase RNA-directed DNA polymerization: a novel induced-fit of 3,5 m-pyridyl bisdistamycin to enzyme-associated template-primer

Five classic DNA minor groove-binding drugs and a series of bis-linked lexitropsins based on netropsin and distamycin have been screened for their effectiveness in inhibiting transcription by HIV-1 reverse transcriptase (RT) on a poly(rA).oligo(dT) template-primer (TP). The two most effective drugs, 3,5 m-pyridyl-linked bisdistamycin (MPyr) and trans-vinyl-linked bisdistamycin (TVin), show (1) enhanced inhibition in reactions initiated with pre-incubated enzyme template-primer (ETP) and (2) reduced affinity for a "free" TP analog, when compared with the parent drug distamycin. All three drugs lack the ability to inhibit processive incorporation of nucleotide, suggesting drug intervention instead at initiation or termination of processive cycles. The two bis-linked drugs exhibit different kinetic behavior with reverse transcriptase's two substrates: template-primer and nucleotide. When primer is the variable substrate, TVin is partially noncompetitive and MPyr is dead-end competitive (Ki = 6.5 microM). With nucleotide as substrate, TVin is noncompetitive at low drug concentrations and MPyr is uncompetitive. Gel band mobility shift assays with MPyr indicate that the drug inhibits via entrapment of TP on the enzyme rather than displacement of TP from the enzyme surface. The conformation of nucleic acid is most likely altered upon MPyr binding, enhancing the induced fit of enzyme to hybrid duplex. The relevance of this novel mode of inhibition is considered in relation to enzyme association/dissociation with TP that occurs prior to (-)-DNA strand transfer, and to the structural implications of an enzyme-bound hybrid RNA/DNA nucleic acid.

Aspects of specific DNA-protein interaction; local bending of DNA molecules by in-register binding of the oligopeptide antibiotic distamycin

Distamycin A binds strongly/moderately to DNA below/above r = 0.08 molecules bound per DNA phosphate. Titration viscometric measurements for high and low molecular weight DNA yielded the relative changes of DNA persistence length, delta alpha/alpha 0, and contour length, delta L/L0 (Nucl. Acids Res. 7 (1979) 1375). delta L/L0 is negligible/positive in the range below/above r = 0.09 at 0.2 M Na+! A two-line covering of the small groove by ligand molecules explains the increase of contour length. The characteristic delta alpha/alpha 0 drop is quantitatively interpreted by local DNA bending (kinking). The underlying theoretical basis is presented in two appendices and applied, in a third one, to literature data for the DNA-actinomycin system. The angle gamma of local DNA bending as induced by complex formation with different distamycin derivatives is presented for DNA species of different base composition. By means of appropriate model, a length mismatch per dinucleotide of (0.03(2) +/- 0.01)nm [or (0.04(3) +/- 0.01)nm] was derived from the experimentally obtained bending angle per dinucleotide of (1.6 +/- 0.4)0 [or (2.1 +/- 0.05)0], independent of DNA base composition and distamycin chain length.

Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin

The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuation of ligand interaction the enzyme cuts along regions containing dG-dC pairs sandwiched between dA-dT pairs. This follows a slow kinetics and is associated with a release of netropsin from those segments. These facts suggests the usefulness of the partial protection of certain DNA sequences in DNAase I cleavage sites in producing DNA fragments in structural studies of the genome. A possible interpretation of the effect of netropsin binding on the enzymatic hydrolysis of phosphodiester bonds of the helix is discussed.

Magnetic circular dichroism study of the binding of netropsin and distamycin A with DNA

The magnetic circular dichroism (MCD) of netropsin and distamycin-A is reported. New data for the interaction with dA ; dT base pairs in DNA were obtained from the MCD of their complexes with DNA duplex polymers. The MCD results allow an interpretation of the induced Cotton effects in the natural CD spectra of netropsin and distamycin-A complexes with DNA. While large distortions of the bases in DNA by the oligopeptide interaction is excluded, some subtle conformational variations of the DNA might explain the inhibition of the enzyme function of netropsin and distamycin-A on DNA.

Thermal denaturation of distamycin A--DNA complexes as followed by hyperchromic spectra

Interaction of distamycin A with calf spleen DNA is investigated by the method of hyperchromic spectra. Hyperchromic spectra of complexes are partitioned into the components corresponding to the denaturation A . T and G . C base pairs and dissociation of the ligand, fractions of respective components are found as a function of temperature. A scheme of melting of successive regions of DNA with different G+C content together with the scheme of distamycin A redistribution in the course of thermal denaturation is presented.

Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides

The specific interaction of distamycin A and analogs with DNA's and synthetic deoxypolynucleotide duplexes were studied in detail by means of circular dichroism and the data were analyzed together with viscosity results of several natural DNA's. At low ligand to nucleotide ratio the previously reported specific binding to (A-T) pairs of DNA is verified by a highly favoured interaction with (A-T)-enriched segments of distamycins containing four and five methylpyrrole carboxamide units. At higher distamycin concentration a second specific binding to (G-C) pairs most probably through hydrogen bonding is established. Viscometric results suggest a distamycin-induced local bending of the helix and could support the idea of a preferential alignment of the ligand molecule along only one strand in the groove which differs from the netropsin interaction mechanism. The possibility of an overlapping binding of the oligopeptides in the small groove is discussed.

The isolation and properties of a DNA-directed RNA polymerase from yeast mitochondria

A method is described for the rapid isolation of yeast mitochondrial DNA-directed RNA polymerase. The enzyme obtained had a specific activity of 1.56 nmol UMP incorporated per mg protein in 20 min at 37 degrees C, and is some 95% pure. This purified enzyme upon polyacrylamide gel elctrophoresis consists of a single polypeptide of 68 000 mol. wt. However, the enzyme forms aggregates easily which are affected by ionic strength, an increase decreasing the apparent molecular weight of the aggregates. This property also explains the presence of two peaks of activity upon DEAE-cellulose chromatography. The purified enzyme is still sensitive to rifamycin and to a number of rifamycin derivatives. The enzyme's sensitivity to rifamycin and rifamycin derivatives was compared with Escherichia coli and yeast nuclear RNA polymerases.

(dA-dT) dependent inactivation of the DNA template properties by interaction with netropsin and distamycin A

The inhibitory effect of the polypeptide antibiotics netropsin and distamycin A on DNA dependent nucleic acid synthesis has been shown to be related to the base composition of the template DNA. A number of natural DNA's of quite different dA-dT content as well as poly (dI-dC)-poly (dI-dC), poly (dA-dT)-poly (dA-dT), poly (dA) - poly (dT) and poly (dG) - poly (dC) has been studied as templates in DNA and in part in RNA polymerase reaction. The highest binding efficiency of netropsin existing for (dA-dT) - containing DNA polymers and the less pronounced interaction with the (dI-dC)-containing polymer shown by the melting and CD spectrral behaviour of the complexes are entirely reflected in the template inactivation. The same is evident for distamycin A. However, in contrast to netropsin the antibiotic distamycin A exhibits some binding tendency to poly (dG) - poly (dC). Binding effects of a netropsin derivative to DNA and (dA-dT) -containing polymers suggest the importance of hydrogen bonds of the peptide groups in the complex formation.

Effect of distamycin A on the primary and secondary immune response of mouse spleen cells in vitro against sheep erythrocytes

The effect of distamycin A (DMC) on the primary and secondary immune response of mouse spleen cells, cultured in vitro in the presence of sheep erythrocytes as an antigen, was studied. It was found that the primary response was extremely sensitive to DMC during the first 24 hrs of culture and then gradually became more and more resistant to the immunosuppressive effect of the drug. Right from the start of culture, however, the secondary response was much more resistant than the primary one to the inhibitory action of DMC. These results could not be reproduced by treating the cultures with inhibitors of DNA-dependent DNA synthesis (such as cytosine arabinoside) or inhibitors of DNA-DEPENDENT RNA synthesis (such as actinomycin D).

Congocidine and distamycin A, antipoxvirus antibiotics

The antibiotics congocidine and distamycin A inhibited the replication of Shope fibroma and vaccinia viruses in BSC(1) cells. Treatment of infected cultures with congocidine for a 12-hr period resulted in an irreversible inhibitory effect on virus development. A longer period of treatment with the antibiotic also resulted in inhibition of the residual infectious virions present in the treated cells. Distamycin A inhibited the replication of poxviruses, but its inhibitory effect was reversed when the antibiotic was removed from the infected cells even as long as 24 hr after treatment. The inhibitory effect of distamycin A and its reversibility resembled the antipoxvirus activity of rifampin.

Optical rotatory dispersion properties of nucleic acid complexes with the oligopeptide antibiotics distamycin A and netropsin

ORD measurements of nucleic acids in the presence of the oligopeptides netropsin and distamycin A have indicated association of the antibiotics with DNA and strong conformational changes of the DNA structure with specificity to AT-rich helical regions. The RNA conformation is relatively unaffected by these antibiotics. The results are explained in terms of a perturbation of the DNA secondary structure as well as of the chromophore system of the oligopeptides.

Effect of distamycin a on the structure and template activity of DNA in RNA - polymerase system

It is shown that native and denatured DNA form complexes with the oligopeptide-antibiotic distamycin A. The pronounced inhibition of the incorporation of AMP into RNA in the DNA directed RNA-polymerase system is due to the interference of the antibiotic with DNA.