Studies on the binding of actinomycin D to DNA and DNA model polymers

Energy transfer and binding competition between dyes used to enhance staining differentiation in metaphase chromosomes

The ability of electronic energy transfer and direct binding competition between pairs of dyes to enhance contrast in human or bovine metaphase chromosome staining patterns is illustrated, and the relative effectiveness of these two mechanism compared. The existence of energy transfer between quinacrine or 33258 Hoechst and 7-amino-actinomycin D in doubly stained chromosomes is demonstrated directly by microfluorometry. The ability of the dyes 7-amino-actinomycin D, methyl green, or netropsin, acting as counterstains, to displace quinacrine, 33258 Hoechst, or chromomycin A3 from chromosomes, is estimated by quantitative analysis of energy transfer data, by photobleaching of the counterstains, or by selective removal of counterstains by appropriate synthetic polynucleotides. Effects on the fluorescence of soluble 33258 Hoechst-DNA complexes due to energy transfer or binding displacement, by actinomycin D or netropsin, respectively, are further differentiated by nanosecond fluorescence decay measurements. Examples are presented of dye combinations for which (a) energy transfer is the primary mechanism operative, (b) binding competition exists, with consequences reinforcing those due to energy transfer, or (c) binding competition is the most important interaction. These analyses of mechanisms responsible for contrast enhancement in doubly stained chromosomes are used to derive information about the relationship between chromosome composition and banding patterns.

New studies on the interaction between 8-methoxypsoralen and DNA in vitro

Some aspects of the interactions between DNA and 8-methoxypsoralen (8-MOP) in its ground state (complex formation) or in its excited state (photobinding) have been investigated. 8-MOP shows a low affinity towards DNA in the complex formation; this fact minimizes the possible biological consequences deriving from this interaction, when it occurs in vivo. In covalent photobinding to DNA, 8-MOP forms mainly monofunctional adducts, and to a lesser extent bifunctional adducts, showing a behavior similar to that of other linearly condensed furocoumarins (psoralens); the ratio between mono- and bifunctional adducts was found to be 9:1. The covalent photobinding to DNA does not occur at random along the macromolecule, but preferentially at the level of specific receptor sites. The regions having an alternate sequence of A-T seem to be the best receptor sites for the formation of monoadducts while the regions containing an alternate sequence of A-T and C-G appeared to be the preferential sites for the cross-linkage formation.

Isolation and characterization of an actinomycin D-sensitive mutant of Saccharomyces cerevisiae

A single mutation in Saccharomyces cerevisiae conferred sensitivity to low concentrations of actinomycin D. Treatment with actinomycin D preferentially inhibited synthesis of rRNA's. Residual rRNA synthesized was processed normally. Total protein synthesis and inducibility of the enzyme maltase were relatively unaffected at concentrations of actinomycin D which severely inhibited rRNA synthesis.

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.

The interaction of daunomycin with polydeoxynucleotides

The ability of daunomycin to bind to various DNA polymers has been sutided by thermal denaturation, spectrophotometric analysis and inhibition of the polymerisation reactions catalysed by Escherichia coli DNA polymerase I and rat liver DNA polymerase alpha. The quantitative binding measurements revealed that the antibiotic binds tightly to all synthetic polydeoxynucleotides studied. The results demonstrated that daunomycin can bind with equal affinity to dG . dC or dA . dT basepaired sequences. However, the number of binding sites per nucleotide for poly(dA) . poly(dT) is significantly lower than that found for poly(dA-dT) . poly(dA-dT), thus indicating an appreciable preference of the drug for the alternating copolymer. The inactivation of the template properties of the synthetic DNA polymers in the DNA polymerase system is consistent with their daunomycin binding ability. However, a lack of correlation was observed between the drug binding ability of different DNA polymers and the binding-induced stabilisation of the double helix to heat denaturation.

The interaction of propidium diiodide with self-complementary dinucleoside monophosphates

The interactions of a quinacrine derivative, methylated at both the aromatic and aliphatic nitrogens, and propidium diiodide with the dinucleoside monophosphates CpG, GpC, UpA and ApU have been investigated using 13C-NMR (for the quinacrine derivative prepared with [13C]methyl substituents and 1H-NMR and ultraviolet-visible spectroscopy. The quinacrine derivative displayed negligible interaction with the dinucleosides at concentrations up to 5 - 10(-4) M. Propidium did form complexes with dinucleosides even at concentrations as low as 10(-4) M. Propidium displayed a pyrimidine-purine binding preference and gave especially large changes in ultraviolet-visible and 1H-NMR spectra in the presence of CpG. This suggests that propidium forms an intercalated complex with a Watson-Crick hydrogen-bonded CpG dimer. At higher concentrations UpA and GpC gave similar spectral changes indicating that they could also form significant amounts of an intercalated complex with propidium under appropriate conditions. The changes caused by ApU were small under all conditions and were more similar to the effects caused by mononucleotides. These results indicate that, at least for phenanthridines, cationic side chains do not greatly inhibit complex formation with dinucleoside monophosphates, and suggest that the weak interaction of the quinacrine derivative with dinucleosides is due to weaker interactions of the acridine ring system with nucleoside bases relative to the phenanthridine ring system.

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.

Preparative fractionation of DNA restriction fragments by reversed phase column chromatography

Reversed phase column chromatography on RPC-5 resin was used to fractionate milligram quantities of DNA fragments generated by restriction endonucleases. Fractionation was on the basis of size, the presence or absence of sticky ends, and at least one as yet undertermined property.

RNA synthesis in Yoshida ascites tumor cells after ultraviolet and gamma irradiation

The residual RNA synthesis in Yoshida ascites tumor cells following exposure to ultraviolet radiation was insensitive to rifampicin AF/013, an inhibitor of initiation of RNA synthesis in eukaryotic cells. On the other hand, residual RNA synthesis in the ascites tumor cells after gamma-irradiation was inhibited by rifampicin AF/013. In vitro synthesis of RNA on ultraviolet-irradiated ascites chromatin likewise was resistant to rifampicin AF/013. Ultraviolet irradiation was found to decrease the number of RNA chain initiation sites on ascites chromatin considerably whereas the number of initiation sites on ascites chromatin increased considerably after gamma irradiation. These results indicate that ultraviolet irradiation may preferentially affect the DNA segments participating in initiation of RNA synthesis.

Diacridines: bifunctional intercalators. III. Definition of the general site of action

Electron microscopy of HeLa cells exposed to spermine diacridine shows nucleolar distortions which disappear after several days despite the persistence of the metabolic changes promoted by spermine diacridine. This compound inhibits ribosomal RNA synthesis and appears to act independently of any particular phase of the cell cycle. The DNA content of the HeLa cells remains unchanged and the cell distribution is not significantly disturbed from its normal distribution in the various phases of the cell cycle. Spermine diacridine and other diacridines inhibit primarily chain initiation but also chain elongation by DNA-directed RNA polymerase of Azotobacter vinelandii.

Spectrophotometric studies on the binding with polynucleotides of 4,4'-diacetyldiphenylurea-bis(guanylhydrazone) and methylglyoxal-bis(guanylhydrazone)

4,4'-Diacetyldiphenylurea-bis(guanylhydrazone) (DDUG), an agent very effective against several animal leukemias and tumors, was found, spectrophotometrically, to interact in a biphasic manner with several natural, native and heat-denatured, and synthetic DNAs. The spectrum of DDUG was shifted towards the visible region with a hypochromic shift reaching a maximum hypochromicity at 316 mmu at a 1 : 1 molar ratio of DDUG to DNA nucleotide. Increasing molarity of DNA nucleotide resulted in a further shift towards the visible end, but with hyperchromicity rather than hypochromicity, and reaching its peak at 323 mmu. The interaction with yeast RNA was much weaker than that with DNA. 4,4'-Diacetyldiphenylurea (DDU) did not show any interaction with DNA; its monoguanylhydrazone (DDUM) showed only a hypochromic interaction. In contrast to DDUG, methylglyoxal-bis( guanylhydrazone (CH3-G), an aliphatic bisguanylhydrazone with antileukemic properties, showed only a hypochromic interaction with DNA at low ionic strength. Unlike DDUG, CH3-G was a very weak inhibitor of the DNA polymerase reaction. The hypochromic shift of the DDUG spectrum with DNA was abolished in the presence of 15 mM sodium citrate or 500 mM NaCl but not in the presence of 150 mM NaCl or 100 mM sodium acetate. The hyperchromic shift was abolished in the presence of 8 M urea. From the results obtained with different DNAs, RNA, synthetic polynucleotides and nucleotides, it appears that the total shift of the DDUG spectrum in the presence of intact DNA can not be ascribed to interaction with a single base although a greater shift occurred in the presence of G-C rich DNA.

The interaction of actinomycin C3 and actinomine with DNA. A small-angle x-ray scattering study

Small-angle X-ray scattering was applied to solutions of calf thymus DNA and calf thymus DNA complexed with various amounts of actinomycin C3 or actinomine in phosphate-saline buffer at pH 6.9 and I equals 0.2. From the measurements of DNA in the absence of dye, two cross-section radii of gyration of R-c equals 0.875 plus or minus 0.015 nm and R-c2 equals 0.81 plus or minus 0.02 nm, and a mass per unit length of M/l equals 1906 plus or minus 43 daltons/nm resulted. The investigation of DNA complexed with dye revealed a decrease of the cross-section radii of gyration as compared to those for the DNA in the absence of dye and a relatively low increase of the mass per unit length on binding of actinomycin and a slight decrease of M/l on binding of actinomine. The latter results are interpreted on the basis of a length increase of the DNA double helix by 0.47 plus or minus 0.03 nm per actinomycin molecule and by 0.355 plus or minus 0.03 nm per actinomine molecule bound. The results for R-c and R-c2 obtained for the various samples of complexed DNA were extrapolated to the limiting binding ratio where each dye molecule is associated with a minimum of six nucleotide pairs. According to this extrapolation, the cross-section radii of gyration of such a complex would amount to (R-c)b equals 0.805 plus or minus 0.015 nm and (R-c2)b equals 0.76 plus or minus 0.015 nm for the complex with actinomycin, and to (R-c)b equals 0.77 plus or minus 0.015 nm and (R-c2)b equals 0.75 plus or minus 0.01 nm for the actinomine complex. On the basis of a core and shell model for solvated DNA, these results can be understood as to indicate a decrease of the radial dimensions of both the core and the shell when the dye is bound. The experimental results are compared with theoretical data calculated from the atomic coordinates of the detailed intercalation model for the actinomycin - DNA complex as recently proposed by Sobell and Jain. The model proves to be consistent fairly well with our data on the length increase of the double helix, but it appears to be unable to explain the experimentally observed decrease of R-c2 on binding of dye.

X-ray crystallographic visualization of drug-nucleic acid intercalative binding: structure of an ethidium-dinucleoside monophosphate crystalline complex, Ethidium: 5-iodouridylyl (3'-5') adenosine

We have cocrystallized the drug ethidium bromide with the dinucleoside monophosphate 5-iodouridylyl(3'-5')adenosine and have solved the three-dimensional structure to atomic resolution by x-ray crystallography. This has allowed the direct visualization of intercalative binding by this drug to a fragment of a nucleic acid double helix.