The interaction of 7-substituted actinomycin D analogs with DNA

DNA Binding Hydroxyl Radical Probes

The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA.

Actinomycin D binding to unstructured, single-stranded DNA

Actinomycin D is an anticancer antibiotic best know for inhibiting transcription by binding double-stranded DNA. Tight, sequence selective binding of actinomycin to single-stranded DNA is also known, however, and is implicated in biological activities including inhibition of (-) strand transfer by HIV reverse transcriptase. Oligonucleotide d(GTTAACCATAG) is one of the rare single-stranded DNAs that lack GC steps yet have high affinity for actinomycin. Oligonucleotide sequence and length requirements for drug binding were investigated by monitoring association of the fluorescent surrogate, 7-aminoactinomycin D, to d(GTTAACCATAG) and 31 related oligomers. The TAG-3' terminal sequence was essential for high-affinity binding, but was not sufficient. Five oligomers with TAG sequences on or near the 3'-end had high affinity [K(d) < or = 200 nM (oligomer)]. A sixth oligomer, d(GTAACCATATG), had moderately lower affinity (Kd = 370 nM), and other homologous oligomers had much lower affinity. The minimum length sequence for tight binding of 7-aminoactinomycin D was identified as only eight nucleotides, corresponding to d(AACCATAG). This octanucleotide is unstructured in the absence of actinomycin, and has the highest drug affinity of all oligomers examined (Kd = 125 nM). These studies show that high-affinity binding of 7-aminoactinomycin, and actinomycin D by extension, to single-stranded DNA does not require pre-existing secondary structure or any apparent propensity for secondary structure. It is proposed that actinomycin D binds to certain single-stranded DNA sequences by an induced-fit mechanism favored by participation of at least eight nucleotides, or the equivalent of four base pairs.

High affinity binding of 7-aminoactinomycin D and 4',6-diamidino-2-phenylindole to human neutrophilic granulocytes and lymphocytes

The binding behavior of the DNA binding dyes 7-aminoactinomycin D (7-AAMD) and 4',6-diamidino-2-phenylindole (DAPI) to human neutrophilic granulocytes and lymphocytes was studied by image cytofluorometry. Peripheral blood leukocytes were prefixed in paraformaldehyde (PFA) and attached to cover glasses. Different fixation, permeabilization, and acid extraction method were applied before the cells were stained to equilibrium using varying concentrations of 7-AAMD or DAPI. The apparent association constant and number of high affinity dye binding sites were estimated for the different cell types, dyes, and treatments. Acid-extracted cells, supposedly containing nucleosome-free DNA, were chosen to represent maximal dye binding. Only about 10% of the 7-AAMD binding sites remained in the unextracted PFA-fixed cells, and the apparent dye affinity was also reduced. We found no major difference in high affinity binding between the cell types, but granulocytes showed more fluorescence from less specifically bound 7-AAMD compared to lymphocytes. DAPI had a much higher affinity than 7-AAMD, independent of the preparation method. It showed a cooperative binding behavior with an apparent saturation of the high affinity binding sites at a dye concentration of about 50 nM. We conclude that both dyes may be useful as probes for chromatin structure in intact cells and that our new technique may contribute to such studies since it allows determination of dye affinities and numbers of high affinity binding sites in situ.

Equilibrium binding of DAPI and 7-aminoactinomycin D to chromatin of cultured cells

The binding of 4',6-diamidino-2-phenylindole (DAPI) and 7-aminoactinomycin D (7-AAMD) to chromatin of intact cultured fibroblast nuclei was studied by cytofluorometry. Staining was performed at equilibrium at varying dye concentrations. By using large volumes of dye solutions, the free dye concentration became approximately equal to total dye concentration, and the estimation of affinity and number of binding sites was performed by Scatchard analysis. Since all Scatchard plots showed a definite curvature, indicating more than one class of binding sites, a two component regression was performed, although only the highest affinity binding sites were determined. The observed affinity constants did not change substantially between different preparational procedures for any of the dyes. The number of DAPI binding sites increased about 30% after detergent extraction. No such increase was observed for 7-AAMD. Fixation in formaldehyde, instead of ethanol, after detergent extraction had no effect on DAPI binding, but decreased the number of 7-AAMD binding sites with about 50%. Extraction of basic proteins with HCl resulted in about 100% increase of the number of binding sites for both dyes. It should be feasible to use this technique as an assay for the identification of proteins or other nuclear components important for the maintenance of chromatin structure.

Application of 7-amino-actinomycin D for the fluorescence microscopical analysis of DNA in cells and polytene chromosomes

The cytochemical properties of a guanine-specific synthetic fluorescent analogue of actinomycin D, 7-amino-actinomycin D, have been studied in fixed and living preparations of L cells and polytene chromosomes of salivary glands of Chironomus thummi thummi and Drosophila lummei (Hackman). 7-Amino-actinomycin D has been shown to bind to DNA-containing structures, thereby inducing in them a bright red fluorescence. No specific fluorescence has been found in RNA-containing structures treated with this fluorescent probe. The fluorescence pattern of some regions of polytene chromosomes with a known nucleotide composition was analysed. It has been established that 7-amino-actinomycin D induces a very weak fluorescence in GC-poor chromosome regions of the Drosophila lummei toromere structure. Data indicating a nonlinear dependence between the fluorescence intensity of a stained chromosome region and the GC content in its DNA have been obtained. The influence of DNA nucleotide composition in a chromosome region on the fluorescence of 7-amino-actinomycin D is discussed. In combination with quinacrine staining and the Feulgen fluorescence reaction, treatment with 7-amino-actinomycin D provides useful information about the distribution of GC base pairs in the chromosome region under study.

Comparison of prometaphase chromosome techniques with emphasis on the role of colcemid

Six different techniques were evaluated to define better those technical factors that are most critical for obtaining prometaphase cells for banding analysis. Our results demonstrate: colcemid exposures of 30 min or less have no effect on increasing the yield of prometaphase cells, colcemid exposures of greater than 0.1 microgram/ml can be toxic, methotrexate depresses the mitotic index significantly and seems to increase the incidence of prometaphase cells only because it suppresses later forms; and (d) the optimum number of cytogenetically satisfactory prometaphase cells can be obtained with a 4-h exposure to a combination of low concentration actinomycin D (0.5 microgram/ml) and colcemid (0.1 microgram/ml). This technique inhibits chromosome condensation while permitting prometaphase cells to accumulate for 4 h.

DNA-binding specificity and RNA polymerase inhibitory activity of bis(aminoalkyl)anthraquinones and bis(methylthio)vinylquinolinium iodides

The determination of DNA-binding specificities for a series of bis(methylthio)vinylquinolinium iodides and two bis (aminoalkyl)-anthraquinones was accomplished by spectral analysis, equilibrium dialysis, elevation of melting temperature, and inhibition of DNA function as a template for Escherichia coli RNA-polymerase transcription activity in vitro. Studies of complex formation were carried out by comparison of difference spectra of the compounds in the presence of native double-stranded DNA and separated-strand DNA. Base specificity of the interaction between DNA and the compounds was demonstrated for both series, particularly for the anthraquinones, for the guanine-cytosine base pair. Comparison of the difference spectra of the compounds in the presence of DNA with varied base-pair ratios showed a strong preference of the anthraquinones for the guanine-cytosine base pair, but the quinolinium compounds showed no preference. The linear-binding isotherm for the quinolinium compounds indicated one type of binding site, while two types of binding sites were apparent for the anthraquinones. Since only one anthraquinone was active in leukemia tests, factors other than DNA binding must account for the activity of the antileukemic derivative.

Raman excitation profiles of actinomycin D

Pre-resonance Raman spectra of actinomycin D have been measured using the exciting lines of an Ar+ laser. The analysis of the excitation profiles provided information on the origin of the electronic states; in particular, the absorption feature between 400 and 500 nm was interpreted as due to a vibrational structure of a single electronic state which is located at 450 nm. In addition, on the basis of the excitation profiles, the number of observed Raman bands, and their frequencies, it has been possible to propose a vibrational assignment of the chromophoric framework of the drug.

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.