Differential fluorescent staining of human chromosomes with daunomycin and adriamycin--the d-bands

Evaluation of Compound Optical Interference in High-Content Screening

Compound optical interference remains an inherent problem in chemical screening and has been well documented for biochemical assays and less so for automated microscopy-based assays. It has also been the assumption that the latter should not suffer from such interference because of the washing steps involved in the process, thus eliminating the residual nonspecific compound effects. Instead, these compounds may have no relevance to the actual target, and as such, compound optical interference contributes to a number of false-positives, resulting in a high attrition rate during subsequent follow-up studies. In this report, we analyze the outcome of a high-content screen using enhanced green fluorescent protein as a reporter in a gain-of-function cell-based assay in search of modulators of the micro RNA (miRNA) biogenesis pathway. Using a previously validated image-based biosensor, we screened a diverse library collection of ~315,000 compounds covering natural and synthetic derivatives in which 1130 positives were identified to enhance green fluorescence expression. Lateral confirmation and dose-response studies revealed that all of these compounds were the result of optical interference and not specific inhibition of miRNA biogenesis. Here, we highlight the chemical classes that are susceptible to compound optical interference and discuss their implications in automated microscopy-based assays.

Anthracyclines induce double-strand DNA breaks at active gene promoters

Doxorubicin is a widely used chemotherapeutic drug that intercalates between DNA base-pairs and poisons Topoisomerase II, although the mechanistic basis for cell killing remains speculative. Doxorubicin and related anthracycline compounds have been shown to increase nucleosome turnover and/or eviction around promoters, which suggests that the resulting enhanced exposure of DNA might underlie cell killing. Previously, we showed that low doses of anthracyclines increase nucleosome turnover around active gene promoters, which suggests that loss of nucleosomes might contribute to cancer cell killing. Here we apply a genome-wide method to precisely map DNA double-strand breaks (DSBs) in cancer cells. We find that spontaneous DSBs occur preferentially around promoters of active genes, and that both anthracyclines and etoposide, a Topoisomerase II poison, increase DSBs around promoters, although CpG islands are conspicuously protected from DSBs. We propose that torsion-based enhancement of nucleosome turnover by anthracyclines exposes promoter DNA, ultimately causing DSBs around promoters.

Microscopical and spectroscopic studies on the fluorescence of a daunomycin-aluminum complex

In this study, the spectroscopic features and microscopical applications of the fluorescent daunomycin-Al3+ complex have been analyzed. In the presence of Al3+, the absorption spectrum of daunomycin showed a deep bathochromic shift and new peaks at 529 and 566 nm, whereas the fluorescence emission was considerably modified. The emission of daunomycin alone (peak at 560 nm under optimal excitation at 470 nm) decreased continuously from 0.5 to 24h after addition of Al3+ ions, and a new emission peak appeared at 580 nm (optimal excitation at 530 nm). Under the fluorescence microscope using green exciting light, nuclei from chicken blood smears and paraffin sections of rat embryos stained with daunomycin showed a weak emission, which greatly increased after treatment with Al3+ ions. The bright and stable fluorescence of chromatin DNA induced by daunomycin-Al3+ could be a valuable labelling method in fluorescence microscopy and DNA cytochemistry.

Establishment of a human leukemia subline resistant to the growth-inhibitory effect of 12-O-tetradecanoylphorbol 13-acetate (TPA) and showing non-P-glycoprotein-mediated multi-drug resistance

We have previously reported that K562/ADM, a typical P-glycoprotein-mediated multi-drug-resistant cell line, is cross-resistant to the growth-inhibitory effect of 12-O-tetradecanoylphorbol 13-acetate (TPA) and non-TPA type tumor promoters. To elucidate the mechanism of cross-resistance to tumor promoters in K562/ADM, we have established a K562 subline resistant to TPA-induced growth inhibition by exposing K562 cells to N-methyl-N'-nitro-N-nitrosoguanidine for 24 hr followed by continuous exposure to TPA. A K562 subline resistant to the TPA-induced growth inhibition, termed K562/TPA, was selected by a limiting dilution technique. K562/TPA was more than 500-fold resistant to TPA compared with parental K562 cells. K562/TPA showed cross-resistance to etoposide, teniposide, adriamycin (ADM), vincristine, vindesine and 3-[(4-amino-2-methyl-5-pyrimidinyl)] methyl-1-(2-chloroethyl)-1-nitrosourea, but showed collateral sensitivity to cisplatin. Although K562/ADM was not cross-resistant to 3'-deamino-3'-morpholino-13-deoxo-10-hydroxycarminomycin (MX2), an anthracycline derivative, K562/TPA was cross-resistant to MX2. By Northern blot analysis, K562/TPA did not express MDR-1. Accumulation of ADM by K562/TPA was no lower than that of K562 although that of K562/ADM was 5-fold lower than K562. We examined the subcellular distribution of ADM by fluorescence microscopy. The fluorescence of ADM was located in the nucleus of K562 and mainly in the cytoplasm of K562/TPA and K562/ADM. The distribution of ADM in K562/TPA, however, was different from that in K562/ADM. These results suggested that K562/TPA had a non-P-glycoprotein-mediated multi-drug-resistance phenotype and that the mechanism of drug-resistance in this cell line might be explained by an alteration in the intracellular drug distribution.

Banding of unfixed mitotic chromosomes in suspension after release from human lymphocytes and fibroblasts

Combined application during chromosome isolation of the non- or weakly fluorescent DNA-intercalators 4'-aminomethyl-4,5',8-trimethylpsoralen and daunomycin as stabilizers of mitotic chromosome structure, and the non-intercalating DNA-binding fluorochromes DAPI and D287 /170 as producers of a visible banding pattern, resulted in clearly banded unfixed floating chromosomes. Chromosomes stabilized by intercalation appeared to be sufficiently stable to allow the reproduction of distamycin A/DAPI or netropsin/DAPI staining in suspension, thus highlighting specific heterochromatic regions on the floating chromosomes. The results of this study demonstrate that the inducibility of bands is an inherent characteristic of mitotic chromosome organization. Possible practical applications of these results in flow cytometry are discussed.

The mechanism of action of quinone antibiotics

The review describes recent studies designed to elucidate the molecular mechanism of action of certain quinone antibiotics which exhibit or have potential for clinical treatment of malignant diseases. Although a large number of quinone antibiotics has been described the review will concentrate on four types, the anthracyclines, the mitomycins, streptonigrin, and the saframycin antibiotics because of their biological significance and because the understanding of their underlying modes of action is perhaps more advanced than in the case of other antibiotics. It will be evident that although the antibiotics bear a common quinone moiety this does not confer a commonality of mechanism. Indeed the variety and precision of the different chemical lesions induced by quinone antibiotics on nucleic acids, their principal cell targets, is remarkable. The particular lesions identified include (i) equilibrium binding, (ii) "permanent' single covalent attachment, (iii) reversible covalent binding, (iv) metal ion sequestration and subsequent DNA binding, (v) DNA groove and base specific binding, (v) interstrand cross-linking, (vi) intercalation with concomitant supercoil relaxation and duplex extension, (viii) redox cycling with production of reactive oxygen species and DNA single strand breaks, and (viii) single strand breaks as a result of phosphotriester formation. In many cases the chemical mechanisms involved in these individual processes may be elucidated in in vitro experiments on purified DNAs by the application of ethidium binding assays in conjunction with certain cellular repair enzymes and utilizing techniques including high field nuclear magnetic resonance and electron paramagnetic resonance spectroscopy. The data obtained in this way complement and extend information from cell culture and in vivo experiments. A coherent description of the multiple cellular effects of these reactive agents is emerging. Such reactions involve bioreductive activation of the quinone the subsequent course of which is precisely controlled by structural and stereochemical factors within the individual antibiotic. The concomitant chemical reactions on cellular macromolecules are beginning to be related to pharmacological properties including in the case of the anthracyclines, a plausible rationale for the molecular origin of the dose limiting cardiotoxicity.

Interaction of anthracyclines with DNA and chromosomes

Daunomycin and adriamycin were previously found to produce Q-like banding patterns on chromosomes. The interaction of several anthracyclines with both natural and synthetic DNAs and chromosomes has been investigated in more detail. Daunomycin fluorescence is almost completely quenched by natural DNAs with varying base composition from 31 to 72% G-C and by the alternating polymer poly-d(G-C).poly-d(G-C). In contrast, daunomycin fluorescence is quenched by only 50% when the dye interacts with synthetic A-T polymers. Thus, differential quenching of daunomycin fluorescence can account for the production of bright bands at contiguous A-T sequences along the chromosome. Slight differences in fluorescence quenching between the repeating and homopolymeric A-T duplex DNAs were observed which can be attributed to differences in affinity of daunomycin for these DNAs. The aminosugar moiety of daunomycin, daunosamine, increases the binding of daunomycin to DNA and also enhances chromosome banding.--Nogalamycin, which displays no differential quenching with the different DNAs in solution, also fails to produce bands on chromosomes.--These findings suggest that non-random nucleotide sequence arrangements along the chromosome are a basic determinant for dye interaction to produce the observed banding patterns. Specific banding procedures may determine the accessibility of these sites within the chromosomal DNA.

Daunomycin-bands are similar to Q-bands on chromosomes of Vicia faba

Lin et al.2 discovered fluorescent bands on human chromosomes stained with daunomycin (D-bands). These bands looked like Q-bands. We demonstrate D-bands, which look like respective Q-bands, in Vicia faba and infer that the similarity between D and Q banding is general.

Mithramycin and DIPI: a pair of fluorochromes specific for GC-and AT-rich DNA respectively

The AT specificity of the fluorochromes DIPI and DAPI and the GC specificity of mithramycin are evidenced by observations in human, mouse, and bovine chromosomes. DIPI and DAPI produce a pattern similar to Hoechst 33258 in all three species, whereas mithramycin results in a reverse pattern. The AT-rich centromeric heterochromatin in mouse is brilliantly stained by DIPI or DAPI and remains nearly invisible after mithramycin staining. In the GC-rich centromeric heterochromatin of cattle the opposite behavior is observed.

DIPI and DAPI: fluorescence banding with only negliglible fading

DIPI and DAPI produce distinct fluorescent bands in human chromosomes similar to quinacrine banding patterns. Additionally, the AT rich secondary constrictions in the chromosomes Nos. 1, 9 and 16 are brightly fluorescent. On the other hand the brilliantly fluorescent regions after staining with quinacrine mustard in the chromosomes Nos. 3 and 4, satellites and some other regions in the acrocentric chromosomes are less striking. The distal part of the Y, however, is clearly discernible. Thus DIPI and DAPI seem to be strictly AT specific fluorochromes like Hoechst 33258. In interphase nuclei the Y chromosome can be identified. However, quinacrines are superior for Y-body analysis in buccal, hair cell and sperm smears. BrdU labeled chromatids show reduced fluorescence intensity. The difference, however, is less apparent than after staining with Hoechst 33 258. DAPI and especially DIPI are highly resistant to UV-irradiation; there is almost no fading within 30 min when using DIPI. Moreover, fluorescence intensity is stronger than in quinicrines. When photographing, exposure times may be reduced to about one quarter compared to quinacrine mustard.

Base specificity in the inhibition of oncornavirus reverse transcriptase and cellular nucleic acid polymerases by antitumor drugs

Adriamycin, daunomycin, acridylmethanesulfonanilide, and alkoxybenzophenanthridine alkaloids (coralyne acetosulfate, fagaronine chloride, and nitidine chloride) inhibit template-directed nucleic acid polymerizing enzyme activities like reverse transcriptase, DNA polymerase, and RNA polymerase. Enzyme reactions with poly(dA-dT), poly(rA)-oligo(dT) and poly(dA)-oligo(dT) are more strongly inhibited by the drugs than those with poly(dC)-poly(dG) and poly(rC)-oligo(dG). These results suggest that the antitumor drugs inhibit nucleic acid polymerases by a specific interaction with A:T base pairs of the templates.

Reverse banding on chromosomes produced by a guanosine-cytosine specific DNA binding antibiotic: olivomycin

Characteristic reverse fluorescent banding patterns (R bands) on human, bovine, and mouse metaphase chromosomes are produced by treating chromosome preparations directly with olivomycin. With the DNA in solution, the repeating polymer poly[d(G-C)] - poly[d((G-C)] (where G is guanine and C is cytosine) enhanced the fluorescence of olivomycin, while the antibotic fluorescence was not affected by the alternating polynucleotide poly]d(A-T)] - poly[d(A-T)] (where A is adenine and T is thymine). Calf thymus DNA, with an intermediate G-C content of about 40 percent, showed a smaller fluorescence enhancement in the presence of olivomycin as was observed for the synthetic polynucleotide poly[d(G-C)] - poly [d(G-C)]. The closely related antibiotic chromomycin A3 showed the same results as were obtained with olivomycin either in the solution interaction with specific DNA's or with the netaphase chromosome preparations. The production of R bands by these G-C-specific DNA binding antibiotics lends credence to the suggestion that the arrangement of the nucleotide sequences along the chromosome is a primary determinant for the appearance of fluorescent bands.

Reverse fluorescent chromosome banding with chromomycin and DAPI

Two DNA binding guanine-specific antibiotics, chromomycin A3 (CMA) and the closely related mithramycin (MM), were used as chromosome fluorescent dyes. Root-tip metaphase chromosomes of three plant species and human metaphase chromosomes were sequentially stained with CMA or MM and the DNA binding AT-specific fluorochrome 4'-6-diamidino-2-phenylindole (DAPI). In some cases a non-fluorescent counterstain was used as contrasting agent: methyl green in conjunction with CMA, and actinomycin D (AMD) in combination with DAPI.--In all three plant species, Vicia faba, Scilla siberica, and Ornithogalum caudatum, the nucleolus organiser regions and/or associated heterochromatin displayed very bright fluorescence with CMA and MM and, in general, heterochromatic segments (C-bands) which were bright with CMA and MM were pale with DAPI whereas segments which were dim with CMA and MM displayed very bright fluorescence with DAPI.--Human metaphase chromosomes showed a small longitudinal differentiation in CMA fluorescence, which was essentially the reverse of the banding pattern obtained with AMD/DAPI double-staining, but of lower contrast. The cma-banding pattern appears to be similar to the pattern found by R-banding procedures.

Mechanisms of chromosome banding. IX. Are variations in DNA base composition adequate to account for quinacrine, Hoechst 33258 and daunomycin banding?

Prior studies on subfractions of mouse and Kangaroo rat DNA have suggested that variations in base concentration within a given genome may not be great enough to account for Q-banding. To examine this with another species, calf DNA was subfractionated by CsCl ultracentrifugation into GC-rich satellites and the main band DNA was further fractionated into AT-rich, intermediate and GC-rich portions. The effect of varying concentrations of these DNAs on quinacrine and Hoechst 33258 fluorescence was examined. Although with both compounds there was less fluorescence in the presence of the GC-rich satellites than main band fractions, these results per se did not answer the question of whether the variation in base composition alone was adequate to account for chromosome banding. To answer this the fluorescence observed in the presence of DNA of a given base composition was related to the fluorescence observed in the presence of DNA of 40% GC content (F/F40). This allowed the derivation of a term B which indicated the relative change in fluorescence per 1% change in base composition of DNA. To determine the percent change in fluorescence observed in Q-banding, the photoelectric recordings of Caspersson et al. (1971) were used. From these data we conclude: 1. Quinacrine is twice as sensitive to changes in base composition as Hoechst 33258. 2. Variation in the base content of DNA along the base content of DNA along the chromosome is sufficient to account for most Q-banding, except possibly for some of the extremes of quinacrine fluorescence. This was further examined with daunomycin. Even though daunomycin gives good fluorescent banding, DNAs varying in base composition from 100 to 40% GC content all resulted in the same relative fluorescence of 0.03. However, in the presence of poly (dA-dT) the relative fluorescence was 0.85, indicating a great sensitivity to very AT-rich DNA. This suggests that with daunomycin and possibly other fluorochromes, stretches of very AT-rich DNA may be more important in fluorescent banding than simple variation in mean base composition.

Rapid nuclear staining method for Saccharomyces cerevisiae

Mithramycin was used to stain nuclei in mitotically dividing and sporulating yeast.