DAPI fluorescence of plant chromosomes prestained with actinomycin D

A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin

Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals. The difficulty in identification of individual chromosomes represents an unresolved problem of this method as the body of the chromosome is stained uniformly and does not have banding pattern beyond C-bands. Here, we present the method that we called CDAG for sequential heterochromatin staining after differential GTG-banding. The method uses G-banding followed by heat denaturation in the presence of formamide with consecutive fluorochrome staining. The new technique is valid for the concurrent revealing of heterochromatin position due to differential banding of chromosomes and heterochromatin composition (AT-/GC-rich) in animal karyotyping.

Uptake, Distribution, and Bioimaging Applications of Aggregation-Induced Emission Saponin Nanoparticles in Arabidopsis thaliana

The application of aggregation-induced emission luminogens (AIEgens) has heralded a new age in the analysis of subcellular events and has overcome many of the limitations of conventional fluorescent probes. Despite the extensive literature investigating AIEgens in mammalian cells, few reports exist of their bioimaging applications in plant cells. In this report, we describe the first systematic investigation of the uptake, distribution, and bioimaging applications of AIEgens and AIE saponin nanoparticles in the plant model system Arabidopsis thaliana. We find that the superior photostability, high colocalization with fluorescent proteins, and unique tissue-specific turn-on emission properties make AIEgens well-suited to tackle the emergent challenges faced in plant bioimaging.

Flow manipulation and cell immobilization for biochemical applications using thermally responsive fluids

A flow redirection and single cell immobilization method in a microfluidic chip is presented. Microheaters generated localized heating and induced poly(N-isopropylacrylamide) phase transition, creating a hydrogel that blocked a channel or immobilized a single cell. The heaters were activated in sets to redirect flow and exchange the fluid in which an immobilized cell was immersed. A yeast cell was immobilized in hydrogel and a 4',6-diamidino-2-phenylindole (DAPI) fluorescent stain was introduced using flow redirection. DAPI diffused through the hydrogel and fluorescently labelled the yeast DNA, demonstrating in situ single cell biochemistry by means of immobilization and fluid exchange.

Cytological and electrophoretic karyotyping of the chestnut blight fungus Cryphonectria parasitica

The karyotypes of nine strains including three transformants of the chestnut blight fungus Cryphonectria parasitica were analyzed by pulsed-field gel electrophoresis (PFGE) and cytology using a fluorescence microscope. Cytology of the mitotic metaphase showed n=9 for both standard strain EP155 and field strain GH2 infected by Cryphonectria hypovirus 3. Chromosomes were morphologically characterized by size, heterochromatic segment, and constriction. PFGE resolved 5 or 6 chromosomal DNA bands ranging from 3.3Mbp to 9.7Mbp, but accurate determination of the chromosome number was hampered by clumping of some bands. Banding profiles in PFGE were similar among the strains except for GH2, in which a chromosome translocation was detected by Southern blot analysis. By integrating the data from cytology and PFGE, the genome size of C. parasitica was estimated to be ca. 50Mbp. This is the first report of a cytological karyotype in the order Diaporthales.

A nanoemulsion formulation of tamoxifen increases its efficacy in a breast cancer cell line

This paper reports on the preparation of a water-soluble nanoemulsion of the highly lipid-soluble drug tamoxifen (TAM). In addition, relative to a suspension of TAM, the nanoemulsion preparation demonstrated a greater zeta potential (increased negative charge) which has previously been associated with increasing drug/membrane permeability. This study also reports that relative to suspensions of TAM with particle sizes greater than 6000 nm, nanoemulsions of TAM, having mean particle sizes of 47 nm, inhibited cell proliferation 20-fold greater and increased cell apoptosis 4-fold greater in the HTB-20 breast cancer cell line. Thus, this work suggests that a nanoemulsion compared to a suspension preparation of TAM increases its anticancer properties relative to breast cancer.

DNA content and genome composition of diploid and triploid water frogs belonging to the Rana esculenta complex (Amphibia, Anura)

The Central European water frog Rana esculenta L., 1758 is a natural hybrid between Rana lessonae Camerano, 1882 (LL) and Rana ridibunda Pallas, 1771 (RR). Hybrids are usually diploid (RL) or triploid (LLR or RRL). Distinguishing LL from RL, RR from RL, and LLR from RRL according to external morphology is ambiguous. In this study we checked whether the DNA content in erythrocyte nuclei measured by image cytometry is useful in determination of the taxonomic status of diploids (LL, RR, and RL) and the genome composition of triploids (LLR and RRL). For exact and direct identification of parental species, as well as for determination of genome composition in hybrids, we applied actinomycin D – 4',6-diamidino-2-phenylindole chromosome staining to metaphase plates. We analyzed 43 LL, 12 RR, and 32 RL diploids, and 37 LLR and 19 RRL triploids. All diploid hybrids had 2n = 26 chromosomes, and all triploid hybrids had 3n = 39 chromosomes. Neither aneuploid nor mosaic hybrids were detected. The expected numbers of 13 R. lessonae (L) and 13 R. ridibunda (R) chromosomes in RL hybrids were recorded in about 31% of individuals. In the rest of the sample the composition was variable, ranging from 9 to 14 R chromosomes and the corresponding number of L chromosomes. The expected composition of 26 L and 13 R chromosomes was detected in about 32% of LLR triploids, whereas in the rest of the sample the composition of chromosomes ranged from 8 to 15 R chromosomes and the corresponding number of L chromosomes. The expected numbers of 26 R and 13 L chromosomes were detected in about 26% of RRL triploids, whereas in the rest of the sample the composition of chromosomes ranged from 19 to 28 R chromosomes and the corresponding number of L chromosomes. The DNA content densitometry showed that RR and RL diploids had 9.5% and 3.8% more DNA, respectively, than LL diploids. These differences, although statistically significant, were not sufficient to unequivocally discriminate LL from RL and RR from RL. Triploids had about 50% more DNA than LL diploids (49% in LLR and 51% in RRL), but these differences were too small for unequivocal determination of their genome composition.

A molecular NAND gate based on Watson-Crick base pairing

[reaction: see text] A DNA-binding dye, 4',6-diamidino-2-phenylindole (DAPI) signals AT base pairing with a shift in the fluorescence emission spectrum. The signaling follows W-C base-pairing rules, and both dAMP and dTMP are required for the largest spectral shift. Thus, the dye with its two phosphate receptor sites functions as a molecular NAND gate accepting nucleotides as inputs. Moreover, when the observation wavelength is changed from 470 to 411.5 nm, the gate functions in TRANSFER logic.

DAPI: a DNA-specific fluorescent probe

DAPI (4',6-diamidino-2-phenylindole) is a DNA-specific probe which forms a fluorescent complex by attaching in the minor grove of A-T rich sequences of DNA. It also forms nonfluorescent intercalative complexes with double-stranded nucleic acids. The physicochemical properties of the dye and its complexes with nucleic acids and history of the development of this dye as a biological stain are described. The application of DAPI as a DNA-specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation in histochemistry and biochemistry is reviewed. The mechanisms of DAPI-nucleic acid complex formation including minor groove binding, intercalation and condensation are discussed.

Lampbrush and mitotic chromosomes of the hemiclonally reproducing hybrid Rana esculenta and its parental species

Mitotic chromosomes of the European water frogs Rana ridibunda and Rana lessonae, the parental species of Rana esculenta, differ significantly in their centromeric regions: when C-banded or when made fluorescent, the centromeres of R. ridibunda (and of ridibunda chromosomes in R. esculenta) are visible as a conspicuous dark granule or as a conspicuous fluorescent spot; the centromeres of R. lessonae (and of the lessonae chromosomes in R. esculenta) are inconspicuous or not fluorescent. Lampbrush chromosomes of these three taxa are described in detail for the first time; those of R. ridibunda and R. lessonae differ significantly in morphostructural characters such as conspicuousness of centromeres and number, form, and location of giant loops as well as in chiasma frequency. Chromosomes of the two parental species can thus be distinguished when present in lampbrush complements of hybrids. Reproduction in both sexes of natural R. esculenta lineages is hemiclonal: only the unrecombined genome of one parental species, usually R. ridibunda, is transmitted to haploid gametes (hybridogenesis). In 18 hybrids from natural populations of Poland, somatic tissues had allodiploid complements with chromosomes from each parental species. In contrast, spermatocytes I of five males and oocytes I of seven of eight females (221 of 222 oocytes) were autodiploid and contained only R. ridibunda chromosomes that formed n bivalents. These 12 hybrids thus were hybridogenetic. A single female hybrid had oocytes I (33 of 34) with genomes of both parental species; they showed various disturbances including tetraploidy, reduced number of chiasmata, and incomplete synapsis resulting in univalents. This individual thus was not hybridogenetic. The irregular lampbrush patterns indicate that such hybrids will have severely reduced fertility and most of their successful gametes will result in allotriploid progeny.

Problem of size dependence in fluorescence DNA cytometry

The relationship among fluorescence intensity, area, thickness, and DNA concentration of DNA-bearing polyacrylamide film, stained with 50 ng/ml DAPI, was studied using an epi-illumination cytofluorometer. Measurements and theoretical analysis suggest the inevitability of the size-dependent effect on human cell nuclei in which the order of the DNA concentration is approximately 10 mg/ml, and that this effect can be virtually negated if the nuclei are stretched and flattened to less than 0.33 microns in thickness on the smears. Alternative practical ways to minimize this effect are to decrease the dye concentration of a staining solution and to make smears as thin and uniform as possible by some means such as hypotonic treatment and/or using an automatic centrifuge smearing apparatus. The size-dependent effect, nevertheless, should be taken into account particularly when determining the DNA content of different cell types and the DNA aneuploidy of tumor cells, regardless of the technique used for measurement.

Monomerizing effect of caffeine, o-phenanthroline, and tannin on cationic dyes: a model system to analyze spectral characteristics of the intercalative binding to nucleic acids

If used as co-solutes in concentrated solutions of cationic planar dyes, caffeine, o-phenanthroline, and tannin induce striking hyperchromic and bathochromic shifts in their absorption spectra. Likewise, the fluorescence of acridine orange at high concentration greatly increases in the presence of caffeine, the emission peak appearing at a shorter wave-length. These spectral changes, which are similar to those produced by organic solvents, detergents, and alpha-cyclodextrin, reflect the disaggregating (monomerizing) capacity of the co-solutes on stacked chromophores. After washing with saturated solutions of caffeine or o-phenanthroline, the chromatin fluorescence by intercalating fluorochromes is reduced or abolished, which suggests competition effects for intercalative binding modes. These results support the use of caffeine, o-phenanthroline, and tannin in spectroscopic and histochemical studies of dye-stuff interactions with DNA and chromatin.

DNA-4'-6-diamidine-2-phenylindole interactions: a comparative study employing fluorescence and ultraviolet spectroscopy

DAPI is a drug that interacts with double-stranded nucleic acids, binding preferentially to A + T base pairs. The interaction is not intercalative, therefore providing a useful model for mimicking the effect of functional molecules in modifying specific sites, namely, A + T segments, of significance in gene expression. Knowledge of the nature of such interaction has been enriched by additional information obtained from comparative analysis of the data acquired by uv spectroscopy and fluorescence. Two classes of binding sites, defined by different apparent affinity constants and numbers of binding sites, are evident. All types of interaction are dependent on the nucleic acid/dye ratio and on the ionic strength of the medium.

Genome evolution in pocket gophers (genus Thomomys). III. Fluorochrome-revealed heterochromatin heterogeneity

Heterochromatin is a dominant component of the genome in the bottae group of the pocket gopher genus Thomomys, having had a major role in the karyotypic evolution of member species. Heterochromatin characteristics of two subspecies of T. bottae and one of T. umbrinus were examined with fluorochrome dyes identifying presumptive GC- and AT-rich regions. In two karyotype forms of T. b. fulvus and in T. umbrinus, chromatin that fluoresces brightly with chromomycin A3 is also C-band positive, although not all heterochromatin fluoresces. However, in T. b. bottae, only euchromatic regions fluoresce brightly with chromomycin. Fluorescence patterns produced with DAPI are the reverse of the chromomycin banding in all karyotypic forms. Heterochromatin in these taxa is thus highly differentiated, exhibiting heterogeneity in staining characteristics, and presumably in underlying DNA sequences, both across the genome within a given chromosomal complement as well as among the different karyotypic races and species of the bottae group of pocket gophers.

Detection and separation of the submetacentric marker chromosome of the WALKER (W-256) carcinoma using flow cytometry and sorting

The chromosomes of WALKER (W-256) carcinoma cells have been separated into different DNA subclasses using DAPI for quantitative DNA staining and laser flow cytometry. The submetacentric marker chromosome could be isolated and its DNA content was determined to be 1.3 pg. One microgram marker DNA was obtained after separation of about 750 000 marker chromosomes by means of electronic flow sorting. The chromosomal composition of sorted fractions was analyzed by microscopy following banding of sorted chromosomes. The average morphological purity obtained was about 83%.

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.

Cytogenetic studies of familial Prader-Willi syndrome

A family in which two first cousins were found to have the Prader-Willi syndrome was investigated cytogenetically. Although G-banding analysis of metaphase chromosomes failed to demonstrate abnormality, close analyses on the fine prometaphase bands by G-banding and the DA-DAPI bands by double stainings revealed a distinct chromosome abnormality in this family. A reciprocal translocation, rcp(14;15)(q11.2;q13), was detected in three family members: the mother, the maternal grandmother, and a maternal uncle of the proband. And, the proband and one of the first cousins had an unbalanced translocation that was derived from their carrier parents. The karyotypes of the affected cousins were determined as 46,XY or XX,-15, + der(14),rcp(14;15)(q11.2;q13). Therefore, they were considered to have an identical cytogenetic abnormality: a partial trisomy of the 14pter leads to q11.2 segment and a partial monosomy of the 15pter leads to q13 segment. Detailed clinical features of the proband and his affected cousin are described, main features associated with the Prader-Willi syndrome having been observed in both cousins. These observations support a definite relationship between the Prader-Willi syndrome and chromosome 15.

Premeiotic chromosome doubling after genome elimination during spermatogenesis of the species hybrid Rana esculenta

Gamete production in the hybridogenetic species hybrid Rana esculenta (Rana ridibunda X Rana lessonae) is preceded by a premeiotic elimination of the R. lessonae genome and subsequent duplication of the remaining R. ridibunda genome, so that only ridibunda chromosomes enter a quasi normal meiosis, and only ridibunda gametes are formed. This is demonstrated by differences in genome specific centromere fluorescence and electrophoretic patterns between somatic and gonadal tissue.

Specific fluorescent bands on chromosomes produced by acridine orange after prestaining with base specific non-fluorescent DNA ligands

Metaphase chromosomes stained with acridine orange exhibit uniform yellow-green fluorescence. Chromosome preparations treated with the non-fluorescent A-T specific antibiotic distamycinA prior to acridine orange staining exhibit longitudinal fluorescent banding patterns similar to those produced by a number of fluorescent R-band techniques. Similarly, chromosome preparations treated with the non-fluorescent G-C specific antibiotic actinomycin D followed by acridine orange staining exhibit "Hoechst-type" banding patterns. Interactions of various ligand-DNA combinations in solution indicate that the base pair specific antibiotics induce banding patterns by selectively altering acridine orange binding sites in chromosomal regions rich in the particular base pair for which the antibiotic exhibits specificity.

Variable substructure in the secondary constriction of the human chromosome 1

The secondary constriction in human chromosome 1 consists of a proximal segment stained by the GC-specific fluorochrome mithramycin and a distal segment stained by such fluorochromes as DAPI or DIPI, which show enhanced fluorescence intensities in AT-rich regions of the chromosomes. A study involving 21 individuals revealed that both parts are independently involved in length variability. In two cases, two GC-rich regions separated by an AT-rich segment and an additional distal AT-rich part were found.

Rapid identification of chromosomes carrying silver-stained nucleolus-organizing regions: application to case of 21/21 Robertsonian translocation

The use of a combination of transmitted light and epiluminescence after silver and fluorescent staining of chromosome preparations makes it possible to achieve simultaneous visualization of silver-stained NORs and flourescent chromosomes. This technique permits exact localization of silver precipitates on normal and BrdU-substituted chromosomes. After previous silver impregnation, fluorescent staining by actinomycin-daunomycin-DAPI was used to induce a banding pattern that enables identification of specific chromosomes while observing silver-stained NORs at the same time. Application of this method to a Down's syndrome patient revealed a 21/21 Robertsonian translocation with NOR'S eliminated.

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.

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.