The use of base pair specific DNA binding agents as affinity labels for the study of mammalian chromosomes

CMA/DAPI Banding of Plant Chromosomes

Chromosome banding based on base-specific fluorochromes, mainly double staining with chromomycin A₃ (CMA) and 4'-6-diamidino-2-phenylindole (DAPI), has been widely used since the 1970s. This technique allows the differential staining of distinct types of heterochromatin. Afterward, the fluorochromes can be easily removed and leave the preparation ready for sequential procedures such as FISH or immunodetection. Interpretations of similar bands obtained with different techniques, however, merit certain caution. Here we present a detailed protocol for CMA/DAPI staining optimized for plant cytogenetics and call attention to the most common sources of misinterpretation of DAPI bands.

Chemical library screen for novel inhibitors of Kaposi's sarcoma-associated herpesvirus processive DNA synthesis

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma and certain lymphoproliferative disorders. The role of KSHV lytic replication has been implicated in the tumor pathogenesis. A highly specific molecular complex formed by the KSHV DNA polymerase (POL8) and processivity factor (PF8) is indispensable for lytic viral DNA synthesis and may serve as an excellent molecular anti-KSHV target. The majority of conventional nucleoside-based anti-herpetic DNA synthesis inhibitors require intracellular phosphorylation/activation before they can exert inhibitory activity as competitive substrates for viral DNA polymerases. Novel and more potent inhibitors of KSHV DNA synthesis may be discovered through POL8/PF8-targeted high throughput screening (HTS) of small molecule chemical libraries. We developed a microplate-based KSHV POL8/PF8-mediated DNA synthesis inhibition assay suitable for HTS and screened the NCI Diversity Set that comprised 1992 synthetic compounds. Twenty-eight compounds exhibited greater than 50% inhibition. The inhibitory activity was confirmed for 25 of the 26 hit compounds available for further testing, with the 50% inhibitory concentrations ranging from 0.12+/-0.07 microM (mean+/-S.D.) to 10.83+/-4.19 microM. Eighteen of the confirmed active compounds efficiently blocked KSHV processive DNA synthesis in vitro. One of the hit compounds, NSC 373989, a pyrimidoquinoline analog, was shown to dose-dependently reduce the levels of KSHV virion production and KSHV DNA in lytically induced KSHV-infected BCBL-1 cells, suggesting that the compound blocked lytic KSHV DNA synthesis. HTS for KSHV POL8/PF8 inhibitors is feasible and may lead to discovery of novel non-nucleoside KSHV DNA synthesis inhibitors.

Characterization of a new aberration of the human Y chromosome by banding methods and DNA restriction endonuclease analysis

Comparative cytogenetic analyses were performed with ten different banding methods on a previously undescribed, inherited structural aberration of a Y chromosome, and the results compared with those of normal Y chromosomes occurring in the same family. The value of the individual staining techniques in investigations of Y chromosomal aberrations is emphasized. The aberrant Y chromosome analyzed can be formally derived from an isodicentric Y chromosome for the short arm with a very terminal long-arm breakpoint, in which the centromere, an entire short arm, and the proximal region on one long arm was lost. This interpretation was confirmed by determining the amount of the two Y-specific DNA sequences (2.1 and 3.4 kb in length) by means of Hae III restriction endonuclease analysis. The karyotype-phenotype correlations in the men with this aberrant Y chromosome, especially the fertility dysfunctions (oligoasthenoteratozoospermia, cryptozoospermia), are discussed. The possibility of the existence of fertility factors involved in the control of spermatogenesis within the quinacrine-bright heterochromatic region of the Y long arm is presented.

Microdissection of pig chromosomes: dissection of whole chromosomes, arms and bands for construction of paints and libraries

Chromosome microdissection is an important means to efficiently generate a large number of markers from a desired region of a genome. The present study was designed to initiate microdissection and amplification of DNA from whole chromosomes, arms, or bands of porcine chromosomes. The following pig (SSC) chromosomes/segments were scraped: SSC1p, SSC1q26-q2.13, SSC2q11-q14, SSC4q12-q25, SSC13, SSC13q12-q31, SSC13q32-q43, SSC13q32-q43, SSC15, and SSC16q21-q23. After amplification and PCR-labelling, the DNA from the dissected segments were painted back to normal metaphase chromosomes to test their identity. Microdissection of some of the segments (on SSC4, 13 and 15) coincides with the mapping of economically important traits. As a first step towards generation of markers, microcloning of amplified product from SSC1p and SSC15 was carried out. The libraries were screened with a (GT)15 oligonucleotide probe. Future prospects of such a work in farm animals are discussed.

DNA-based monitoring of total bacterial community structure in environmental samples

Determining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between micro-organisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA-binding dye bisbenzimidazole which imposes G+C-dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G+C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.

Deciphering the fluorescent variability of human genomic heterochromatin by DA/DAPI technique

A number of selective staining techniques have been utilized to decipher the variability of pericentromeric heterochromatin. One such technique is called DA/DAPI and it is believed to be stain specific. However, we demonstrate otherwise and suggest that pericentromeric regions of all human chromosomes stain positive by DA/DAPI-technique. It must be emphasized that the incidence of DA/DAPI positive stained chromosomes, other than 1, 9, 15, 16 and Y, is a rare occurrence and only a small portion of the pericentromeric region is DA/DAPI positive, as reported here using 50 normal individuals.

Fluorophotometric quantitation of DNA in articular cartilage utilizing Hoechst 33258

A sensitive fluorophotometric assay was developed for the measurement of DNA in articular cartilage. The tissue was digested with Proteinase K and dodecyl sodium sulfate, followed by analysis with Hoechst 33258 dye. DNA content was determined on both fresh and lyophilized material containing as little as 50 ng DNA. The results are comparable to values for other fluorophotometric and spectrophotometric methods reported in the literature. In addition, this method can be incorporated into existing methodology, allowing quantitation of specific glycosaminoglycans in the same cartilage sample in terms of DNA.

Evolutionary diversity of reverse (R) fluorescent chromosome bands in vertebrates

Mitotic chromosomes, interphase cell nuclei, and male meiosis of 41 species representing all vertebrate classes were analyzed with distamycin A/mithramycin counterstaining. The purpose of the study was to recognize differences and common characteristics in the reverse (R) fluorescent banding patterns in the chromosomes of vertebrate species at various stages of evolution. In contrast to the warm-blooded mammals and birds, the euchromatic segments in the chromosomes of most reptiles, amphibians, and fishes contain no multiple fluorescent R-bands. This is thought to be due to the absence of the long homogeneous regions (isochores) in the DNA of the cold-blooded vertebrates. Distamycin A/mithramycin banding specifically reveals the GC-rich constitutive heterochromatin in all vertebrates. In most of the vertebrate chromosomes examined, the heterochromatic regions have opposite staining properties with mithramycin and quinacrine. Mithramycin labels the nucleolus organizer regions very brightly in the karyotypes of fishes, amphibians, reptiles and birds, but not of mammals. The lack of mithramycin fluorescence at the nucleolus organizer regions of mammals is attributed to the relatively low level of redundancy of the GC-rich ribosomal DNA in their genomes. Studies on the various meiotic stages of the cold-blooded vertebrates show that the mithramycin labeling of the nucleolus organizers is independent of their state of activity. This can be confirmed by mithramycin fluorescence at the nucleoli of actinomycin-treated cells.

Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands

Combining high resolution in situ hybridization with quantitative solid state imaging, we show that human metaphase chromosome Giemsa/Quinacrine and Reverse bands are each characterized by distinct families of interspersed repeated sequences: the SINES, Alu family dominates in Reverse bands, and the LINES, L1 family dominates in Giemsa/Quinacrine positive bands. Alu is 56% guanine plus cytosine, and L1 is 58% adenine plus thymine, and each may comprise 13%-18% of the total DNA in a chromosome band. Therefore, the distribution of these sequences alone may account for a large part of human chromosome banding seen with fluorescent dyes. With the exception of some telomeric regions, and the chromosomal regions of simple sequence DNA, Alu and L1 are precisely inversely distributed, suggesting an inverse functional relationship. This finding links genome organization with chromosome structure and function.

Interaction of Hoechst 33258 with repeating synthetic DNA polymers and natural DNA

Fluorescence, circular dichroism and sedimentation through cesium chloride gradient techniques were performed to study the physical properties of the binding of the bisbenzimidazole dye Hoechst 33258 (H33258) to natural DNAs and synthetic polynucleotides of defined repeating units. These studies show that Hoechst 33258 exhibits at least two modes of interaction with duplex DNA: (1) a strong base pair specific mode which requires at least 4 consecutive AT base pairs and (2) a weaker mode of binding which is significantly reduced in the presence of high salt (0.4 M NaCl) and exhibits no apparent base specificity. The H33258 binding was found to be sensitive to the substitutions in the minor groove elements of a series of synthetic polynucleotides supporting the model of H33258 binding in the minor groove of the DNA with AT rich sequences. Similar mode of binding was predicted in natural DNAs by methylation of dye-DNA complexes. Footprint analysis of the complex of dye to a pBR322 fragment also supports that a minimum of 4 consecutive AT base pairs are required for H33258 binding to DNA.

Correlation between constitutive heterochromatin and restriction enzyme resistant chromatin in Arcyptera tornosi (Orthoptera)

Fixed mitotic chromosomes of A. tornosi have been analysed by means of C-banding, DA-DAPI and Chromomicin A3 fluorescence, as well as by digestion in situ with Alu I, Hae III, Hinf I and Hind III restriction endonucleases. From the results obtained at least nine types of chromatin can be distinguished in A. tornosi. Some C-band positive areas (constitutive heterochromatin) which show a characteristic fluorescence pattern are digested by specific endonucleases, whilst others are undigested. C-band negative areas (euchromatin) are digested by some restriction endonucleases but not by others. Regions digested are supposed to contain highly repetitive DNAs. It is noteworthy, however, that the heterochromatin associated with NORs is not attacked by any of the enzymes we used, while regions believed to contain AT-rich DNA (DA-DAPI positive) are digested by Hae III that cleaves the GG decreases CC base sequence target.

Nucleolus organizer regions and heterochromatin in the zebu (Bos indicus L.)

Ag-NOR staining and a counterstain enhanced fluorescence technique (chromomycin A3/distamycin A/DAPI-staining = CDD-method) and G-banding, respectively, have been applied to the zebu (Bos indicus L.) chromosomes. The nucleolus organizer regions (NORs) were found in the telomeric regions of chromosomes nos. 2, 3, 4, 11, and 28. CDD staining led to a well-defined R-banding pattern along the chromosome arms and to the visualization of centric heterochromatic bands of variable sizes.

Relative position of constitutive heterochromatin and of nucleolar structures during mouse spermiogenesis

In this study, the selective fluorochrome staining of constitutive heterochromatin and a specific ultrastructural silver-staining of nucleolar material (i.e., the nucleolus organizing regions) were undertaken to be used as indicators for the chromosomal arrangement during mouse spermiogenesis. Since in mice all somatic chromosomes are telocentric and the constitutive heterochromatin and nucleolar organizing regions are closely associated to the centromeres, this combination of techniques provided for the first time ultrastructural evidence 1) for the dispersion of the constitutive heterochromatic chromocentre and a centrifugal migration to the postacrosomal portion of the nuclear envelope where constitutive heterochromatin seems to mediate the assembling of microtubules in the so-called manchette. As elongation continues, the constitutive heterochromatin migrates back into central position and forms the "focous of earlier condensing chromatin", which initiates further chromatin condensation. 2) The fate of the nucleolus during spermiogenesis could also be further clarified: The nucleolus is first associated with the chromocentre, but starts to disintegrate during elongation phase. However, argyrophilic remnants are still visible in the centre of the nucleus, pointing to an ongoing transcriptional activity. When they final disappear, they leave behind "nuclear vacuoles" in the dense chromatin mass of the mature sperm nucleus.

Multiple malformation of bovine spermatozoa with special reference to their lightmicroscopic fluorescing pattern and electron-microscopic structure

The light microscopic examinations of sperm samples from a sterile Fleckvieh-bull stained by the AT specific fluorochrome Hoechst 33258 showed beneath the constantly occurring paraxial tail numerous other malformations, which appeared under the electron microscope as multiple defects of essential cell organelles: defects of the acrosome as irregular thickening or forming of overturned folds "knobbed acrosome", sometimes with vesicles and inclusions inside, partial separation of the acrosome lamina from the nucleus. The defects of the nucleus were present as double-headed sperms, macro- and microcephalic forms besides bizarre shaped heads with gigantic cavities, often filled with membranes, cytoplasm and canaliculi even as heads with ridges which extended from the base to the apex. The main tail defect was a paraxial inserted tail, sometimes coiled, folded or bent down and combined with duplication or even multiplication of the tail with one or two implantation fossae. This multiplication was followed by extensive disturbances of the tail elements as lack or excessive numbers up to the isolation of tubules, fibers and mitochondria. Often there was no contact between tail and implantation fossa. Another defect was the existence of voluminous cytoplasmic droplets covering not only great parts of the tail but also the total head which included "arch like double membranes" and up to 15 tail segments. The persisting cytoplasmic droplet even as the generally occurring paraxial inserted tail are discussed in connexion with the existing hormonal imbalance as probably genetic damage leading to extensive defects during spermiogenesis.

Effects of Hoechst 33258 on different cell cycle events. I. Inhibition of synthetic activities in bone-marrow cells of the mole rat Bandicota bengalensis

A study of the effects of the A-T base-specific ligand Hoechst 33258 on the cell cycle events of the bone-marrow cells of the mole rat Bandicota bengalensis reveals that (1) the G2 phase is prolonged by 2 h; (2) the chromosomes are undercondensed to varying degrees in about 30% metaphases; (3) DNA as well as RNA synthesis is partially inhibited. Study on DNA fibre autoradiograms shows that despite the inhibition of DNA synthesis the average replicon size and rate of fork migration remain unchanged, but there is a marked asynchrony of initiation of replicons in replicon clusters in H-treated cells in comparison with control. It is suggested that these inhibitory effects result from the stabilization of the double-stranded organization of DNA (dsDNA) by the drug so that the unwinding of DNA at the replication or transcription origin sites is greatly impaired. It is likely that this introduces asynchrony in the initiation of replicons within replicon clusters which may retard the overall rate of replication. In addition, it appears that the reduction in transcription is at least one cause for the prolongation of G2 phase.

Fluorescence patterns of heterochromatin in mitotic and polytene chromosomes in seven members of three sub-groups of the melanogaster species group of Drosophila

A comparative study of fluorescence patterns of heterochromatin in mitotic and polytene chromosomes of seven species belonging to 3 subgroups (melanogaster sub-group: D. melanogaster and D. simulans; montium sub-group: D. kikkawai and D. jambulina; ananassae sub-group: D. ananassae. D. malerkotliana and D. bipectinata) of the melanogaster species group of Drosophila (Sophophora) has been made. Hoechst 33258 (H) fluorescence patterns of mitotic chromosomes reveal differences correlated to the taxonomic groupings of these species. The melanogaster sub-group species have H-bright regions on heterochromatin of all chromosomes; the montium subgroup species have H-bright regions mainly on the 4th and Y-chromosomes; in the ananassae sub-group, while D. ananassae chromosomes do not show any H-bright regions. D. malerkotliana and D. bipectinata have small H-bright segments only on their 4th chromosomes. The H- and quinacrine mustard (QM) fluorescence patterns of larval salivary gland polytene chromocentre in these species, however, do not show the same taxonomic correlation. While D. ananassae and D. kikkawai polytene nuclei lack any H- or QM-bright region in the chromocentre, the remaining species have prominent H- and/or QM-bright region(s). In D. jambulina, the QM-bright regions are generally bigger than H-bright regions, while in D. malerkotliana and D. bipectinata the situation is reversed. Actinomycin D counterstaining prior to H-staining of polytene preparations of each species confirms that the H-bright region/s in the chromocentre are composed of A-T rich sequences. In vivo labelling of salivary gland polytene nuclei with 5-bromo-deoxyuridine for 24 to 48 h and subsequent H-staining reveals that in all the species, the H-bright regions do not replicate in 3rd instar stage and presumably represent the non-replicating alpha heterochromatin. Significantly, in all the species (excepting D. kikkawai and D. ananassae), the size, location and the number of H- and/or QM-bright regions were seen to vary in different polytene nuclei in the same gland. It seems that the organization and the extent of under-replication of alpha heterochromatin varies in different polytene nuclei. Present studies also show that even closely related species differ in the content and organization of H-bright heterochromatin. The 81F band at the base of 3R in D. melanogaster, but not in D. simulans, appears to contain non-replicating H-bright sequences in addition to replicating chromatin.

Interactions between pairs of DNA-binding dyes: results and implications of chromosome analysis

A number of DNA-binding dyes, with spectral properties making them suitable as components of energy donor-acceptor pairs, are described. If such pairs are used to stain metaphase chromosomes, and if the energy acceptor (e.g., actinomycin D or methyl green) has a binding specificity opposite to the binding or fluorescence specificity of the donor (e.g., 33258 Hoechst, quinacrine or chromomycin A3), contrast in donor fluorescence can be enhanced, leading to patterns selectively highlighting standard or reverse chromosome bands or particular polymorphic regions. Such results presumably reflect chromosomal regions enriched in 10-20 base pair clusters to which the donor binds and fluoresces but to which the acceptor cannot bind. For other pairs, involving counterstains such as netropsin or echinomycin, which are not suitable as energy acceptors, specific changes observed in polymorphic region fluorescence are most likely due to binding competition between dyes. Dye pairs producing contrast by either method can be used to differentiate between homologous chromosomes or to facilitate detection of specific chromosomal rearrangements. Preliminary data indicate that contrast enhancement generated in fixed metaphase chromosomes spread on microscopic slides can also be observed in suspensions of unfixed metaphase chromosomes, reinforcing the expectation that the methodology described will be of use in flow cytometry.

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.

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.

Porcine (Sus scrofa domestica) chromosome identification and suggested nomenclature

Various banding techniques have been used for chromosome analysis in domestic pigs (Sus scrofa domestica). The techniques used in karyotype analysis were Q-banding by (CMA)2S, trypsin-G-banding, BrdU-Acridine-Orange R-Banding and C-banding. Sequential staining techniques of quinacrine-Giemsa were used to record the length of each chromosome and determine arm ratios. Sequential Quinacrine-Giemsa-Ag-AS treatment was used to locate the nucleolar organizer (NOR) on specific chromosomes. A G-C specific fluorochrome was used for reverse fluorescent banding and to differentiate certain chromosome regions which may contain G + C rich DNA. Unequivocal identification of all individual autosomes and sex-chromosomes in the porcine complement is now possible. The X-chromosome of the species has a banding pattern similar to the human X-chromosome. A nomenclature system similar to that used for human chromosomes is proposed for the G-banded and Q-banded karyotype of the domestic pig. The results of C-banding and olivomycin fluorescent banding suggest that at least three types of heterochromatin are contained in the porcine genome.

Cytochemical studies of metaphase chromosomes by flow cytometry

The cytochemical properties of metaphase chromosomes from Chinese hamster and human cells were studied by flow cytometry. This technique allows precise quantitation of the fluorescence properties of individual stained chromosome types. Chromosomes were stained with the following fluorescent DNA stains: Hoechst 33258, DAPI, chromomycin A3, ethidium bromide, and propidium iodide. The relative fluorescence of individual chromosome types varied depending on the stain used, demonstrating that individual chromosome types differ in chemical properties. Flow measurements were performed as a function of stain and chromosome concentration to characterize the number and distribution of stain binding sites. Flow analysis of double stained chromosomes show that bound stains interact by energy transfer with little or no binding competition. For most hamster chromosomes, there is a strong correlation between relative fluorescence and stain base preference suggesting that staining differences may be determined primarily by differences in average base composition. A few hamster chromosome types exhibit anomalous staining which suggests that some other property, such as repetitive DNA sequences, also may be an important determinant of chromosomal staining.