Chromosome regions containing DNAs of known base composition,specifically evidenced by 2,7-di-t-butyl proflavine

After staining by a new proflavine derivative (2,7-di-t-butyl proflavine, DBP), which specifically binds to the A-T base pairs of DNA by an external process, the constrictions of the human chromosomes 1, 16 and to a lesser extent 9 and the centromeric regions of the chromosomes (except the Y) of Mus musculus are brightly fluorescent. These chromosome regions are known to contain repetitive DNAs rich in A-T. On the contrary, the centromeric regions of the autosomes of Bos taurus, which contain a G-C rich DNA, are faintly fluorescent. The arms of the chromosomes of the three species display a banding similar to, but fainter than, the Q-banding. These results are discussed in correlation with physico-chemical studies on the binding and fluorescence processes of the dye bound to DNA and to nucleohistone. The staining properties of DBP are compared to those of quinacrine, quinacrine mustard and proflavine, three intercalative dyes which are also supposed to reveal the A-T base pairs along the chromosomes, but are faintly fluorescent on the human and murine A-T rich regions. This comparison leads us to discuss the mechanisms responsible for the chromosomal banding in relation to DNA base composition and repetitiveness, protein distribution and packing of the chromatin fibers, along the chromosomes.     

Optical studies of complexes of quinacrine with DNA and chromatin: implications for the fluorescence of cytological chromosome preparations

The fluorescence and circular dichroism of quinacrine complexed with nucleic acids and chromatin were measured to estimate the relative magnitudes of factors influencing the fluorescence banding patterns of chromosomes stained with quinacrine or quinacrine mustard. DNA base composition can influence quinacrine fluorescence in at least two ways. The major effect, evident at low ratios of quinacrine to DNA, is a quenching of dye fluorescence, correlating with G-C composition. This may occur largely prior to relaxation of excited dye molecules. At higher dye/DNA saturations, which might exist in cytological chromosome preparations stained with high concentrations of quinacrine, energy transfer between dye molecules converts dyes bound near G-C base pairs into energy sinks. In contrast to its influence on quinacrine fluorescence, DNA base composition has very little effect on either quinacrine binding affinity or the circular dichroism of bound quinacrine molecules. The synthetic polynucleotides poly(dA-dT) and poly(dA)-poly(dT) have a similar effect on quinacrine fluorescence, but differ markedly in their affinity for quinacrine and in the circular dichroism changes associated with quinacrine binding. Quinacrine fluorescence intensity and lifetime are slightly less when bound to calf thymus chromatin than when bound to calf thymus DNA, and minor differences in circular dichroism between these complexes are observed. Chromosomal proteins probably affect the fluorescence of chromosomes stained with quinacrine, although this effect appears to be much less than that due to variations in DNA base composition. The fluorescence of cytological chromosome preparations may also be influenced by fixation effects and macroscopic variations in chromosome coiling.     

Mechanisms of quinacrine binding and fluorescence in nuclei and chromosomes

The mechanisms has been investigated whereby quinacrine binds to the DNA of nuclei and chromosomes in cytological preparations fixed in methanol-acetic acid. A variety of evidence is consistent with the idea that the quinacrine binds by intercalation. This is supported by a high value for the affinity of quinacrine for DNA, together with a saturation value of 0.2 quinacrine molecules/nucleotide; binding in the presence of strong salt solutions; and inhibition of fluorescence and banding by denaturation or depurination of DNA. At high quinacrine concentrations, weak binding of quinacrine to nuclei and chromosomes also occurs, but this is not relevant to the production of strong fluorescence or Q-banding patterns. A number of factors were tested which might have affected quinacrine fluorescence and banding. These included: pH; blocking protein amino groups by acetylation or benzoylation; introduction of hydrophobic groups by benzoylation; and dephosphorylation. All these treatments were without effect. However, comparison of the quinacrine fluorescence of human and onion nuclei, which differ substantially in the base composition of their DNA, shows that quinacrine fluorescence can be enhanced in cytological preparations by AT-rich DNA.     

Mechanisms of quinacrine binding and fluorescence in nuclei and chromosomes

Summary The mechanism has been investigated whereby quinacrine binds to the DNA of nuclei and chromosomes in cytological preparations fixed in methanol-acetic acid. A variety of evidence is consistent with the idea that the quinacrine binds by intercalation. This is supported by a high value for the affinity of quinacrine for DNA, together with a saturation value of 0.2 quinacrine molecules/nucleotide; binding in the presence of strong salt solutions; and inhibition of fluorescence and banding by denaturation or depurination of DNA. At high quinacrine concentrations, weak binding of quinacrine to nuclei and chromosomes also occurs, but this is not relevant to the production of strong fluorescence or Q-banding patterns.A number of factors were tested which might have affected quinacrine fluorescence and banding. These included: pH; blocking protein amino groups by acetylation or benzoylation; introduction of hydrophobic groups by benzoylation; and dephosphorylation. All these treatments were without effect. However, comparison of the quinacrine fluorescence of human and onion nuclei, which differ substantially in the base composition of their DNa, shows that quinacrine fluorescence can be enhanced in cytological preparations by AT-rich DNA.In honour of Prof. P. van Duijn     

Clearly differentiated and stable chromosome bands produced by a spermine bis-acridine, a bifunctional intercalating analogue of quinacrine

Characteristic fluorescent banding patterns on human metaphase chromosomes are produced by treating chromosome preparations directly with a spermine bis-acridine fluorochrome (CMA)₂S. The clearly differentiated bands are similar to those produced by quinacrine (Q-banding), but show enhanced definition between bright and dull regions as compared with the banding patterns obtained by the quinacrine technique. In addition, the bands on chromosomes produced by (CMA)₂S show insignificant fluorescence fading over extended periods of excitation. Solution interactions between DNA and (CMA)₂S showed a greater fluorescence differential between fluorescence enhancement by the alternating polymers poly d(A-T) · poly d(A-T) and fluorescence quenching by the polynucleotide poly d(G-C) · poly d(G-C) for this fluorochrome than was observed for quinacrine. The increased definition in Q-type bands produced by the spermine bis-intercalating derivative and the lack of fluorescence fading make this fluorochrome an excellent one for routine clinical cytogenetic analysis.     

Further evidence of intraspecific heterochromatin variants in Drosophila melanogaster

The analysis of inter-strain heterochromatin polymorphism in mitotic chromosomes of Drosophila melanogaster was extended to some stocks characterized by chromosomal mutations. In particular, the present investigation aims to compare, in the same cell, the quinacrine banding of two different Y chromosomes of male hybrids derived from crosses using special stocks. A direct comparison of homologous heteromorphic chromosomes in F₁ hybrids provided additional evidence of differences in the fluorescence pattern of the Y chromosome, as well as in the length of the heterochromatin segment of the X chromosome.     

Fluorometric properties of the bibenzimidazole derivative hoechst 33258, a fluorescent probe specific for AT concentration in chromosomal DNA

A new fluorescent probe of chromosomal DNA structure in situ, the bibenzimidazole derivative Hoechst 33258, shows enhanced fluorescence with both AT- and GC-rich DNA; however, enhancement by AT-rich DNA is greater than enhancement with GC-rich DNA. When this compound is used as a probe, it produces localized fluorescence which can be correlated with AT concentration in specific chromosome regions. By the use of 33258, Hilwig and Gropp (1972) were able to demonstrate the relatively AT-rich DNA present in centric regions of mouse chromosomes; these regions do not fluoresce brightly when treated with quinacrine because of the presence of guanine residues which are spaced with high periodicity and which therefore efficiently quench quinacrine fluorescence. The data obtained in this study with DNA polymers of defined structure or composition, as test model compounds, suggest that 33258 is a useful cytochemical reagent for generally identifying all types of AT-rich regions in chromosomes, including those which are not demonstrable with quinacrine.     

The distribution of repetitive DNA in the chromosomes of cultured cells of Drosophila melanogaster

The distribution patterns of different stains (orcein, quinacrine and Giemsa) in an established cell line of Drosophila melanogaster (GM₃ WS) were compared. Each chromosome stained both with quinacrine and with Giemsa shows up a specific banding pattern for heterochromatin. The comparison between the two patterns suggests a hypothesis concerning the significance of the fluorescence; moreover it permits the conclusion that heterochromatin in D. melanogaster mitotic chromosomes is all constitutive and that there is a correspondence between repetitive DNA and sections poor in mappable genes.This work was supported by a grant of the Consiglio Nazionale delle Ricerche Roma.     

Giemsa banding,quinacrine fluorescence and DNA-replication in chromosomes of cattle (Bos taurus)

Almost all the 30 chromosome pairs of cattle can be identified by their banding patterns made be visible by a Giemsa staining technique described previously. The banding pattern of the X chromosome shows striking similarities with the banding pattern of the human X chromosome. — The centromeric region of the acrocentric autosomes contains a highly condensed DNA. This DNA is removed by the Giemsa staining procedure as can be shown by interference microscopic studies. If the chromosomes are stained with quinacrine dihydrochloride these centromeric regions are only slightly fluorescent. — Autoradiographic studies with ³H-thymidine show that the DNA at the centromeric regions starts and finishes its replication later than in the other parts of the chromosomes.     

Q and G banding patterns of the chromosomes of some Primates

A study of the Q (quinacrine fluorescence) and G (Giemsa) banding patterns of the chromosomes of Pan troglodytes and Gorilla gorilla gorilla shows that they are almost identical. The differences include a pericentric inversion in pairs 5, 9, 19 and the X-chromosome, a possible translocation between pairs 7 and 17 of gorilla and a deletion of part of the long arms of the Y-chromosome in the chimpanzee. Several species of the genera Macaca, Papio and Cercocebus have the same karyotype and identical banding patterns. This suggests that speciation in this group may have taken place on purely genic grounds, without, involving any karyological changes.     

Hoechst 33258 banding of Drosophila nasutoides metaphase chromosomes

Hoechst 33258 banding of D. nasutoides metaphase chromosomes is described and compared with Q and C bands. The C band positive regions of the euchromatic autosomes, the X and the Y fluoresce brightly, as is typical of Drosophila and other species. The fluorescence pattern of the large heterochromatic chromosome is atypical, however. Contrary to the observations on other species, the C negative bands of the large heterochromatic chromosome are brightly fluorescent with both Hoechst 33258 and quinacrine. Based on differences in the various banding patterns, four classes of heterochromatin are described in the large heterochromatic chromosome and it is suggested that each class may correspond to an AT-rich DNA satellite.     

In situ localization and characterization of different classes of chromosomal DNA: acridine orange and quinacrine mustard fluorescence

In situ denaturation of metaphase chromosomes with alkali results in a shift from green to yellow, orange, brown and red fluorescence with acridine orange, indicating increasing denaturation of chromosomal DNA. The kinetics and characteristics of denaturation are described. Mouse and Microtus agrestis chromosomes denature uniformly but human cells show sequential denaturation. With increasing concentrations of alkali, the secondary constrictions in chromosomes 1, 9 and 16 are the first, and the distal half of the Y chromosome the last, to become denatured. — Reassociation of chromosomal DNA occurs within seconds after the start of incubation in salt solution. Areas containing repetitious DNA, e.g. mouse centromeres, fluoresce much more strongly than other regions with acridine orange after prolonged reassociation. Since human and Microtus centromeric regions behave similarly, it is proposed that they, too, contain repetitious DNA. — Reassociation treatment leads to enhancement of bright quinacrine mustard fluorescence in regions already bright before treatment. Furthermore, regions containing repetitious DNA, e.g. the secondary constrictions in human chromosomes 1, 9 and 16, whose fluorescence is dull before treatment, turn bright after reassociation. — The methods of fluorescence analysis of mammalian chromosomes with acridine orange and quinacrine mustard permit the localization and study of different classes of chromosomal DNA.     

A comparison between quinacrine fluorescence banding and 3H-thymidine incorporation patterns in human chromosomes

Summary Late ³H-thymidine incorporation patterns and quinacrine fluorescence banding patterns were analyzed in metaphase chromosomes prepared from human blood cultures. In general, late-labeling regions correspond to the strongly fluorescent bands in the chromosomes. However, the dully fluorescent secondary constrictions of the chromosomes Nos. 1, 9 and 16 may show late replication in some instances. In contrast, the brilliantly fluorescent distal part of the Y chromosome is not labeled during the latest phase of the DNA replication. In the male X and in the isopycnotic X of the female the labeling pattern also agrees with the quinacrine fluorescence banding. The heteropycnotic X of the female is still more strikingly late-labeling. However, the pattern of its late replication agrees also with the quinacrine fluorescence bands.

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Zusammenfassung An aus menschlichen Blutkulturen gewonnenen Chromosomenpräparaten wurden vergleichende Untersuchungen über die späten Replikationsmuster (mittels ³H-Thymidin-Autoradiographie) und die Quinacrin-Fluorescenz-Bänderungsmuster durchgeführt. Im allgemeinen stimmen die spät replizierenden Abschnitte mit den intensiv fluorescierenden Regionen der Chromosomen überein. Allerdings können die nur schwach fluorescierenden sekundären Constrictionen der Chromosomen Nr. 1, 9 und 16 manchmal auch eine späte Replikation zeigen. Auf der anderen Seite wird der stark fluorescierende Abschnitt des Y-Chromosoms in den letzten Phasen der DNS-Replikation nicht mehr markiert. Beim X-Chromosom des Mannes und beim isopyknotischen X der Frau wird ebenfalls eine Übereinstimmung des Spät-Replikationsmusters und der Quinacrin-Bänderung gefunden. Das heteropyknotische X der Frau zeigt eine noch deutlichere Spät-Replikation; das Muster der Silberkörner stimmt aber ebenfalls mit den Quinacrine-Bändern überein.

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This study was supported by the österreichischen Fonds zur Förderung der Wissenschaftlichen Forschung.     

On the Chemical Basis of Chromosome Banding Patterns

A comparative study of the staining characteristics of four reagents for human chromosomes has been carried out. The four reagents are: (I) quinacrine mustard, as an alkylating agent, (II) the dihydrory derivative of quinacrine mustard, (III) quinacrine, and (IV) 9-amino-6-chloro-2-methoryacridine. The last reagent does not possess the amino substituted side chain even though it has the same intercalating nucleus. Comparison of the first three compounds in their staining and banding behavior suggested the initial step leading to banding may be the displacement of the nucleoprotein sites in chromosomes. The Q and G banding could he blocked experimentally by treating the chromosome preparation with dimethylamine solution. This result may suggest that these sites have weaker basic proteins (nonhistone proteins?). The use of compound IV, which does not have the side chain in the molecuk but docs have the same intercalating chromophore, did not lead to handing and gives indirect support to this hypothesis. A combined use of compound IV and quinacrine may be useful for the determination of total DNA vs. banding DNA.     

Banding pattern analysis of human chromosomes by use of a urea treatment technique

A new technique to reveal the banding pattern of human chromosomes is described. Slides prepared by the routine air drying technique were treated with urea-Sörensen buffer solution for ten minutes at pH 6.8 at 37° C. Individual pairs of all human chromosomes exhibited a characteristic banding pattern by this technique, and by its use the karyotypes were analysed. With the exception of some minor differences the banding patterns obtained by the present technique appeared to be identical with those obtained by the Giemsa staining and quinacrine fluorescence methods carried out by previous workers.Contribution No. 877 from the National Institute of Genetics, Japan. Supported by grant-in-aid No. 92332 from the Ministry of Education of Japan.     

Characterization of Drosophila heterochromatin

The C- and N-banding patterns of D. melanogaster, D. simulans, D. virilis, D. texana, D. ezoana and D. hydei were studied in comparison with quinacrine and Hoechst banding patterns. In all these Drosophila species the C bands correspond to the heterochromatin as revealed by the positive heteropycnosis in the prometaphase chromosomes. The N bands have the following characteristics: 1) they are always localized on the heterochromatin and generally do not correspond to the C bands; 2) they do not correspond to the nucleolar organizing regions; 3) they are inversely correlated with fluorescence, i.e., they correspond to regions which are scarcely, if at all, fluorescent after Hoechst 33258 or quinacrine staining; 4) they are localized both on regions containing AT rich satellite DNA and on those containing GC rich satellite DNA.     

Genomic analyses of the Formosan harvest mouse (Micromys minutus) and comparisons to the brown Norway rat (Rattus norvegicus) and the house mouse (Mus musculus)

The harvest mouse, Micromys minutus (MMIN), has a very wide range of distribution (from the British Isles across the Euroasian continent to Japan and Taiwan). We studied an isolated population of MMIN in Taiwan, which is at the southeastern margin of the species’ geographic distribution, and compared its genetic complement with those of the same species previously reported from other geographic locations and with two model rodent species, the house mouse (Mus musculus) and the brown Norway rat (Rattus norvegicus). The diploid number (2N) of MMIN was 68, consistent with that reported for other populations. However, variations were noted in the fundamental number (FN) and the shape and banding patterns of the individual chromosomes among populations. The FN of MMIN was estimated to be 72, including 2 bi-armed autosomes, 31 one-armed autosomes, and one pair of one-armed sex chromosomes. Here, we propose the first ideogram for MMIN. C-banding, Ag-NOR, and the locations of 18S rRNA gene sequences (MMIN chromosomes no. 10, 14, 19, 29, 31, 33, and X) mapped by fluorescence in situ hybridization (FISH) are also reported. Additionally, we compared the 18S rDNA sequences and performed cross-species X chromosome painting (FISH) for M. minutus, M. musculus, and R. norvegicus. The results indicate that both genetic elements are rather conserved across species. Thus, implications for the phylogenetic position of Micromys were limited.     

Quantitative analysis of fluorescence profiles of chromosomes : Influence of DNA base composition on banding

Chromosome banding has been analysed in terms of DNA content and base composition distribution along five human chromosomes. Three intercalative dyes (quinacrine, proflavine and ethidium bromide) whose fluorescence quantum yield in the presence of DNAs of different base compositions has been determined, have been used to examine the influence of base composition on the chromosome patterns. Considering that the amount of DNA as determined by the Feulgen reaction is almost constant along the chromosome arms and assuming that base composition is the only factor influencing the fluorescence of these dyes, a distribution of the A-T base pair content along the chromosomes has been calculated from the fluorescence intensity profiles. From the ratio of the intensity profiles obtained with quinacrine and proflavine, patterns showing the variation of the DNA content and of the A-T base pair content could also be obtained independently. The validity of these different approaches is discussed.     

The chromosomal localisation of human satellite DNA I

The major concentrations of human satellite DNA I (1.688 g/ml) have been localised on human chromosome preparations by the technique of in situ hybridisation using radioactive complementary RNA synthesised in vitro. Chromosomes were identified by prior study using quinacrine fluorescence microscopy. The satellite DNA is concentrated, mainly in centromeric constitutive heterochromatin, on many chromosomes but is especially obvious in the fluorescent distal segment of the Y chromosome.     

On the chemical basis of chromosome banding patterns.

A comparative study of the staining characteristics of four reagents for human chromosomes has been carried out. The four reagents are: (I) quinacrine mustard, as an alkylating agent, (II) the dihydroxy derivative of quinacrine mustard, (III) quinacrine, and (IV) 9-amino-6-chloro-2-methoxyacridine. The last reagent does not possess the amino substituted side chain even though it has the same intercalating nucleus. Comparison of the first three compounds in their staining and banding behavior suggested the initial step leading to banding may be the displacement of the nucleoprotein sites in hcromosomes. The Q and G banding could be blocked experimentally by treating the chromosome preparation with dimethylamine solution. This result may suggest that these sites have weaker basic proteins (nonhistone proteins?). The use of compound IV, which does not have the side chain in the molecule but does have the same intercalating chromophore, did not lead to banding and gives indirect support to this hypothesis. A combined use of compound IV and quinacrine may be useful for the determination of total DNA vs. banding DNA.