A simple method for the fluorescence analysis of nucleic acid-dye complexes in cytological preparations

Summary This communication describes a simple method for recording fluorescence emission spectra of cytological preparations using a conventional fluorescence spectrophotometer. The emission characteristics of in situ complexes between some basic fluorochromes (DAPI, 33258 Hoechst, acridine orange, pyronin Y, and ethidium bromide) and nucleic acid containing structures from smears of chicken blood and Ehrlich tumor cells (chromatin, basophilic cytoplasm) are briefly described.     

A simple method for the fluorescence analysis of nucleic acid-dye complexes in cytological preparations

This communication describes a simple method for recording fluorescence emission spectra of cytological preparations using a conventional fluorescence spectrophotometer. The emission characteristics of "in situ" complexes between some basic fluorochromes (DAPI, 33258 Hoechst, acridine orange, pyronin Y, and ethidium bromide) and nucleic acid containing structures from smears of chicken blood and Ehrlich tumor cells (chromatin, basophilic cytoplasm) are briefly described.     

Optical studies on complexes between DNA and pseudoisocyanine.

Linear dichroism (LD) results when pseudoisocyanine=PIC (1,1-diethy1-2,2-cyannine iodide) binds to flow-oriented DNA. LD may be used to follow the complexation both stoichmetrically and structurally, since when specified to unti complex concentration LD provides a measure of the average orientation of the absorbing transition dipole. Two different types of complexes can be distinguished: I. One strong, ionic-strength insensitive complex with monomeric PIC with an orientation indication intercalation. II. Several weaker complexes of electrostatic nature (only observed at I less than 0.2M Na Cl) among which those with dimeric (IIa) and with polymeric (IIb) PIC are concluded both from LD and from circular dichroism (CD). The dimer is probably formed by employing one intercalated PIC as a second site. The polymer complex is characterized by a very sharp absorption band at 553 nm polarized parallel to the DNA-axis (with positive LD and positive CL). The structure, a right-handed helical array of PIC molecules, is discussed in terms of exciton theory in relation to that of polymeric free PIC ("Scheibe polymer") which is also shown to interact with DNA (IIc) yielding a large aggregate which is degraded at a distinct flow force field...     

Optical studies of the interaction of 33258 Hoechst with DNA,chromatin, and metaphase chromosomes

The interaction of the bisbenzimidazole dye 33258 Hoechst with DNA and chromatin is characterized by changes in absorption, fluorescence, and circular dichroism measurements. At low dye/phosphate ratios, dye binding is accompanied by intense fluorescence and circular dichroism and exhibits little sensitivity to ionic strength. At higher dye/phosphate ratios, additional dye binding can be detected by further changes in absorptivity. This secondary binding is suppressed by increasing the ionic strength. A-T rich DNA sequences enhance both dye binding and fluorescence quantum yield, while chromosomal proteins apparently exclude the dye from approximately half of the sites available with DNA. Fluorescence of the free dye is sensitive to pH and, below pH 8, to quenching by iodide ion. Substitution of 5-bromodeoxyuridine (BrdU) for thymidine in synthetic polynucleotides, DNA, or unfixed chromatin quenches the fluorescence of bound dye. This suppression of dye fluorescence permits optical detection of BrdU incorporation associated with DNA synthesis in cytological chromosome preparations. Quenching of 33258 Hoechst fluorescence by BrdU can be abolished by appropriate alterations in solvent conditions, thereby revealing changes in dye fluorescence of microscopic specimens specifically due to BrdU incorporation.     

AluI-resistant chromatin of chromosome 18: classification,frequencies and implications

The pericentric chromatin of chromosome 18 was found to be far more heterogeneous for restriction endonuclease AluI (5 ··· AG CT···3) than previously thought. The extent of such heterogeneity was characterized using 50 normal Caucasians and 5 cases of trisomy 18 or Edwards' Syndrome. The AluI-resistant chromatin can arbitrarily be classified into at least five sizes by comparison with the length of the short arm (p) of chromosome 18. They are: negative (1), small (2), medium (3), large (4) and very large (5) with incidences of 11.30%, 19.13%, 29.57%, 29.57% and 10.43%, respectively. In addition the location of the chromatin can be classified into four types depending upon the position relative to the primary constriction. For example: Type I (absent); Type II (present on p arm only); Type III (present on q arm only); Type IV (present on centromere and extending into both p and q arms). The incidences of types I, II, III, and IV were 11.30%, 62.61%, 0.87%, and 25.22%, respectively. Based on limited data, AluI-resistant chromatin was found to be predominantly large and very large in Edwards' Syndrome samples. In addition, no case with negative Alu-resistant chromatin was noted. Therefore, it is tempting to speculate that the amount of chromatin present on the centromere might play a role in non-disjunction in Edwards' Syndrome cases. Although the variation observed in the present study is continuous, the proposed classification has some important implications for future investigations.     

Biochemical and cytological studies of bleomycin actions on chromatin and chromosomes

Interaction of bleomycin with nuclei isolated from a variety of mammalian cells resulted in the release of nucleosomes. When isolated mononucleosomes (core plus linker) were re-treated with bleomycin, no further degradation of DNA occurred. The results suggest that the bleomycin cleavage sites in chromatin are present only in the linker region and that there are probably only one or two cleavage sites per linker. The repeat lengths of nucleosomal DNA released by bleomycin from nuclei of different species are different; this variability is considered to reflect the length of the linker. Incorporation of BrdU into DNA did not alter the bleomycin action on nucleosomes. When mitotic cells were held at metaphase for a prolonged period, bleomycin caused a gradual disintegration of chromosomes, although the bleomycin cleavage sites in metaphase chromosomes were found to be the same as those in interphase nuclei.     

Optical absorption and fluorescence spectroscopy studies of ground state melanin-cationic porphyrins complexes.

Optical absorption and fluorescence spectroscopies were employed in the study of the interaction between synthetic L-dopa (dihydroxyphenylalanine) melanin and the cationic porphyrins tetrakis(4-N-methylpyridyl) porphyrin (TMPyP), tetrakis(4-N-benzylpyridyl)porphyrin (TBzPyP), zinc tetrakis(4-N-methylpyridyl)porphyrin (ZnTMPyP) and zinc tetrakis (4-N-benzylpyridyl)porphyrin (ZnTBzPyP). Optical absorption and fluorescence properties of the porphyrins were dependent on the symmetry of the central ring. No evidence was found for dimerization of the porphyrins in phosphate buffer, pH 7, in the concentration range between 4 x 10(-8) to 5 x 10(-5) M. Addition of L-dopa melanin red shifted the optical absorption spectra of porphyrins, concomitant to broadening and reduction in intensity of the bands. L-Dopa melanin also strongly quenched the fluorescence of the porphyrins. Time resolution of the fluorescence decay of porphyrins showed at least two lifetimes that were only slightly modified in the presence of melanin. The interaction between melanin and porphyrin resulted in the formation of non-fluorescent ground state complexes. It was found that there are two different classes of binding sites in melanin for complexation with cationic porphyrins and the values of dissociation constants are of the order of 10(-8) M. These values and the number of binding sites are dependent on the nature of the porphyrins. It was shown that the binding has electrostatic origin, but it is also affected by metal coordination and hydrophobic interaction.     

Molecular and cytological characteristics of nuclear DNA and chromatin for angiosperm systematics: DNA diversification in the evolution of four orchids

The species- and genus-specific DNA content, average base composition of nuclear DNA, presence or absence of satellite DNA, the percentage of heterochromatin and other characteristics of nuclear DNA and nuclear structure allow to deduce the molecular changes which accompanied, or more probably caused, cladogenesis in the orchids studied. It is suggested that saltatory replication (generative amplification) of certain DNA sequenes, diversification of reiterated DNA sequences, and loss of DNA play an important role in the evolution of orchids.—The relationship between changes of genome composition and of nuclear structure and ultrastructure is discussed on the basis of cot curves, heterochromatin staining with Giemsa (C banding), electron microscopy of nuclei, and molecular hybridization in situ.Some aspects of this paper have been presented at the Helsinki Chromosome Conference, August 1977 (Nagl & Capesius 1977).     

Specific and non-specific interactions of ParB with DNA: implications for chromosome segregation

The segregation of many bacterial chromosomes is dependent on the interactions of ParB proteins with centromere-like DNA sequences called parS that are located close to the origin of replication. In this work, we have investigated the binding of Bacillus subtilis ParB to DNA in vitro using a variety of biochemical and biophysical techniques. We observe tight and specific binding of a ParB homodimer to the parS sequence. Binding of ParB to non-specific DNA is more complex and displays apparent positive co-operativity that is associated with the formation of larger, poorly defined, nucleoprotein complexes. Experiments with magnetic tweezers demonstrate that non-specific binding leads to DNA condensation that is reversible by protein unbinding or force. The condensed DNA structure is not well ordered and we infer that it is formed by many looping interactions between neighbouring DNA segments. Consistent with this view, ParB is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from two different DNA molecules in trans. The experiments provide no evidence for the promotion of non-specific DNA binding and/or condensation events by the presence of parS sequences. The implications of these observations for chromosome segregation are discussed.     

Filter combinations and light sources for fluorescence microscopy of quinacrine mustard or quinacrine stained chromosomes

Summary The efficiency of various combinations of primary and secondary filters, and light sources for the fluorescence microscopy of chromosomes stained with quinacrine mustard or quinacrine has been studied quantitatively. Using epi-illumination, strong fluorescence could be obtained with a mercury or xenon lamp in combination with two KP 490 short-wave pass interference filters (tilted to an angle of 60° with the excitation beam) as primary filter, and a K 490 as a secondary filter. The combination of a mercury lamp and a narrow band interference filter with a maximal transmission at about 436 nm as a primary filter together with a K 490 secondary filter results in a good visual image contrast, sufficiently strong fluorescence, and a relatively slow rate of fading.     

Structural heterogeneity of chromatin preparations at the level of DNA topology

The structural heterogeneity of calf thymus chromatin preparations was studied at the level of DNA topology by analysing the influence of ethidium bromide on the chromatin viscosity in deproteinizing medium. In 0.7 M NaCl the chromatin was separated into the fractions with linear DNA (3--36% in various preparations) and with supercoiled circular DNA (scc DNA), which differ from each other in their adhesive properties. Reduction of disulfide bonds in residual chromatin protein with 5% mercaptoethanol linearized scc DNA, present in chromatin preparations as nuclear matrix subunits containing some loops of scc DNA on the protein globule.     

DNA and chromatin imaging with super-resolution fluorescence microscopy based on single-molecule localization

With the expansion of super-resolution fluorescence microscopy methods, it is now possible to access the organization of cells and materials at the nanoscale by optical means. This review discusses recent progress in super-resolution imaging of isolated and cell DNA using single-molecule localization methods. A high labeling density of photoswitchable fluorophores is crucial for these techniques, which can be provided by sequence independent DNA stains in which photoblinking reactions can be induced. In particular, unsymmetrical cyanine intercalating dyes in combination with special buffers can be used to image isolated DNA with a spatial resolution of 30-40 nm. For super-resolution imaging of chromatin, cell permeant cyanine dyes that bind the minor groove of DNA have the potential to become a useful alternative to the labeling of histones and other DNA-associated proteins. Other recent developments that are interesting in this context such as high density labeling methods or new DNA probes with photoswitching functionalities are also surveyed. Progress in labeling, optics, and single-molecule localization algorithms is being rapid, and it is likely to provide real insight into DNA structuring in cells and materials.     

Molecular cytological differentiation of active from inactive X domains in interphase: implications for X chromosome inactivation

A fluorescence in situ hybridization method using a biotinylated DNA probe specific for the centromeric region of the human X chromosome was used to differentiate the genetically active from the inactive X in interphase cells. With this technique, we were able to interpret both the relative position and the degree of condensation of the X chromosomes within the nucleus. We first established the specificity of fluorescence labelling of the hybridized probe by comparing its location and appearance (either dense or diffuse) when associated with a sex chromatin body (SCB) in early passage normal human female fibroblasts. In these cells, where the presence of inactive X chromatin was verified by identification of a 4',6-diamidino-2-phenyl indole (DAPI)-positive SCB in 85% of the cells examined, the X chromatin fluorescence was always associated with the SCB. The signal was dense in structure in 98% and peripheral in location in 80% of the nuclei. A second type of signal, diffuse in form, was observed in 85% of the nuclei and presumably represents the location of the active X chromosome. It was located peripherally or centrally with equal frequency and was not associated with any identifiable nuclear component. This diffuse signal was the major type associated with human male fibroblasts. In rodent x human hybrid cells containing a human inactive X, the fluorescent signal was associated with an SCB-like structure in only 13% of the nuclei; it was dense in 66% of the nuclei and equally peripheral or central in location. This indicates an alteration in the interphase structure of the human inactive X chromosome in hybrid cells which may explain its known instability with respect to genetic activity in such systems.     

Specific detection of kinetoplast DNA in cytological preparations of trypanosomes by hybridization with complementary RNA

Fibroblasts from patients with Xeroderma pigmentosum (X.P.) were used together with normal fibroblasts, in order to test (1) whether complementation takes place in heterokaryons formed by these cells; (2) whether the ‘factor’ defective in X.P. limits the rate of DNA repair synthesis in normal fibroblasts. Proximity to normal fibroblasts as well as treatment with their extract does not significantly affect the DNA repair synthesis of the abnormal cells, as measured by autoradiography. By contrast, in heterodikaryons a corrective substance rapidly diffuses into the abnormal nuclei which then perform a normal amount of DNA repair synthesis. Such complementation does not require de novo protein synthesis, since it occurs in the presence of daunomycin or cycloheximide. Furthermore, the dilution of normal ‘factor’, which follows diffusion, does not prevent each nucleus in these hybrids from showing a normal amount of DNA repair synthesis even after UV doses capable of saturating the DNA repair system of the normal parental cells. Thus it seems that in normal fibroblasts the factor defective in X.P. is not rate limiting.Nevertheless, a comparison of heteropolykaryons with a high (3:1) and a low (1:1.25) average ratio of X.P. to normal nuclei shows that, in the former, DNA repair synthesis is reduced. This effect, which seems rather long lasting, indicates that the carrier state for X.P. could be detected using the dosimetric help of heteropolykaryons.     

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.