Cytophotometric determination of unscheduled DNA synthesis

We describe a cytophotometric assay for unscheduled DNA synthesis (UDS) in asynchronously growing cells. Monolayer cultures of human HEp-2 and mouse MCa-11 cells were incubated with the carcinogen methyl-methane sulfonate (MMS), as well as with hydroxyurea and (3H)thymidine. Slides were prepared, and the DNA contents and areas of nuclei were measured by absorption cytophotometry. The labeling of the nuclei, determined on the basis of their DNA content to be in G0/G1, was selectively measured after the preparation of autoradiographs. The labeling of the G0/G1 cells increased with increasing doses of MMS. We also found that the increased nuclear labeling after MMS treatment was not due to induction of replicative DNA synthesis or selective destruction of G0/G1 cells. The results of this assay compared favorably with a standard biochemical method for measuring unscheduled DNA synthesis by benzoylated naphthoylated DEAE cellulose chromatography.     

Cytophotometric determination of DNA in mesotheliomas and reactive mesothelial cells

Cytophotometry was used to study the nuclear DNA content of cells in Feulgen-stained effusion specimens from 18 patients with mesothelioma and 14 patients with reactive mesothelial proliferations. The mean DNA content (MDNA) of mesothelioma cells was significantly higher than that of reactive mesothelial cells (P less than .001). Other parameters reflecting the DNA content also differed significantly between the two kinds of cells, including (1) the ratio of mean mesothelial DNA to mean lymphocyte DNA, (2) the percentage of mesothelial cells with DNA content exceeding three times the lymphocyte MDNA and (3) the coefficient of variation of the DNA content. Since these parameters were highly correlated, only one was accepted in a stepwise linear discriminant model for distinguishing reactive from mesotheliomatous effusions. The model correctly classified all of the reactive effusions studied and 89% of the mesotheliomatous effusions. These results indicate that DNA analysis, using the Feulgen stain and cytophotometry, yields criteria that may be useful in distinguishing benign reactive mesothelial cells from malignant mesothelioma in effusions when used in conjunction with other traditional parameters.     

Cytophotometric DNA determination correlated to karyotype, particularly in cancer

Variation from the normal in the distribution patterns of the DNA content of interphase tumor cells is considered in relation to the chromosome abnormalities that occur in these cells. The possible diagnostic and prognostic significance of the DNA distributions, particularly the modal values, of human tumors is discussed. Tumors with normal or near-normal modes frequently have a favorable prognosis, but this is not true for all tumor sites or types, including squamous-cell carcinomas of the cervix uteri and carcinomas of the large bowel, in which near-triploid tumors may have a relatively favorable prognosis.     

G-quadruplex DNA binding by a series of carbocyanine dyes.

We have examined a number of carbocyanine dyes for their ability to bind intramolecular G-quadruplex DNA structures (G4'-DNA) using a Taq polymerase stop assay. Of the five dyes examined, only one, N,N'-diethylthiacarbocyanine iodide (DTC), was found to bind to G4'-DNA. DTC was also the only dye found to inhibit human telomerase at 50 microM concentration.     

Modulation of binding of DNA to the C-terminal domain of p53 by acetylation

The binding of nonspecific DNA to the C-terminal negative regulatory domain (CTD) of p53 modulates its activity. The CTD is a natively unfolded region, which is subject to acetylation and phosphorylation at several residues as part of control. To measure the effect of covalent modification on binding to DNA, we synthesized a series of fluorescein-labeled CTD peptides with single and multiple acetylations at lysine residues that we had identified by NMR as making contact with DNA, and developed an analytical ultracentrifugation method to study their binding to DNA. Binding depended on ionic strength, indicating an electrostatic contribution. Monoacetylation weakened DNA binding at physiological ionic strength 2- to 3-fold, diacetylations resulted in further 2- to 3-fold decrease in the affinity, and tri- and tetraacetylations rendered DNA binding undetectable. Phosphorylation at S392 did not affect DNA binding. NMR spectroscopy showed binding to DNA did not induce significant structure into CTD, apart possibly from local helix formation.     

Linear dichroism studies of binding site structures in solution: Complexes between DNA and basic arylmethane dyes

The interaction between B-form DNA and twelve cationic triaryl-methane dyes was studied with respect lo optical properties and stabilities, using linear dichroism (LD) and aqueous two-phase partition techniques. Monovalent dyes derived from crystal violet as a rule form a single strong complex (K₁ ca 10⁵ M^?1; site density per nucleotide base n₁ ca 0.1 at 0.1M ionic strength) in which the plane of the dye is at an angle of less than 50° to the local DNA helix axis. The complex with fuchsin is weaker (10⁴M^?1) but can be explained by a similar orientation. For some of the dyes (those with pseudo-C_2v symmetry) XXXre angular orientations of two molecule-fixed axes can be obtained. For the divalent methyl green a second complex appears to be formed at low ionic strength. Methyl green (and to some extent 2-thiophene green and malachite green) show exciton splitting in the LD spectrum and circular dichroism assignable to exciton coupling between transition dipoles roughly parallel to the helical strands, indicating a dye-dye interaction. Tne optical data, supported by fitting experiments with space-filling models, suggests a general structure for the binding site. The dye is not intercalated but is bound to exposed hydrophobic regions in the major groove. The ligand is in part (the charged amino groups) in contact with the phosphoribose chain but its main surface lies against the hydrophobic base-pair stack. For a diphenylmethane dye, Michler's hydrol blue, a perpendicular orientation was observed, possibly due to intercaiation.     

Modification of the method for staining DNA with basic dyes]

The author studied the mechanisms and the applicability in histochemistry of the sodium bisulfate treatment with subsequent toluidine and methylene blue staining after Felgen's hydrolysis. Bisulfite treatment proved to increase the reaction intensity 11/2-fold; the stain is bound stoichiometrically. Toludidine blue results in a metachromatic and anisotropic staining of the cell nuclei. The method is recommended as a sensitive test for DNA in cytochemical investigations and for the study of dichroism of the DNA-containing structures.     

Cytophotometric determination of the DNA content in epithelial and connective tissue cells of the human prostate

A study of the quantitative parameters of DNA in cells nuclei of epithelium and connective tissue allowed establishing certain periods which are characterized by an increase in the percentage of ploidy. The causes and importance of this phenomenon for the development of pathological processes in tissues of the prostate gland and the possibility of its use for the diagnosis are discussed.     

Substitution of basic amino acids in the basic region stabilizes DNA binding by E12 homodimers.

The E2A gene encodes two alternatively spliced products, E12 and E47. The two proteins differ in their basic helix-loop-helix motifs (bHLH), responsible for DNA binding and dimerization. Although both E12 and E47 can bind to DNA as heterodimers with tissue-specific bHLH proteins, E12 binds to DNA poorly as homodimers. An inhibitory domain in E12 has previously been found to prevent E12 homodimers from binding to DNA. By measuring the dissociation rates using filter binding and electrophoretic mobility shift assays, we have shown here that the inhibitory domain interferes with DNA binding by destabilizing the DNA-protein complexes. Furthermore, we have demonstrated that substitution of basic amino acids (not other amino acids) in the DNA-binding domain of E12 can increase the intrinsic DNA-binding activity of E12 and stabilize the binding complexes, thus alleviating the repression from the inhibitory domain. This ability of basic amino acids to stabilize DNA-binding complexes may be of biological significance in the case of myogenic bHLH proteins, which all possess two more basic amino acids in their DNA binding domain than E12. To function as heterodimers with E12, the myogenic bHLH proteins may need stronger DNA binding domains.     

On the mechanism of sequence-specific DNA-dependent acetylation of p53: the acetylation motif is exposed upon DNA binding

P53 acetylation requires p300-docking to two contiguous sites in the activation domain that in turn mediates DNA-dependent acetylation of the tetramer. In an attempt to further define the mechanism of DNA-dependent acetylation of p53, an in vitro system has been reconstituted with distinct p53 isoforms and has been used to reveal conformational constraints on p53 acetylation. Two native p53 tetrameric isoforms purified from Sf9 cells differing by the extent of phosphorylation within the C-terminal acetylation site are both acetylated in a sequence-specific DNA-dependent manner. By contrast, p53 purified from an Escherichia coli expression system is in a largely denatured conformation and its acetylation is DNA-independent. Heating native p53 to destroy the folded structure restores DNA-independent acetylation similar to that seen with bacterially expressed p53. There are at least two sites of conformational flexibility in the p53 tetramer: the first in the flexible S10 beta-sheet within the MDM2 ubiquitination sequence and the second in the C-terminal regulatory domain. We analysed therefore whether DNA-dependent acetylation correlated with conformational changes in either of these two regions. DNA-dependent acetylation of p53 is maintained in a dose-dependent manner by low concentrations of consensus site DNA under conditions where flexibility in the S10 beta-sheet region is maintained. Oligonucleotide DNAs that promote acetylation stimulate the binding of monoclonal antibodies PAb421 and ICA-9; two antibodies whose contiguous epitopes overlap the C-terminal acetylation motif. By contrast, bent oligonucleotide DNAs that conceal both the S10 beta-sheet from binding of the monoclonal antibody DO-12 and attenuate binding of the monoclonal antibody PAb421 can preclude acetylation. These data suggest that, in the absence of DNA, the acetylation motif of p53 is in a cryptic state, but after DNA binding, allosteric effects mediate an exposure of the acetylation motif to allow DNA-dependent acetylation of the tetramer.     

Equilibrium shift by target DNA substrates for determination of DNA binding ligands

An equilibrium containing the thiol derivative of Hoechst33258 (Ht-SH), glutathione (G-SH), and the corresponding homo and hetero disulfides was shifted by the addition of the duplex DNA. It was shown from the analysis of the components that the hetero disulfide Ht-SS-G increased by binding with the DNA (CA14) with an A(3)T(3) binding motif for the structure of Hoechst33258, and that the different equilibrium shift was observed in the presence of CT14 with no A(3)T(3) binding motif.     

Cytophotometric determination of the nuclear DNA content of 23 Mexican and 18 non-Mexican isolates ofPhytophthora infestans

The nuclear DNA content of zoospores ofPhytophthora infestans was determined by Feulgen cytophotometry. Isolates from Mexico, where the sexual stage of the fungus is common, were compared with isolates from the United States and Europe. The mean nuclear DNA content of 23 Mexican isolates was 0.59 arbitrary units (a.u.; range, 0.48–0.79), while that of 18 non-Mexican isolates was 0.92 a.u. (range, 0.56–1.11). Mexican isolates are very likely diploid, as indicated by cytological studies of other workers. The non-Mexican group, by contrast, appears to include isolates that are diploid, triploid, tetraploid, and aneuploid. Of three non-Mexican isolates with DNA contents similar to those of the Mexican isolates (apparent diploids), two originated from Southern California and may be of recent Mexican origin.     

Photohemolysis sensitized by deuteroporphyrin-IX derivatives: determination of binding strength of dyes to erythrocytes

A comparative analysis of the ability of 4-(1-methyl-3-hydroxybutyl)-deuteroporphyrin-IX (I) and 2,4-di-(1-methyl-3-hydroxybutyl)-deuteroporphyrin-IX (II) to photosensitize hemolysis of human erythrocytes was performed. The photohemolytic efficiency of dye I was shown to be about 60 times higher than that of dye II. It was found that a part of each dye tightly binds to erythrocyte membranes and is not removed by washing. A method for estimating the share of the dye tightly bound to the membrane (beta) was proposed, which takes into account the shielding effect produced by the free dye and the photohemolytic efficiency of the bound dye. It was shown that the beta values for dyes I and II are 86 and 61% and correlate with the coefficients of distribution of the dyes in the octanol/water system (20.7 and 17.0, respectively).