Nuclear labeling in immunoperoxidase studies of mouse tissue as detected by staining at acid pH.

Several peroxidase-Ig conjugates were applied to sections of fixed mouse tissue. When the peroxidase staining reaction was done at pH 4.5 instead of pH 7.4, a striking reaction on nuclear membrane, chromatin, or chromosomes was observed. This staining was prevented by pretreatment of sections with DNase but not with RNase or after acid elution of histones. It is suggested that at acid pH a redistribution and binding DNA of oxidized chromogen or of a chromogen-conjugate complex to DNA may account for the results observed.     

A role for DNA in the formation of nuclear estradiol-receptor complex in a cell-free system

Destruction of the DNA component of the nuclear pellet fraction of rat uterus homogenates with DNase prevented the formation of “nuclear” estradiol-receptor complex upon subsequent incubation with supernatant fraction containing 8S cytoplasmic estrogen-receptor complex. Nuclear pellet pretreatment with RNase had no effect on the reaction. DNase did not appear to release any component capable of binding estradiol or the 8S estradiol-receptor complex.     

Romanowsky-type staining: Enzymatic analysis of nuclear metachromasia in formalin-fixed paraffin sections

The red color of nuclei produced in formol-fixed paraffin sections stained with toluidine blue has been investigated by using deoxyribonuclease (DNase), ribonuclease (RNase) and 0.1 M Tris buffer. The action of DNase on formol-fixed material is not fully reliable, but clear-cut when positive. Nuclear basophilia and metachromasia is removed, nucleolar and cytoplasmic RNA is preserved. The picture produced by RNase depends to some extent on the concentration and acidity of the toluidine blue used for subsequent staining. Cytoplasmic RNA is always removed, while the red stain in nuclei usually remains intact. With 0.1% toluidine blue in 1% acetic acid, a nuclear color change from red to pale green is observed. Using this same staining solution, it can be shown that 0.1 M Tris buffer (overnight extraction at 37° C) will remove cytoplasmic RNA but leave intact the nuclear material that stains red. A red to green shift can subsequently be produced by RNase. From this it is deduced that there is a chromatin-associated nuclear RNA fraction which can be removed by the enzyme, but is stable to the buffer solution.     

Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids

The S9.6 antibody is broadly used to detect RNA:DNA hybrids but has significant affinity for double-stranded RNA. The impact of this off-target RNA binding activity has not been thoroughly investigated, especially in the context of immunofluorescence microscopy. We report that S9.6 immunofluorescence signal observed in fixed human cells arises predominantly from ribosomal RNA, not RNA:DNA hybrids. S9.6 staining was unchanged by pretreatment with the RNA:DNA hybrid–specific nuclease RNase H1, despite verification in situ that S9.6 recognized RNA:DNA hybrids and that RNase H1 was active. S9.6 staining was, however, significantly sensitive to RNase T1, which specifically degrades RNA. Additional imaging and biochemical data indicate that the prominent cytoplasmic and nucleolar S9.6 signal primarily derives from ribosomal RNA. Importantly, genome-wide maps obtained by DNA sequencing after S9.6-mediated DNA:RNA immunoprecipitation (DRIP) are RNase H1 sensitive and RNase T1 insensitive. Altogether, these data demonstrate that imaging using S9.6 is subject to pervasive artifacts without pretreatments and controls that mitigate its promiscuous recognition of cellular RNAs.     

Anti-native DNA antibodies from autoimmune sera also bind to DNA in mitochondria

Sera from 20 patients with systemic lupus erythematosus (SLE), selected for elevated titers of antibody to native DNA (nDNA), were examined by indirect immunofluorescence (IF) on tissue culture Hep-2 and rabbit kidney cells. Twelve sera showed a particulate cytoplasmic staining, in addition to nuclear IF. Double IF staining by using a mouse monoclonal anti-nDNA and a human serum containing anti-mitochondrial antibody as probes showed that the cytoplasmic structures recognized by these 12 SLE sera were mitochondria. SLE sera showing mitochondrial staining had high anti-nDNA levels, as assessed by ELISA (3.5 +/- 1.9 O.D.), compared with those not showing this staining pattern (0.8 +/- 0.4 O.D.). Mitochondrial staining was abolished by DNase I pretreatment of the substrates. Liquid phase absorption of serum anti-nDNA with S1 nuclease-treated calf thymus DNA or purified mitochondrial DNA also removed staining. These findings demonstrate that anti-nDNA antibodies from patients with SLE bind to DNA in intact mitochondria. Therefore, mitochondrial IF staining on tissue culture cells in the presence of nuclear staining should be interpreted with caution, because the phenomenon could be entirely related to anti-native DNA. These observations might also provide new insights concerning the nature of immunogenic cellular components stimulating anti-DNA production.     

Reactions of seven basic fluorochromes with unfixed cells obtained from the salivary glands of the dipteran fly Megaselia scalaris Loew (Phoridae)

Seven basic fluorochromes with varying specificities were used to stain the large squamous epithelial cells isolated from the larval salivary glands of Megaselia scalaris (Phoridae). Although the EDTA-based method selected for isolating the cells produced permeabilization and a loss of viability of the cells, consistent results were obtained with the various fluorochromes. The "classical" pattern of green nuclear and red cytoplasmic fluorescence observed in cells stained with acridine orange could be changed to green cytoplasmic and red nuclear fluorescence by pretreatment with RNase. The predominantly cytoplasmic and nucleolar fluorescence obtained with pyronine Y could be changed to mainly nuclear fluorescence by RNase pretreatment. The other five fluorochromes tested were not affected appreciably by extraction with RNase. Quinacrine mustard, dicarbocyanine (DiOC3(3)), and rhodamine 123 produced primarily cytoplasmic and nucleolar fluorescence, while nile red revealed mainly cytoplasmic lipid droplets. Phosphine 3R initially stained lipid droplets but very rapidly redistributed throughout the cytoplasm and nucleus. Because of their large size, flatness, and content of histochemically demonstrable components, the cells of Megaselia are especially appropriate for use as "optical objects" or controls in various studies. New methods of isolating the cells, however, will be needed to prevent permeabilization and loss of viability of the cells.     

Activité DNA-polymérase nucléaire dans les spermatozoides de souris et évolution de cette activité au cours de la spermatogenèse

The presence of a nuclear DNA polymerase activity has been demonstrated in the mouse testis by a cytochemical method. The enzyme was present in the nuclei of the various cell types of mouse spermatogenesis, including spermatozoa. The nuclear activity increased during meiotic prophase and then decreased in spermatids and spermatozoa. A peculiar attention was devoted to the properties of the nuclear DNA polymerase present in spermatozoa. All four deoxyribonucleoside-triphosphates were needed for optimal activity; the acid-insoluble radioactive product obtained by polymerization in situ was completely removed by DNase, but not by RNase nor by pronase. The reaction of polymerization was DNA-dependent, sensitive to high concentrations of KCl and not affected by NEM nor by PHMB.     

Tests for Nucleic Acid Selectivity of Einarson's Gallocyanin-Chrome Alum Stain on Monolayers of Strain L-929 Mouse Fibroblasts

L-929 fibroblasts, fixed on coverslips, were stained with gallocyanin-chrome alum after various treatments for removal of nucleic acid or for methylation or deamination. For nucleic acid, trichloroacetic acid and NaCl extractions and sequential incubation in DNase and RNase yielded cells unstainable with the dye complex. Methylated cells showed no cytoplasmic staining and a reduced nuclear staining, compared with the unblocked controls. Deamination had little effect. All results were dependent on the types of fixative used, times and temperatures of incubation, and in the case of nucleases, their concentration. Conventional dehydration and melted paraffin infiltration was associated with little or no staining of deaminated cells and intense staining of methylated cells. The paraffin effects were also dependent on fixatives. The evidence shows that gallocyanin-chrome alum combines with groups (presumably phosphate or carboxyl, or both) which are blocked by methylation, and which can be removed from L cells by sequential RNase and DNase treatment.     

DNA-Dependent RNA Polymerase Activity Associated with Subviral Particles of Polyhedral Cytoplasmic Dexoyribovirus

Polyhedral cytoplasmic deoxyribovirus virions contain a DNA-dependent RNA polymerase which catalyzes the incorporation of ribonucleotides into an acid-precipitable product. Treatment of virions with sodium deoxycholate and dithiothreitol resulted in the formation of subviral particles which could be separated from virions by rate zonal centrifugation in sucrose gradients. Subviral particles were RNA polymerase-positive and more active per unit mass of protein than virions. In vitro enzyme activity associated with subviral particles required addition of ribonucleotides, Mg(2+), and exogenous denatured DNA template. Optimal enzyme activity occurred over a broad pH (7.2 to 8.8) and Mg(2+) concentration (2 to 10 mumol) range. The specific activity of the RNA polymerase was maximal at 37 C. Addition of DNase or actinomycin D to the reaction mixture reduced the incorporation of [(3)H]UMP into an acid-precipitable product. The product of the reaction was sensitive to degradation by RNase but not to DNase or Pronase. These data suggest that the enzyme copies DNA into RNA.     

Double-stranded RNA and male sterility in rice

Summary Double-stranded RNA (dsRNA) was isolated from rice Oryza sativa ssp. japonica, but not from other subspecies. The dsRNA has been found in all of the examined cytoplasmic male-sterile (CMS) lines of BT (Chinsurah Boro II)-type rice, but was not detected in their companionate maintainer lines. It is uniquely and positivley correlated with the CMS trait in BT-type rice. Recently, the dsRNA was also found in a nuclear malesterile (NMS) rice, Nongken 58s, but was not found in its normal Nongken 58. The molecular weight of this dsRNA was estimated to be about 18 kb. Electron microscopic analysis reveals that it is linear snapped. The double strandedness of the RNA molecules was characterized by CF-11 cellulose column chromatography and nuclease treatments. It bound to CF-11 cellulose in the presence of 15% ethanol. It was sensitive to RNase A at low salt concentrations, but insensitive to DNase I, SI nuclease, and RNase A at high salt concentrations. The dsRNA was detected in both mitochondrial and cytoplasmic fractions. Dot-blot hybridization reveals that there is no sequence homology between this dsRNA and mtDNA, but there is homology between this dsRNA and nuclear genomic DNA. We have not been able to transmit this dsRNA to fertile rice.     

Isolating and sequencing the infrequent 3'-ends of a specific mRNA

Procedures are described for identification of very infrequent in vivo 3'-ends of RNA. After purification by filter hybridization, the 3'-ends were labeled with [5'-32P] cytosine-3'-P in the RNA ligase reaction. Significantly fewer counts were incorporated in the ligase reaction than in the polynucleotide kinase reaction to label 5'-ends. The incorporation was increased by increasing the RNA concentration 5-10 fold by using only one round of filter hybridization. Non-specific RNA binding could be eliminated by RNase A treatment of the filter if a great excess of denatured heterologous DNA was immobilized along with the DNA probe. Significant amounts of DNA were released when eluting the hybrid RNA from such filters. DNA inhibited the ligase reaction, while its DNase products were even more inhibitory. Treatment of the DNase products with alkaline phosphatase completely eliminated the inhibition. We detected no spurious 5'- or 3'-ends generated in the hybrid RNA by RNase A activity used to reduce the non-specific RNA. Also, RNase T1 could be used in place of RNase A to eliminate non-specific RNA binding, but about 25 times more RNase T1 (microgram/microgram) was needed. We used partial alkali digestion to sequence 3'-ends. A major (one hit) and minor (two hit) set of products were produced which could be distinguished from each other by alkaline phosphatase treatment and homochromatography of the products.     

Cytochemical significance of acridine orange staining of human plasmodia with some comments on double-stranded DNA

Summary Air-dried blood smears and erythrocyte suspension from patients infected with Plasmodium falciparum, stained under optimal conditions with acridine orange, permit easy detection of plasmodia with fluorescence microscopy together with a clear cytochemical colour differentiation of nuclear DNA (green or green-yellow) and cytoplasmic RNA (orange-red fluorescence). Judging from fluorescence characteristics of nuclei (DNase sensitive and RNase resistant green or green-yellow), the plasmodial DNA appears to be double-stranded.     

Antibodies against RNA hydrolyze RNA and DNA

Immunization of animals with DNA leads to the production of anti-DNA antibodies (Abs) demonstrating both DNase and RNase activities. It is currently not known whether anti-RNA Abs can possess nuclease activities. In an attempt to address this question, we have shown that immunization of three rabbits with complex of RNA with methylated BSA (mBSA) stimulates production of IgGs with RNase and DNase activities belonging to IgGs, while polyclonal Abs from three non-immunized rabbits and three animals immunized with mBSA are catalytically inactive. Affinity chromatography of IgGs from the sera of autoimmune (AI) patients on DNA-cellulose usually demonstrates a number of fractions, all of which effectively hydrolyze both DNA and RNA, while rabbit catalytic IgGs were separated into Ab subfractions, some of which demonstrated only DNase activity, while others hydrolyzed RNA faster than DNA. The enzymic properties of the RNase and DNase IgGs from rabbits immunized with RNA distinguish them from all known canonical RNases and DNases and DNA- and RNA-hydrolyzing abzymes (Abzs) from patients with different AI diseases. In contrast to RNases and AI RNA-hydrolyzing Abs, rabbit RNase IgGs catalyze only the first step of the hydrolysis reaction but cannot hydrolyze the formed terminal 2',3'-cyclophosphate. The data indicate that Abzs of AI patients hydrolyzing nucleic acids in part may be Abs against RNA and its complexes with proteins. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Preparation of the bifunctional enzyme ribonuclease-deoxyribonuclease by cross-linkage.

Protease-free bovine pancreatic deoxyribonuclease (DNase) (1.6 X 10(-4) mmol) was thiolated on the NH2 groups with N-acetyl-DL-homocysteine thiolactone (2.4 X 10(-2) mmol) at pH 10.5 with imidazole (2.4 X 10(-2) mmol) as the catalyst in the presence of 4,4'-dithiodipyridine (4.2 X 10(-2) mmol). The product obtained after 16 h at 4 degrees C, 2-acetamido-4-(4'-dithiopyridyl)butyryl-DNase, isolated by gel filtration, contained an average of 0.87 +/- 0.13 mol of mixed disulfide per mol of DNase. Ribonuclease (RNase) was thiolated in a similar manner, but under N2 in the absence of 4,4'-dithiodipyridine. The protein N-acetylhomocysteinyl-RNase contained on the average 0.94 +/- 0.11 mol of sulfhydryl groups per mol of RNase. The coupling of RNase ot DNase was accomplished by thiol-disulfide interchange at pH 6.2 and 25 degrees C for 90 min. The hybrid enzyme (yield 25--33%, based upon the DNase derivative used) was freed from unreacted DNase, RNase, and homodimers by gel filtration, affinity chromatography, and salting-out chromatography. The purified enzyme contained one molecule each of DNase and RNase and hydrolyzed thymus deoxyribonucleic acid (DNA) and yeast or transfer ribonucleic acid (RNA) with 75 and 40% of the efficiencies, respectively, of the parent enzymes. The RNA strand of the hybrid substrate, phage f1 DNA-[3H]RNA, prepared from phage DNA with RNA polymerase, was hydrolyzed rapidly by the hybrid enzyme but was not hydrolyzed by RNase alone. A conjugate of the two enzymes offers the possibility in vivo of delivering two enzymes that differ in size, charge, and biological function to the same site at the same time.     

Cytotoxic effects of methylnitrosourea on developing brain

The effect of methylnitrosourea (MNU) on cerebellar and cerebral DNA, RNA, protein, lysosomal enzymes (acid DNase, RNase, phosphatase, and beta-glucuronidase), and 2',3'-cyclic nucleotide 3'-phosphohydrolase (2',3'-CNPase) activities was studied in rats from birth through 12 days of age. Subcutaneous injection of MNU in a dose of 0.625 mmol/kg caused a suppression of increase in weights and content of DNA, RNA, and protein of cerebellum, but no changes in those of the cerebrum or in body weight. Ratios of protein and RNA to DNA were substantially elevated by MNU in the cerebellum but not in the cerebrum. Acid DNase and acid RNase activities of MNU-treated rats were significantly elevated beyond the increase of these activities in controls in the cerebellum, but no change in these activities by MNU was observed in the cerebrum. A slight elevation in acid phosphatase activity was observed in the cerebellum but not in the cerebrum after MNU pretreatment. Beta-glucuronidase and 2',3'-CNPase activities were not changed in the cerebellum or in the cerebrum. These results suggest that in the developing brain, especially in the cerebellum at the mitotic stage, MNU caused cell damage and inhibited cell mitosis.     

DETERMINATION OF RNA AND DNA CONCENTRATIONS IN NATURAL PLANKTON SAMPLES USING THIAZOLE ORANGE IN COMBINATION WITH DNASE AND RNASE DIGESTIONS1

A fluorometric technique, based on the combination of RNase and DNase incubation with the use of thiazole orange (RNase/DNase method), was investigated to determine DNA and RNA concentrations in marine plankton. Tests were performed to optimize both RNase and DNase assay conditions. The RNase assay should be conducted at 37° C for 20 min with 0.5 μg·mL^?1 of DNase-free RNase. An incubation at 25° C for 20 min with 10 units ·mL^-1 of RNase-free DNase were the optimal conditions required for DNA digestion by DNase. The detection limits in terms of minimum biomass for reliable measurements of DNA and RNA were 7.5 and 10 μg of protein · (mL assay)^?1, respectively. RNA and DNA concentration were estimated in oligotrophic water samples using the RNase/DNase and other available methods (e.g. a double fluorochrome method). The different techniques provided similar DNA estimations. However, the RNase/DNase method provided the highest sensitivity and a low variability for the estimation of RNA.     

Reverse differential staining of sister chromatids induced by Hoechst plus black light and endonuclease

A differential Giemsa staining between sister chromatids was obtained by treating chromosomes replicated twice in medium containing 5-bromodeoxyuridine (BrdU) with Hoechst 33258 plus black light at 55 degrees C (HB pretreatment) and deoxyribonuclease (DNase) I, II, or micrococcal nuclease. In this staining pattern the BrdU bifilarly substituted chromatids were darkly and the unifilarly substituted chromatids lightly stained. This staining pattern was obtained only by staining the HB-DNase I-treated chromosomes with Giemsa and methylene blue, not by several other dyes tested. Relatively more DNA labelling was removed from the non-BrdU-substituted than the BrdU-substituted chromosomes, when the HB-pretreated chromosomes were digested with DNase I. But the protein labelling was not removed appreciably in the same treatment. The differential DNase I sensitivity between the non-BrdU-substituted and BrdU-substituted chromosomes disappeared when the HB-pretreated chromosomes were incubated with proteinase K before The DNase I digestion. Moreover, no differential DNase I sensitivity was found between the HB-pretreated isolated DNA containing and not containing BrdU. We propose that during the HB pretreatment, more DNA-protein cross-linkings are induced in BrdU bifilarly substituted than the unifilarly substituted chromatids. This structure protects the chromosomal DNA against the DNase I digestion. Thus, a reverse differential Giemsa staining between sister chromatids is obtained by the HB-DNase I treatment.     

Intranuclear localization of the Ki-67 reactive antigen in HeLa cells. Flow cytometric analysis

The intranuclear localization of the Ki-67 reactive antigen was immunocytochemically investigated using flow cytometry. HeLa S3 cells were immunocytochemically stained with the monoclonal antibody, Ki-67, after in situ treatments with various kinds of compounds, namely: HCl; NaCl; RNase; Sl nuclease and DNase I. The only treatment that markedly diminished the immunofluorescence intensity of the cells was exposure to DNase I. Nuclear fluorescence was no longer observed in the cells digested with relatively high concentrations of DNase I. These results suggest that the antigen recognized by Ki-67 is closely associated with DNA, but is not directly associated with either the nuclear matrix or histones.     

Intranuclear localization of the Ki-67 reactive antigen in HeLa cells. Flow cytometric analysis

The intranuclear localization of the Ki-67 reactive antigen was immunocytochemically investigated using flow cytometry. HeLa S3 cells were immunocytochemically stained with the monoclonal antibody, Ki-67, after in situ treatments with various kinds of compounds, namely: HCl; NaCl; RNase; S1 nuclease and DNase I. The only treatment that markedly diminished the immunofluorescence intensity of the cells was exposure to DNase I. Nuclear fluorescence was no longer observed in the cells digested with relatively high concentrations of DNase I. These results suggest that the antigen recognized by Ki-67 is closely associated with DNA, but is not directly associated with either the nuclear matrix or histones.     

Co-localization of non-histone protein BA with U-snRNPs to the same regions of the cell nucleus

Using indirect immunofluorescence, nuclear non-histone protein BA was localized in a normal rat liver cell line. Protein BA antibodies immunostained nuclear structures producing a speckled immunofluorescent staining pattern. Nuclear structures stained with protein BA antibodies were sensitive to DNase I digestion, but not to RNase. The speckled pattern of nuclear fluorescence observed with protein BA antibodies was similar to that reported earlier for Sm antibodies, which react with U-snRNPs. Using double-label indirect immunofluorescence, the Sm antigen was shown to be concentrated in the same regions of the nucleus which contain protein BA. Immunoblot analysis of total nuclear proteins with the two antibodies demonstrated that protein BA and the major Sm antigen have similar molecular weights, but are antigenically distinct. In addition, they differ in their extractabilities from the cell nucleus.