A refined method for silver staining of nucleic acids fixed on nitrocellulose

A refined silver staining method was developed to stain nucleic acids fixed onto nitrocellulose membranes and nylon-based membranes. Approximately 4 ng RNA or DNA can be stained with this method with no protein interference. This method involves simple repetition of immersions of membranes in three solutions prepared from common chemicals. The total staining time is less than 30 min.     

Microscale autoradiographic method for the qualitative and quantitative analysis of apoptotic DNA fragmentation

A method combining the advantages of electrophoretic DNA fractionation and autoradiography is described for the qualitative and quantitative analysis of internucleosomal DNA fragmentation that occurs during apoptosis, or “programmed cell death”. This procedure utilizes terminal transferase enzyme to uniformly add one molecule of [α ³²P]-to the 3′-of DNA fragments. Following gel electrophoresis and autoradiographic analysis, the total amount of radiolabel incorporated into the low molecular weight DNA fraction can be quantitated and used to estimate the degree of apoptotic DNA fragmentation in any given sample. This method requires as little as 15 ng of total cellular DNA and increases the sensitivity of apoptotic DNA detection by at least 100-fold over the widely used ethidium bromide staining method. The procedure should prove valuable for the analysis of apoptosis in minute quantities of tissues and cultured cells. © 1993 Wiley-Liss, Inc.     

A visible dye-based staining method for DNA in polyacrylamide gels by ethyl violet

We describe a visible dye-based staining method for DNA in polyacrylamide gels using ethyl violet (EV). The novel method is a background-free, sensitive, economical, and simple procedure involving only staining and washing steps that can be completed within 30 min. As little as 0.8-1.6 ng of φX174 DNA/HaeIII can be detected by EV, which is about eightfold more sensitive than Nile blue (NB) stain and twofold less sensitive than ethidium bromide (EB) stain.     

两种核酸染料染色效果的比较研究

用前染和后染两种不同的染色方法,研究比较SYBRGreenI和溴化乙锭(EB)两种核酸染料对凝胶中DNA的染色效果和灵敏度,及SYBRGreenI取代EB用于常规凝胶中核酸染色的可能性。结果表明,用前染法染色SYBRGreenI对琼脂糖凝胶中的核酸染色效果与EB相当;用后染法染色前者要优于后者,可显示5ng以下的DNA条带,在完全相同的操作条件下,其染色DNA条带背景清晰,灵敏度较高。因此,无致突变性新型染料SYBRGreenI可替代强致突变性染料EB用于检测凝胶中DNA片段大小、含量等,从而减少由于使用EB带来的环境污染和人体健康危害。     

A silver stain for the rapid quantitative detection of proteins or nucleic acids on membranes or thin layer plates

A relatively simple silver stain which takes less than 15 min to perform has been developed for the detection of nanogram quantities of proteins and DNA on cellulose membranes and thin layer plates. This stain demonstrates a reproducible curvilinear relationship between silver density and the amount of protein or DNA, over an averaged concentration range from 1 to 300 ng for proteins and 10 to 710 ng for DNA. The ease of staining proteins and DNA on membranes, combined with the stain's sensitivity and reproducibility, permits the use of this procedure for the quantitative determination of nanogram amounts of proteins and DNA. The simplicity of this silver stain has also permitted a survey of the staining properties of individual amino acids, purine and pyrimidine bases, nucleosides, nucleotides, homopolymers, and small peptides of known sequence. This survey demonstrated the importance of the basic amino acids, particularly lysine and histidine, and the sulfur-containing amino acids in the detection of proteins. It also indicated that the purine bases may play an important role in the detection of DNA.     

Ultrasensitive staining of nucleic acids with silver

A method for ultrasensitive detection of proteins on polyacrylamide gels by staining with silver, recently described by C. R. Merril, D. Goldman, S. A. Sedman, and M. H. Ebert (Science211, 1437–1438 (1981)), was applied with slight modifications to staining nucleic acids. Silver staining of double-stranded DNA was at least 100 times as sensitive as fluorescence staining with ethidium bromide, and at least 20 times as sensitive as staining with ammoniacal silver. The limit of detection of double-stranded DNA was approximately 25–50 pg/band with a cross-sectional area of 5 mm². The intensities of silver staining of double-stranded fragments 271 bp or longer from HaeIII endonuclease digests of φX174 RF DNA were linear over a concentration range of 0.25 to 4 ng DNA/band. RNA and single-stranded DNA species as short as 10 to 20 nucleotides were detected with high sensitivity after electrophoresis on denaturing gels containing urea, suggesting that silver staining may be applicable to the sequencing of a few micrograms of unlabeled DNA. Methods for staining DNA using ammoniacal silver were relatively insensitive for small DNA fragments.     

A simple method of protein determination in polyacrylamide gel using silver staining

A simple and relatively rapid method is elaborated for development of electrophoregram in PAAG by silver binding directly with protein. This permits avoiding the gel staining, considerably improves the quality of staining and promotes better reproducibility of the results. Sensitivity of the method permits detecting 1 ng of protein in the band.     

Detection of DNA in agarose gels using berberine and Mordant Yellow 3R.

A nontoxic and simple staining method for the detection of DNA in agarose gels is described. After eletrophoretic separation, the gels were stained with 5 microg/ml of berberine (BB) prepared in distilled water and then the gels were soaked in 20 microg/ml of aqueous Mordant Yellow 3R (MY3R) solution. Employment of MY3R as a counterion dye efficiently quenched unwanted background fluorescence of BB. This method can detect as little as 10 ng of plasma membrane H(+)-ATPase cDNA obtained from Arabidopsis thaliana L. (AHA1, 3.2 kb) under a long wavelength of UV irradiation (366 nm) within 1 h.     

Rapid staining of proteins on polyacrylamide gels and nitrocellulose membranes using a mixture of fluorescent dyes

The present work describes a novel, fluorescence-based method for staining proteins on SDS-PAGE and membrane(s). In this method, proteins are stained using a mixed-dye (sulfo-rhodamine B and 1-anilino-8-naphthalene sulfonic acid (NH(4)(+))) solution. The mixed-dye staining protocol can detect proteins up to a concentration of 15 ng. This method is generally applicable to all proteins and is more sensitive than the conventional Coomassie blue method. The staining method is rapid and efficient. Staining-destaining of proteins using the mixed-dye protocol takes less than half an hour. Another interesting feature of the staining protocol described here is the applicability to the staining of proteins on nitrocellulose membranes.     

Interaction of cyanine dyes with nucleic acids: XXXI. Using of polymethine cyanine dyes for the visualization of DNA in agarose gels

Fifteen polymethine cyanine dyes were studied as fluorescent stains for DNA in electrophoretic gels. Among studied cyanines, two dyes CPent V and CCyan 2-O most effectively visualized covalently closed and linear double-stranded DNA molecules in gels under standard conditions using UV-illumination, green filter and black-and-white photo film. Ethidium bromide was 1.2-1.6 times more effective as compared to cyanine dyes in staining of DNA in the concentration range of 8-18 ng, while studied cyanines were more sensitive to DNA quantity above 50 ng.     

DNA staining in agarose gels with Zn²+-cyclen-pyrene

A pyrene-labeled Zn2+-cyclen complex for the staining of DNA in agarose gels is reported. The metal chelate coordinates reversibly to the DNA phosphate backbone, which induces the formation of pyrene excimers. The typical pyrene excimer emission is used for the detection of the DNA. Staining is limited to agarose gels and is less sensitive than ethidium bromide, but DNA amounts as low as 10 ng and short DNA strands (～300 b.p.) are detectable. Gel extraction as a standard technique in molecular biology was successfully performed after staining with Zn2+-cyclen-pyrene. Cytotoxicity tests on HeLa and V-79 cells reveal that the zinc-cyclen pyrene probe is significant less toxic compared to ethidium bromide.     

Dynamic functional and structural analysis of living cells: New tools for vital staining of nuclear DNA and for characterisation of cell motion

Increasing interest has been paid to applications of fluorescence measurements to analyze physiological mechanisms in living cells. However, few studies have taken advantage of DNA quantification by fluorometry for dynamic assessment of chromatin organization as well as cell motion during the cell cycle. This approach involves both optimal conditions for DNA staining and cell tracking methods. In this context, this report describes a stoichiometric method for nuclear DNA specific staining, using the bisbenzimidazole dye Hoechst 33342 associated with verapamil, a calcium membrane channel blocker. This method makes it possible to correlate variations of nuclear DNA content with cell motion in cells that are maintained alive. Motion measurement is the second goal of this paper and it explains the snake-spline method, and the associated cell following method.     

Detection of a few picograms of DNA on polyacrylamide gels by silver staining

DNA fragments separated on polyacrylamide gels are silver stained in ethanolamine solution. The staining procedure can be completed in 3 1/2 h. Illumination of the gels on a black background increases the sensitivity of detection compared with the usual transillumination. The limit level of detection is 3-5 pg per band with a cross-sectional area of 5 mm2. Five to fifty picograms of DNA may be detected quantitatively by scanning the gels. The method will detect 0.1 to 1 ng per band of low-molecular-weight RNA components.     

DNA Staining in Agarose Gels with ZN2+-Cyclen-Pyrene

A pyrene-labeled Zn²⁺-cyclen complex for the staining of DNA in agarose gels is reported. The metal chelate coordinates reversibly to the DNA phosphate backbone, which induces the formation of pyrene excimers. The typical pyrene excimer emission is used for the detection of the DNA. Staining is limited to agarose gels and is less sensitive than ethidium bromide, but DNA amounts as low as 10 ng and short DNA strands (～300 b.p.) are detectable. Gel extraction as a standard technique in molecular biology was successfully performed after staining with Zn²⁺-cyclen-pyrene. Cytotoxicity tests on HeLa and V-79 cells reveal that the zinc-cyclen pyrene probe is significant less toxic compared to ethidium bromide.     

A rapid single step staining technique for DNA analysis by flow microfluorimetry

A new procedure is reported for the staining of DNA, for flow microfluorimetry. It allows the production of stained cell nuclei in a single step by incorporating the DNA stain with a solution of the nonionic detergent Triton-X-100. This method has been found to be applicable to all DNA fluorochromes tested (ethidium bromide, propidium iodide, mithramycin, DAPI, Hoechst 33342). DNA histograms obtained in this way are comparable to those using conventional staining techniques, e.g., ethanol fixation followed by staining. Using this procedure the DNA content distribution of solid tissue or cells from suspension or monolayer cultures can be generated in less than 5 min.     

Live-cell assay for detection of apoptosis by dual-laser flow cytometry using Hoechst 33342 and 7-amino-actinomycin D

This protocol describes a rapid and simple method for the identification of apoptotic cells. Owing to changes in membrane permeability, early apoptotic cells show an increased uptake of the vital DNA dye Hoechst 33342 (HO342) compared with live cells. The nonvital DNA dye 7-amino-actinomycin D (7-AAD) is added to distinguish late apoptotic or necrotic cells that have lost membrane integrity from early apoptotic cells that still have intact membranes as assayed by dye exclusion. The method is suitable to be combined with cell surface staining using Abs of interest labeled with fluorochromes that are compatible with HO342 and 7-AAD emissions. Surface antigen staining is carried out according to standard methods before staining for apoptosis. The basic assay can be completed in 30 min, and extra time is needed for cell surface antigen staining.     

DNA cytofluorometry on large and small cell nuclei stained with pararosaniline Feulgen

Summary To examine reliability of DNA cytofluorometry with conventional Feulgen staining, measurement was carried out on smears of small and large neurons of human cerebellum, using a Digital-Microfluorometer with incident green light excitation. Nuclear fluorescence of the inner granule neuron and the Purkinje cell came to good agreement with each other when the staining was reduced so that the maximal extinction of the excitation beam nowhere exceeded the value of 0.1. The reduction of the feulgen staining is realized with unimpaired proportionality by treatment with 0.05% Schiff's reagent (pH 2.3) at 7–10° C for 10 min. It is concluded that this staining condition assures accurate determination of DNA content irrespective of size of the nucleus and of pattern of the chromatin distribution.     

Immunocytochemical detection of sulphonylated DNA in tissue sections. An alternative to Feulgen staining of DNA

We report here on a new sensitive and highly specific DNA staining technique which we have called sulpho-DNA staining. DNA staining is based on a sulphonylation reaction of 2'-deoxycytidine or cytidine that takes place in the 6th position of cytosine with ensuing immunodetection of the sulphonylated DNA. The specificity of DNA staining is introduced by the use of an antibody recognizing only modified DNA but not modified RNA, by recourse to an additional acid hydrolysis step which destroys RNA but not DNA. We describe here the optimal conditions for the sulphonylation of DNA using O-methylhydroxylamine and metabisulphite as reactants. The new DNA stain labels all nuclei in either normal human tissue or in tumor cells. For nuclear DNA the staining signal is higher for the sulpho-DNA staining than for the Feulgen staining for nuclear DNA. This new DNA staining technique is suitable for use on tissue sections as well as on cytosmears.     

Preliminary studies on DNA retardation by MutS applied to the detection of point mutations in clinical samples

MutS ability to bind DNA mismatches was applied to the detection of point mutations in PCR products. MutS recognized mismatches from single up to five nucleotides and retarded the electrophoretic migration of mismatched DNA. The electrophoretic detection of insertions/deletions above three nucleotides is also possible without MutS, thanks to the DNA mobility shift caused by the presence of large insertion/deletion loops in the heteroduplex DNA. Thus, the method enables the search for a broad range of mutations: from single up to several nucleotides. The mobility shift assays were carried out in polyacrylamide gels stained with SYBR-Gold. One assay required 50-200 ng of PCR product and 1-3 microg of Thermus thermophilus his6-MutS protein. The advantages of this approach are: the small amounts of DNA required for the examination, simple and fast staining, no demand for PCR product purification, no labelling and radioisotopes required. The method was tested in the detection of cancer predisposing mutations in RET, hMSH2, hMLH1, BRCA1, BRCA2 and NBS1 genes. The approach appears to be promising in screening for unknown point mutations.     

The staining behavior of oocyte cytoplasm with the alcoholic Feulgen variant and with methyl green

Summary A variant of the Feulgen reaction which has been proposed as a method for demonstrating cytoplasmic DNA in oocytes has been tested on ovarian material from a variety of species. While Schiff positive staining was developed, this was not removable by pretreatment with DNase and could be reproduced by using oxidants used in the pseudoplasmal reaction. This method was not considered useful for demonstrating cytoplasmic DNA.When chloroform extracted solutions of methyl green were used to stain ovaries, cytoplasmic staining identical in pattern to that obtained with other basic dyes was observed. The cytoplasmic staining was prevented by pretreatment of sections with RNase, but was not affected by DNase pretreatment. In somatic cells with high concentrations of cytoplasmic RNA, only nuclear staining was observed. This nuclear staining was labile to DNase but not to RNase.This work was supported by U.S. Public Health Service grants GM-10003-03 and K-3-6176-03.Contribution number 376 of the Bermuda Biological Station.