Measurement of DNA single-strand breaks by alkaline elution and fluorometric DNA quantification

The method presented is based on the alkaline elution procedure for the determination of DNA single-stand (ss) breaks developed by Kohn and on the principles of DNA quantification after binding with the dye Hoechst 33258. In the present study, modification of the alkaline elution procedure with regard to the elution solution volume was performed. The influences of the DNA strandedness, the ethylenediaminetetraacetate/tetraethylammonium hydroxide denaturation and elution solution presence, the DNA solution pH, the dye amount, and the incubation time for the formation of the dye-ssDNA complex on the DNA fluorometric quantification were also studied. The modified DNA alkaline elution procedure followed by the optimized fluorometric determination of the ssDNA was applied on liver tissue from both untreated and treated (N-nitroso-N-methylurea- administered) Wistar rats. The criteria for the selection of the appropriate estimator and statistical analysis of the obtained results are also presented. The method of the DNA alkaline elution followed by fluorometric determination of ssDNA as modified and evaluated is an accurate and reliable approach for the determination of in vivo induced ssDNA strand breaks.     

A modified method of quantitative colorimetric DNA-DNA hybridization on membrane filters for bacterial identification

Based on conventional membrane filter dot hybridization protocols, a modified method for the quantitative measurement of DNA-DNA reassociation is described. Labeled DNA probes are prepared with Photobiotin and hybridized with immobilized target DNAs on nitrocellulose filters. The extent of hybridization is detected by an enzyme linked assay in microtiter plates using streptavidine-alkaline phosphatase conjugates as reporter enzymes and nitrophenylphosphate as the colorimetric substrate. The procedure is non-destructive and allows the re-use of the filter holding the target DNAs. The results of the membrane filter hybridizations have been compared to spectroscopic DNA-DNA hybridizations and the limits and the applicability of the method for bacterial taxonomy and bacterial identification are discussed.     

The TEACL method of DNA-DNA hybridization: Technical considerations

Summary This paper emanated from a conference concerning the value, accuracy, and technical considerations of DNA-DNA hybridization for evolutionary studies. Our laboratory has been performing the so-called TEACL (tetraethylammonium chloride) method, and we have amassed sufficient data to indicate that this method is very powerful if performed properly with correct analyses. Here we address five technical considerations: (1) We present empirical data that size correction for tracer length is legitimate and accurate. (2) We show that the error of Tm measurement does not significantly increase with increasing distance up to at least 10°C. (3) The error distribution for Tm does not deviate from the expected normal distribution indicating parametric statistics are probably legitimate for analyses. (4) Using a known phylogeny we examined the resolving power of the technique by showing that at least five taxa can be correctly placed in phylogenies with a maximum Tm of 2.5°C. (5) To data, all our data sets based on DNA-DNA hybridization are very robust with respect to analytical procedures in that every algorithm used on the data sets has yielded identical trees with nearly identical branch lengths. Nevertheless, we point out that theoretical analyses of distance data (as generated by DNA-DNA hybridization) are lacking, especially with regard to tests of the molecular clock hypothesis.     

The phylogeny of the hominoid primates,as indicated by DNA-DNA hybridization

Summary The living hominoid primates are Man, the chimpanzees, the Gorilla, the Orangutan, and the gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. The composition of the Hominoidea is not in dispute, but a consensus has not yet been reached concerning the phylogenetic branching pattern and the dating of divergence nodes. We have compared the single-copy nuclear DNA sequences of the hominoid genera using DNA-DNA hybridization to produce a complete matrix of delta T₅₀H values. The data show that the branching sequence of the lineages, from oldest to most recent, was: Old World monkeys, gibbons, Orangutan, Gorilla, chimpanzees, and Man. The calibration of the delta T₅₀H scale in absolute time needs further refinement, but the ranges of our estimates of the datings of the divergence nodes are: Cercopithecoidea, 27–33 million years ago (MYA); gibbons, 18–22 MYA; Orangutan, 13–16 MYA; Gorilla, 8–10 MYA; and chimpanzees-Man, 6.3–7.7 MYA.     

Development of a fast DNA-DNA hybridization method based on melting profiles in microplates

DNA-DNA hybridization is still the “gold standard” for the genotypic delineation of bacterial species. However, it is not widely used because traditional DNA-DNA hybridization techniques are rather time-consuming and not easy to perform in routine laboratories. In the present study, DNA of reference strains was digested with Sau3A, ligated with linker oligonucleotides S1/2 and in vitro amplified. The amplified DNA fragments were immobilized on MaxiSorb 96-well plates. DNA isolated from target strains was also digested with Sau3A, ligated with linker oligonuleotides P1/2 and in vitro amplified in the presence of digoxygenin modified dUTP. The labeled amplificate was hybridized to the immobilized reference DNA under isothermal conditions. Thermal denaturation curves of the DNA-DNA hybrids were obtained by using washing solutions of increasing stringency. Remaining hybrids were colorimetrically detected with anti-digoxygenin-horseradish peroxidase anti-bodies. The new method was validated with strains of the genus Pedioccocus for which DNA-DNA similarities have also been determined by the filter hybridization method. In addition, DNA-DNA hybridizations were performed with genotypically defined Enterobacter species.     

Rapid RAPD screening of plant DNA using dot blot hybridization

Scoring of the results of RAPD analysis using gel electrophoresis imposes a constraint on throughput. To circumvent this barrier, dot-blot hybridization was substituted for electrophoresis. Arbitrarily amplified fragments from barley and wheat genomic DNA were labelled and used as probes for the identification of identical fragments in subsequent amplification reactions. None of the twelve fragments used as probes exhibited significant levels of croos-hybridization to other fragments amplified by the same arbitrary primer. The strength of the hybridization signal facilitates more accurate and more sensitive detection of diagnostic fragments than gel electrophoresis. In addition, the defined spatial orientation (microtitre dish format) of the ± results provide an excellent format for automated data collection. The use of dot blot hybridization to analyse PCR products well decrease the cost and time requirements of marker-assisted selection. This technique will also facilitate the rapid application of PCR-based maps.     

Psoralen-DNA crosslink repair in human lymphocytes: Comparison of alkaline elution with electron microscopy

Much interest has surrounded the question of the removal of psoralen interstrand crosslinks in DNA of eukaryotic organisms. A commonly employed method for the study of psoralen repair is alkaline elution. In this study we have used alkaline elution to assess psoralen crosslink repair in human lymphocytes. The lymphocytes were treated with 8-methoxypsoralen or 4,5′,8-trimethylpsoralen and allowed to repair for different periods of time. Analysis by alkaline elution showed elution patterns compatible with crosslink removal. When the crosslink removal under comparable conditions was studied by the use of electron microscopy under totally denaturing conditions, no repair of the crosslinks could be detected.     

DNA-DNA and rRNA-DNA hybridization studies in the genus Ectothiorhodospira and other purple sulfur bacteria

DNA-DNA hybridization reveals low DNA homologies (about 14%) between the species of Ectothiorhodospira genus and indicate clearly that the degree of divergence within this genus exceeds the interspecific level. The degree of genome similarities of E. mobilis and E. vacuolata (more than 80% homology) is high and characteristic for the strains of one and the same species.The results of rRNA-DNA and secondary DNA-DNA hybridization indicate the following: Ectothiorhodospira and Thiocapsa are far less related than the genera of one and the same family; the genus Ectothiorhodospira is equidistant from both families of purple sulfur and nonsulfur bacteria. Thus Ectothiorhodospira is a taxon of a higher rank than a genus; we agree with Imhoff's proposal of a new family Ectothiorhodospiraceae.     

The alkaline hydrolysis of phosphotriesters in alkylated mammalian DNA

Isolated DNA was alkylated with $\text{N-[}{}^{14}\text{C]methyl}\text{-N-}\text{nitrosourea}$ or $\text{N-[}{}^{14}\text{C]ethyl}\text{-N-}\text{nitrosourea}$. Sedimentation analysis of the alkylated DNA before and after alkaline hydrolysis was used to determine the number of single-strand breaks introduced by hydrolysis of the triesters. Vacuum distillation from alkylated DNA solutions before and after alkaline hydrolysis was used to determine the numbers of triesters hydrolysing to the alcohol.     

DNA损伤检测技术

检测DNA损伤的方法有很多,根据其原理大致可以分为3类：基于损伤DNA理化性质的改变检测DNA损伤、基于分子杂交检测DNA损伤以及基于DNA损伤后形成的产物检测DNA损伤。检测DNA损伤的方法目前还在不断快速发展、完善中。本文就DNA损伤的检测方法及其发展做一综述。     

Study of the quality of aminated substrates used for hybridization analysis

A set of methods for analysis of the quality of aminated substrates that could be a basis for the large-scale manufacturing of biological microchips is suggested. The analysis includes the determination of the number of amino groups, their availability for the immobilization of phosphorylated oligonucleotides, and the characterization of surface properties of the substrates in respect to the nonspecific sorption of reagents during hybridization. A simple procedure was suggested for determination of the density/number of amino groups. It is based on the use of dimethoxytrityl chloride with the subsequent spectrophotometric determination of dimethoxytrityl cation. The availability of amino groups was estimated by covalent attachment of an oligonucleotide probe containing a fluorescently labeled group to the aminated surface and the subsequent comparison of the intensity of fluorescing zones formed on the chip. The sorption properties of the surface were investigated with the help of a model hybridization reaction. A comparative analysis of aminated glasses manufactured by various firms and in our laboratory showed that the glasses with the amino group density from 0.7 to 2.0 groups/nm² prepared by our procedure have the best properties for the hybridization analysis.     

Development of sensitive methods for the detection of myobacteria by DNA probes

A sensitive method allowing the detection of mycobacteria by DNA probing has been developed. Besides the choice of a relevant probe encoding for part of the ribosomal RNA genes, the critical step allowing this high sensitivity was the method by which mycobacteria were lysed. Sonication of mycobacteria in the presence of chloroform followed by dot blot by this lysate gave the highest sensitivity in the detection of sequences homologous to the DNA probes.     

Reverse dot blot hybridization: A useful method for the direct identification of lactic acid bacteria in fermented food

Abstract A rapid method for a reliable and simultaneous identification of different lactic acid bacteria in fermented food has been developed. Various 16S and 23S rRNA-targeted, species-specific oligonucleotides were applied as capture probes in a non-radioactive reverse dot blot hybridization. A simple and fast DNA extraction method in combination with in vitro amplification of rRNA gene fragments enables the direct detection of typical starter organisms without any preceding enrichment or cultivation steps. Various lactic acid bacteria occurring in cheese, yogurt, sausages, sauerkraut and sourdough could be identified at the species level within 1 day.     

Covalently immobilized DNA plate for luminometric DNA-DNA hybridization to identify viridans streptococci in under 2 hours

Abstract Single-stranded chromosomal DNA was covalently bound to a microdilution plate and used for quantitative DNA-DNA hybridization. After 30 min, hybridized DNA was quantitatively detected by alkaline phosphatase and a chemiluminescent substrate. This method was successfully used for the rapid identification of viridans streptococci.     

Voltammetric determination of gamma radiation-induced DNA damage

Homopolydeoxyribonucleotides, poly[dGuo], poly[dAdo], poly[dThd], and poly[dCyd], and calf thymus single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) aqueous solutions previously exposed to gamma radiation doses between 2 and 35 Gy, were studied by differential pulse voltammetry using a glassy carbon electrode. The interpretation of the voltammetric data was also supported by the electrophoretic migration profile obtained for the same ssDNA and dsDNA gamma-irradiated samples by nondenaturing agarose gel electrophoresis. The generation of 8-oxo-7,8-dihydroguanine, 2,8-dihydroxyadenine, 5-formyluracil, base-free sites, and single- and double-stranded breaks in the gamma-irradiated DNA samples was detected voltammetrically, with the amount depending on the irradiation time. It was found that the current peaks obtained for 8-oxoguanine increase linearly with the radiation dose applied to the nucleic acid sample, and values between 8 and 446 8-oxo-7,8-dihydroguanine (8-oxoGua) per 10(6) guanines per Gy were obtained according to the nucleic acid sample. The results showed that voltammetry can be used for monitoring and simultaneously characterizing different kinds of DNA damage caused by gamma radiation exposure.     

A new method for rapid screening of bacterial species- or subspecies-specific DNA probes

A simple assay for the rapid screening of bacterial species- or subspecies-specific DNA probes for the random cloning method is presented, involving the use of genomic DNAs as probes and recombinant plasmid DNAs containing genomic DNA digested with HindIII as targets. The optimal amount of target DNAs and the concentration of digoxigenin-labeled genomic DNA probes were 20 ng and 100 ng ml(-1) (or 10 ng and 200 ng ml(-1)), respectively. The method was applied to the development of Fusobacterium nucleatum subspecies-specific probes. Our results showed that four out of 96 probes were F. nucleatum subspecies-specific, which was confirmed by Southern blot analysis. Our results indicate that the new method can be used for the rapid screening of species- or subspecies-specific probes.     

Alzheimer's disease fibroblasts have normal repair of N-methyl-N'-nitro-N-nitrosoguanidine-induced DNA damage determined by the alkaline elution technique

Cultured fibroblast strains from two normal persons and from two patients with the neurodegeneration of Alzheimer's disease were exposed to the alkylating chemical N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Immediately after exposure and also after a 24-h repair incubation period the single-strand breaks in the cells' DNA were quantified by the alkaline elution technique. In contrast to a report by others using alkaline elution, MNNG, and these same strains, we found no evidence of deficient repair of MNNG-induced DNA damage in the Alzheimer's disease cells. The putative DNA repair defect in Alzheimer's disease should be investigated by methods other than the alkaline elution technique which measures only a small fraction of the damage induced by an alkylating chemical such as MNNG.