32P-postlabeling determination of DNA adducts in the earthworm Lumbricus terrestris exposed to PAH-contaminated soils.
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Animals↗
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Results for “DNA Contamination”
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Quantification of X-chromosome inactivation patterns using RT-PCR of the polymorphic iduronate-2-sulphatase gene and correlation of the results obtained with DNA-based techniques.
Most studies using X-chromosome inactivation patterns (XCIPs) to determine clonality in females have used polymorphic DNA loci, but interpretation may be complicated by the complexity of the differential methylation patterns necessary to distinguish active and inactive X-chromosomes. Recent description of polymorphisms within the transcribed region of three X-chromosome genes has enabled XCIP analysis of allele expression at the RNA level, which should circumvent this problem. We report here a quantitative RT-PCR assay for one of these loci, the iduronate-2-sulphatase (IDS) gene, using a mismatch primer to introduce a Bc/l cutting site in one of the alleles. DNA samples from 150 females were screened and 61 (41%) were found to be informative for the polymorphism. Reproducible results were obtained from clonal analysis of 56 RNA samples covering the complete spectrum of XCIP ratios. The values correlated closely with those obtained from the corresponding DNA samples analyzed using either PGK or HUMARA (r=0.98) provided that the number of amplification cycles was limited to 25 to reduce heteroduplex formation. However, sample purity is of greater importance than in the DNA-based assays as contaminating red cells and platelets will still contain the relevant transcripts and could influence the result.
Base Sequence↗
HPLC preparation of highly purified single-stranded M13 DNA.
Closed-circular, single-stranded viral DNAs are widely employed in DNA cloning and sequencing experiments. Because of their well-defined structure and sequence, closed-circular, single-stranded DNAs have also been used for ligand binding experiments and light scattering measurements. However, there is a high molecular weight impurity observed in light scattering experiments, which sometimes contaminates single-stranded DNA purified from phage that has been precipitated in polyethylene glycol, average molecular weight 8000, and purified by standard phenol-chloroform extraction. Three methods have been examined that remove this impurity from closed-circular, single-stranded M13mp19 DNA (SS M13 DNA). One employs a commercial peparation. This procedure yields pure but degraded SS M13 DNA, as shown by light scattering measurements and HPLC. Another employs a Whatman DE52 (diethylamino cellulose) column. This procedure yields intact DNA, but in poor yield (less than 20% of that obtained by phenol-chloroform extraction). The last was the most successful. This employs HPLC with a Waters AP-1 column with DEAE 8HR bedding. This procedure, which provides DNA in high yield (80%-90% column recovery) with an intact structure, is an efficient method for the isolation of high-purity, closed-circular, single-stranded viral DNA suitable for physical investigations and ligand binding measurements.
Artifacts↗
ILG1 : a new integrase-like gene that is a marker of bacterial contamination by the laboratory Escherichia coli strain TOP10F'.
BACKGROUND: Identification of differentially expressed genes between normal and diseased states is an area of intense current medical research that can lead to the discovery of new therapeutic targets. However, isolation of differentially expressed genes by subtraction often suffers from unreported contamination of the resulting subtraction library with clones containing DNA sequences not from the original RNA samples. MATERIALS AND METHODS: Subtraction using cDNA representational difference analysis (RDA) was performed on human B cells from normal or common variable immunodeficiency patients. The material remaining after the subtraction was cloned and individual clones were sequenced. The sequence of one clone with similarity to integrases (ILG1, integrase-like gene-1) was used to obtain the full length cDNA sequence and as a probe for the presence of this sequence in RNA or genomic DNA samples. RESULTS: After five rounds of cDNA RDA, 23.3% of the clones from the resulting subtraction library contained Escherichia coli DNA. In addition, three clones contained the sequence of a new integrase, ILG1. The full length cDNA sequence of ILG1 exhibits prokaryotic, but not eukaryotic, features. At the DNA level, ILG1 is not similar to any known gene. At the protein level, ILG1 has 58% similarity to integrases from the cryptic P4 bacteriophage family (S clade). The catalytic domain of ILG1 contains the conserved features found in site-specific recombinases. The critical residues that form the catalytic active site pocket are conserved, including the highly conserved R-H-R-Y hallmark of these recombinases. Interestingly, ILG1 was not present in the original B cell populations. By probing genomic DNA, ILG1 could only be detected in the E. coli TOP10F' strain used in our laboratory for molecular cloning, but not in any of its precursor strains, including TOP10. Furthermore, bacteria cultured from the mouth of the laboratory worker who performed cDNA RDA were also positive for ILG1. CONCLUSIONS: In the course of our studies using cDNA RDA, we have isolated and identified ILG1, a likely active site-specific recombinase and new member of the bacteriophage P4 family of integrases. This family of integrases is implicated in the horizontal DNA transfer of pathogenic genes between bacterial species, such as those found in pathogenic strains of E. coli, Shigella, Yersinia, and Vibrio cholera. Using ILG1 as a marker of our laboratory E. coli strain TOP10F', our evidence suggests that contaminating bacterial DNA in our subtraction experiment is due to this laboratory bacterial strain, which colonized exposed surfaces of the laboratory worker. Thus, identification of differentially expressed genes between normal and diseased states could be dramatically improved by using extra precaution to prevent bacterial contamination of samples.
Amino Acid Sequence↗
Pseudomonas aeruginosa PA-I lectin gene molecular analysis and expression in Escherichia coli.
This communication describes a Pseudomonas aeruginosa DNA fragment (cloned in lambda gt11) which contains the structural gene coding for the galactophilic PA-I lectin (pa-1L, 369 bp) and an additional downstream 237 bp sequence. This DNA is relatively rich in G + C (54%), and exhibits a strong codon preference biased for XXC and also for XXG. The Shine-Dalgarno site of the gene is preceded by an adjacent ATATAT sequence resembling the -10 sequence of the Escherichia coli promoter. The stop codons are followed by a stem and loop structure--typical of the rho-independent transcriptional stop element. This lambda gt11-cloned DNA was expressed in E. coli Y1090 cells. The resulting cell lysates exhibited a galactose-specific hemagglutination and a protein with electrophoretic mobility similar to that of the native PA-I, which were both absent from E. coli lysates infected with ovalbumin gene-bearing bacteriophages. The recombinant PA-I, purified by gel filtration and affinity chromatography, was shown to be a galactophilic hemagglutinin resembling the native lectin in molecular weight and selective reactivity with rabbit anti native PA-I serum. These results are important for development of a safe Pseudomonas aeruginosa vaccine using recombinant DNA techniques, thus avoiding contamination with toxic products of this bacterium.
Adhesins, Bacterial↗
Comparison of "Gen-Probe" DNA probe and PCR for detection of Listeria monocytogenes in naturally contaminated soft cheese and semi-soft cheese.
A comparison was made of three approaches for the detection of Listeria monocytogenes in naturally contaminated soft cheese and semi-soft cheese after enrichment. Enrichment broths were tested by plating them onto different selective agars, by "Gen Probe" DNA hybridization and by the polymerase chain reaction (PCR). Based on two-step enrichment, all three approaches showed high specificities (90% or more) in detecting L. monocytogenes. In contrast, the sensitivity of the Gen-Probe test was low (33% or less), whereas high sensitivities were obtained with selective plating and PCR (83% or more). Based on one-step enrichment, specificities again were high for selective plating and PCR assay (100%), whereas for the Gen-Probe assay the specificity was lower (88% or more). The best sensitivities were observed with selective plating (67%) and PCR (75%). In terms of sensitivity, specificity and analysis time, PCR applied to a two-step enrichment was the most powerful assay for detecting L. monocytogenes in soft and semi-soft cheese.
Cheese↗
[Nuclear factor A5 from the rat liver that requires a metal for specific interaction in vitro with distal element of the tyrosine aminotransferase gene promoter].
To detect nuclear protein factors which might account for a tissue-specific and inducible expression of the rat tyrosine aminotransferase (TAT) gene promoter, extracts from rat liver and spleen nuclei have been fractionated by heparin-sepharose chromatography and the fractions assayed for sequence-specific binding to the distal TAT gene promoter element (sequence between -313 and -210). Gel retardation experiments carried out in the presence or absence of Mg2+, Ca2+, or Zn2+ ions showed that there are at least two nuclear factors (A3 and A4) binding to the distal promoter element only in the presence of the chelator (20 mM EDTA). Incubation of the protein fractions with Zn2+ or Ca2+ instead of commonly used Mg2+allowed: (i) to avoid 3 2P-DNA-probe degradation by "contaminating" endogenous nucleases; and (ii) to detect another sequence-specific nuclear factor, A5. No other specific binding activities were found in the rat-liver nuclear fractions tested under these conditions. As the metal ions became inaccessible to chelation in excess of EDTA and EGTA when protein factor A5 was complexed to DNA we assumed that factor A5 is metalloprotein which requires Zn or Ca to maintain a structure of its DNA-binding domain. To identify the polypeptide possessing this domain, a protein gel blotting procedure was employed. By incubating gel blots with the 3 2P-DNA-probe in the buffer containing Zn2+, specific binding to the only polypeptide with approximate Mr 30 kDa was clearly revealed. Both gel retardation and gel blotting assays consistently showed that nuclear factor A5 is present in the liver, but not in the spleen extracts.
Animals↗
Applicability of rabbit microsatellite primers for studies of hybridisation between an introduced and a native hare species.
Introduced species may hybridise with relatives in the native fauna or flora and thereby compete for matings and transmit alien DNA. Such interference may contaminate unique genepools, disturb existing ecological balances and may ultimately result in the extinction of the native species. In Sweden, the introduced brown hare (Lepus europaeus Pall.) hybridise with the native mountain hare (L. timidus L.), both relatively common members of the present Swedish fauna. This hybridisation has resulted in the transmission of mitochondrial DNA from the mountain hare to the brown hare, but absence of species differences in karyotype and allozymes have prevented investigations of the amount of nuclear gene flow. More polymorphic genetic markers are needed to analyse evidence of hybridisation in the nuclear genome. The conservation of microsatellite loci across taxa usually enables PCR amplification of microsatellites in closely related species with the same primers. We have used five microsatellite primer pairs, developed for the European wild rabbit (Oryctolagus cuniculus L.) to amplify microsatellites in the two species of hare in Sweden. The obtained allelic variation was used to construct a genetic distance tree based on the amount of shared alleles between all pairs of individuals (shared-allele index). This method offered sufficient differences to arrange all individuals in two groups, one for each species. Identification of individual hybrids based on the number of alleles shared between the species is not possible with these five microsatellite markers.
Animals↗
[Ochratoxin A, ubiquitous mycotoxin contaminating human food].
Ochratoxin A (OTA) a mycotoxin produced by molds of the Aspergillus and Penicillium genera, contaminates animal feeds and human foods. It has been shown to induce renal adenomas and hepatocellular carcinomas in rodents. OTA is implicated in Balkan endemic nephropathy, a disease followed by a high incidence of urinary tract tumours. Concerning the genotoxicity of OTA, we have recently shown, using the [32P]-phosphate postlabelling method, that several DNA-adducts are formed in four mice organs treated with OTA. Some of the adducts were specific of every analyzed tissue. These results, allow us to state that OTA metabolism in different from organ to organ. The influence of OTA metabolism on its genotoxic effect was studied. Preliminary results have shown the possibilities of oxidative pathways in OTA metabolism leading to genotoxic compounds. Effects of some vitamins such as retinol (A), ascorbic acid (C) and tocopherol (E), which are known to act as superoxide anion scavengers, were tested on genotoxicity of OTA. Pretreatment of mice by vit E induced a decrease of the DNA-adducts by 80% in kidney, and by 55% in liver. Vit A and vit C decreased DNA-adduct levels by 70% in kidney. In liver, DNA adduct level was essentially decreased by vit C (90%). Vit A decreased only the level by 25% in this organ. The involvement of oxidative metabolism in the genotoxicity of OTA led us to investigate the effect of prostaglandin H synthase (PHS) which is known to cooxidase xenobiotics. Aspirin and indomethacin which inhibit this enzyme were given prior to OTA administration to mice in order to test this metabolic pathway. The decrease observed with aspirin was of about 90% and 30% in kidney and liver respectively, and of 90% and 80% with indomethacin in kidney and liver. These results confirmed that OTA is activated to genotoxic metabolites by cooxydation by the prostaglandin synthase route. Human bronchial epithelial cells (BEAS-2B) expressing or not human cytochrome P450s (CYP) (1A2, 2A6, 2D6, 2E1 and 3A4) were incubated with 0.5 microM OTA for 24 h. DNA-adducts were detected in all cells. Total DNA-adduct levels ranged from 4 to 85 adducts per 10(9) nucleotides. Some adducts were common to all cell types including cells expressing only normal phase II enzymes, but no cytochromes P450. Some other DNA-adducts were only induced by specific CYPs. The highest DNA-adduct level was found in cells where CYP 1A2 was expressed. Nevertheless, more different types of DNA-adducts were formed in cells expressing CYP 2D6.(ABSTRACT TRUNCATED AT 400 WORDS)
Abnormalities, Drug-Induced↗
Reexamination of the effect of endotoxin on cell proliferation and transfection efficiency.
Plasmid DNA purified from bacterial cells can be contaminated with endotoxin to different extents, depending on the purification method. Earlier reports indicate that endotoxin can decrease transfection efficiency in many eukaryotic cell lines; however, the amount of endotoxin required for inhibition is unclear. We determined endotoxin effects in several cell lines and observed that endotoxin levels greater than or equal to 10,000 endotoxin units (EU) were needed to significantly affect cell proliferation and viability; levels greater than 2000 EU/mu g DNA were required to significantly inhibit transfection for all but one (Huh-7) of the cell lines tested. These endotoxin levels are significantly higher than endotoxin contamination in plasmid DNA purified by anion exchange, CsCl2 gradient and endotoxin-free purification technology, but not as high as a crude alkaline lysis preparatory method. Plasmid DNA prepared using anion exchange technology was comparable to endotoxin-free technology in terms of transfection efficiency. Even Huh-7 cells, which are markedly more sensitive to endotoxins, have comparable transfection efficiencies using plasmid DNA purified by either of these two methods. We conclude that for those cell lines commonly used for transfection studies, endotoxin-free, quality DNA is not necessary because significantly higher levels of bacterial endotoxins are required to inhibit either cell proliferation or transfection.
Animals↗
Novel DNA-Sepharose purification of the FadR transcription factor.
A DNA sequence bound by the FadR transcription factor of Escherichia coli was covalently attached to Sepharose by two different approaches: by chemical coupling or by template-directed enzymatic synthesis using a DNA polymerase. The two kinds of DNA-Sepharose were packed into small columns and used for the purification of the FadR protein; chromatography was without using competitor DNA and the supports contained single-copy, non-repetitive DNA sequences. Comparison showed that the enzymatically prepared support, while having less bound DNA, bound more FadR protein than did the chemically prepared support. This probably results from the lack of detrimental DNA modification by the gentle enzymatic procedure. The chemically prepared support was of lower capacity but yielded purer FadR protein when compared under the same elution conditions. This may be explained by the simpler DNA sequence which could be coupled chemically; less contaminating proteins were bound by the simpler DNA sequence. However, the enzymatically prepared support could also yield comparable purity if the protocol was modified to include additional washes with salt containing buffers. In all cases, FadR was eluted from the DNA using high-salt (0.8 M) mobile phase; ligand-specific elution of FadR using a fatty acyl-coenzyme A thiol ester was ineffective. Affinity chromatography on DNA-Sepharose provided a more rapid, simple purification of FadR than conventional purification techniques and yielded biologically active protein.
Bacterial Proteins↗
Partial purification and characterization of a human 3-methyladenine-DNA glycosylase.
A DNA glycosylase was purified about 30-fold from cultured human lymphoblasts (CCRF-CEM line) and was found to cleave 3-methyladenine from DNA alkylated with methyl methanesulfonate. The enzyme did not promote the release of 1-methyladenine, 7-methyladenine, or 7-methylguanine from DNA nor did it act on denatured methylated DNA. It produced apurinic sites in DNA alkylated with N-methyl-N-nitrosourea and ethyl methane-sulfonate as well as methyl methanesulfonate but not in untreated DNA or in DNA alkylated with nitrogen mustard or irradiated with ultraviolet light or X-rays. The glycosylase was free of detectable endonuclease activity in experiments with untreated DNA or DNA exposed to ultraviolet light; low levels of endonuclease activity, obtained when X-irradiated, alkylated, or depurinated DNA was the substrate, were attributed to contaminant apurinic endonuclease activity. This 3-methyladenine-DNA glycosylase has an estimated molecular weight of 34,000, is not dependent on divalent metal ions, and shows optimal activity at pH 7.5--8.5.
Adenine↗
AdDeam: a fast and scalable tool for estimating and clustering reference-level damage profiles.
MOTIVATION: DNA damage patterns, such as increased frequencies of C→T and G→A substitutions at fragment ends, are widely used in ancient DNA studies to assess authenticity and detect contamination. In metagenomic studies, fragments can be mapped against multiple references or de novo assembled contigs to identify those likely to be ancient. Generating and comparing damage profiles, however, can be both tedious and time-consuming. Although tools exist for estimating damage in single reference genomes and metagenomic datasets, none efficiently cluster damage patterns. RESULTS: To address this methodological gap, we developed AdDeam, a tool that combines rapid damage estimation with clustering for streamlined analyses and easy identification of potential contaminants or outliers. Our tool takes aligned ancient DNA (aDNA) fragments from various samples or contigs as input, computes damage patterns, clusters them, and outputs representative damage profiles per cluster, a probability of each sample pertaining to a cluster, as well as a Principal Component Analysis of the damage patterns for each sample for fast visualisation. We evaluated AdDeam on both simulated and empirical datasets. AdDeam effectively distinguishes different damage levels, such as uracil-DNA glycosylase-treated samples, sample-specific damages from specimens of different time periods, and can also distinguish between contigs containing modern or ancient fragments, providing a clear framework for aDNA authentication and facilitating large-scale analyses. AVAILABILITY AND IMPLEMENTATION: AdDeam is publicly available at https://github.com/LouisPwr/AdDeam and can also be installed via Bioconda. It is implemented in Python and C++. All analysis scripts and datasets are available at https://github.com/LouisPwr/AdDeamAnalysis and on Zenodo under: 10.5281/zenodo.15052427.
Software↗
Formation of acrolein adducts with 2'-deoxyadenosine in calf thymus DNA.
Acrolein is a ubiquitous environmental contaminant that has been found to be mutagenic in prokaryotic and eukaryotic cells. In the present study, we examined the reactions of acrolein with 2'-deoxyadenosine and calf thymus single- and double-stranded DNA in aqueous buffered solutions at physiological conditions. The deoxynucleoside adducts were isolated by reversed-phase liquid chromatography, and their structures were determined by their UV absorbance, mass spectrometry, and 1H and 13C NMR spectroscopy. The reaction of 2'-deoxyadenosine with acrolein resulted in the formation of four structurally different adducts (dAI, dAII, dAIII, dAIV). The structures of the novel acrolein adducts, dAIII and dAIV, were assigned as 3-[N(6)-(2'-deoxyadenosinyl)]propanal (dAIII) and 9-(2'-deoxyribosyl-6-(3-formyl-1,2,5,6-tetrahydropyridyl)purine (dAIV), respectively. The adduct dAIII was found to arise via a Dimroth rearrangement of adduct dAI, while the adduct dAIV was shown to be formed upon further reaction of acrolein with dAIII. In the reaction of acrolein with calf thymus DNA, all studied 2'-deoxyadenosine-acrolein adducts were observed. For the first time, it is shown that the N(6)-adduct and the adducts which are derived from two acrolein units are formed in calf thymus DNA.
Acrolein↗
Thiophilic interaction chromatography for supercoiled plasmid DNA purification.
Supercoiled plasmid DNA was selectively purified from its open circular form by thiophilic interaction chromatography, performed in the presence of high concentrations of water-structuring salts. To identify optimal conditions for purification, various aromatic thioether ligands were coupled to a chromatographic support and screened for their ability to separate plasmid isoforms from each other and from other host cell contaminants, including RNA, genomic DNA, protein, and endotoxins. Selectivity of the chromatographic medium depended on the structure of the ligands, with characteristics of the substituents on the aromatic ring determining the resolution between the different plasmid DNA isoforms. Optimal resolution was obtained with ligands consisting of an thioaromate, substituted with highly electronegative groups. When 2-mercaptopyridine was used as a ligand, the difference in conductivity for eluting open circular and supercoiled plasmid DNA is only 6 mS/cm. However, with 4-nitrothiophol the resolution for plasmid DNA separation on the media increased, resulting in a 20 mS/cm difference. When used in combination with a prior group separation step, these aromatic thioether ligands facilitated the isolation of highly purified supercoiled plasmid DNA, suitable for use in gene therapy and DNA vaccine applications.
Chromatography↗
Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification.
BACKGROUND: Complex mixtures of DNA may be found in environmental and medical samples. There is a need for techniques that can measure low concentrations of target DNAs. For a multiplexed, flow cytometric assay, we show that the signal-to-noise ratio for fluorescence detection may be increased with the use of 3DNA dendrimers. A single fluorescent DNA molecule per bead could be detected with conventional flow cytometry instrumentation. METHODS: The analyte consisted of single-stranded (ss) DNA amplicons that were hybridized to capture probes on the surface of fluorescent polystyrene microspheres (beads) and initially labeled with streptavidin-R-phycoerythrin (single-step labeling). These beads have a low reporter fluorescence background and high efficiency of DNA hybridization. The DNA/SA-RPE complex was then labeled with 3DNA dendrimers and SA-RPE. The bead complexes were detected with a Luminex 100 flow cytometer. Bead standards were developed to convert the intensity to the number of SA-RPE labels per bead and the number of dendrimers per bead. RESULTS: The dendrimer assay resulted in 10-fold fluorescence amplification compared with single-step SA-RPE labeling. Based on concentration curves of pure target ss-amplicons, the signal-to-noise ratio of the dendrimer assay was greater by a factor of 8.5 over single-step SA-RPE labeling. The dendrimer assay was tested on 16S ribosomal DNA amplified from filter retentates of contaminated groundwater. Multiplexed detection of a single dendrimer-labeled DNA molecule per bead was demonstrated. CONCLUSIONS: Multiplexed detection of DNA hybridization on a single molecule level per bead was achieved with conventional flow cytometry instrumentation. This assay is useful for detecting target DNAs at low concentrations.
Calibration↗
A study of sex identification of trace, dried bloodstains using a Y-chromosome-specific deoxyribonucleic acid (DNA) probe.
A new method is discussed which examines trace, dried bloodstains by gel in situ hybridization using a Y-chromosome-specific deoxyribonucleic acid (DNA) probe to determine the sex of the bloodstain for forensic medicine application. The complete DNA is transferred directly by electrophoresis onto the gel intact, bypassing the possibilities of impurities contaminating the sample and of DNA degradation. The method has proven accurate for small (2.5-mm-diameter) samples aged up to eight years and is quick, simple, and easily read.
Adult↗
[Detection of bacterial DNA using the polymerase chain reaction (PCR)].
Enzymatic amplification of DNA using the polymerase chain reaction (PCR) is a very sensitive and rapid way of detecting specific DNA sequences. Bacterial DNA can be detected in a wide variety of samples provided at least partial sequence information is available. For a great number of bacteria PCR detection methods have been published. Most important for the pathologist are mycobacteriae (M. tuberculosis, avium, etc.). Borellia burgdorferi, Listeria monozytogenes and chlamydiae (Ce. trachomatis, C. psittaci). Fresh or fixed paraffin embedded tissues, exfoliated cells, whole blood, serum, sputum, urine, ascites or pleural fluid etc. can be analyzed. The time needed to perform the analysis varies between 5 hours and 2 days mostly depending on the DNA extraction method. Several potential pitfalls have to be avoided. The most common problem is contamination of reagents with target DNA. Amplification of DNA from biological samples may be prevented by enzyme inhibitors (salts, proteins). This problem can at least partially be avoided by changing the DNA purification method. Several additional problems may arise if bacterial DNA has to be amplified. Bacterial walls may have to be disrupted using heat or detergent for accessibility of target DNA. Positive results have to be judged carefully. Unlike the situation in retroviral infections with the virus sometimes present in the absence of disease, in the majority of bacterial infections the presence of bacteria signals manifest disease. A possible exception may be the finding of mycobacterial DNA in sarcoidosis patients who can be treated with steroids without provoking tuberculosis. PCR is especially useful in situations where rapid results are necessary or only fixed tissue is available.(ABSTRACT TRUNCATED AT 250 WORDS)
Bacteria↗