Single-step elimination of contaminating DNA prior to reverse transcriptase PCR.
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Animals↗
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Results for “DNA Contamination”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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Differentiating vector-derived mRNA from contaminating DNA templates by inverse RT-PCR.
Inverse RT-PCR was used for detecting doxycycline-induced mRNA expression after viral transduction with a retroviral vector harboring human TDAG51. After the circularization of double-stranded cDNA, induced transcripts originating from integrated vector genomes were selectively amplified, even in the presence of DNA templates. Thus, DNase treatment before amplification was unnecessary.
Anti-Bacterial Agents↗
An immunoenzymatic test designed for the detection of small amounts of contaminant DNA in biological preparations.
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Adenosine↗
Removal of contaminating DNA from PCR reagents by ultrafiltration.
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Chromatography, High Pressure Liquid↗
Effects of preservation methods, parasites, and gut contents of black flies (Diptera: Simuliidae) on polymerase chain reaction products.
Molecular analysis of biological specimens usually requires extraction of high-molecular weight DNA free of foreign DNA contaminants. DNA was extracted from black flies at different life stages that had been preserved by 4 methods: larvae and adults in ethanol, larvae in Carnoy's solution, adults on card-points, and adults hand-swatted and sun-dried. Using specific primers for the mitochondrial ND4 gene, a 257-bp amplicon was obtained from specimens preserved by ethanol, card-point mounting, and sun-drying. Successful amplification often required DNA dilutions > or = 1:20 (< 1-10 ng). DNA from specimens preserved in Carnoy's solution (ethanol: acetic acid, 3:1) yielded degraded DNA, resulting in fewer successful amplications. Parasitic nematodes and, to a lesser extent, gut contents resulted in extra products when amplified with randomly amplified polymorphic DNA (RAPD) primers. Sufficient DNA was extracted from the head of a larva for a successful polymerase chain reaction (PCR), eliminating the need to remove the contaminating gut and parasites.
Animals↗
Spurious genotypes in female nematodes resulting from contamination with male DNA.
Females of many invertebrates contain stored sperm or fertilized eggs or both, causing potential genotyping errors. We investigated errors caused by male DNA contamination by amplifying 5 microsatellites in DNA isolated from various tissue types in the nematode Ascaris lumbricoides. We observed additional alleles in 30/135 uterus-derived samples when compared with muscle controls, resulting in 20/135 (15%) incorrect genotypes and an underestimation of inbreeding. In contrast, we observed additional alleles in only 5/143 ovary-derived samples, resulting in 4/143 (3%) incorrect genotypes and no significant influence on inbreeding estimates. Because uterus constitutes approximately 17% of a female's organ weight, a substantial proportion of samples isolated from female tissue may contain male-derived DNA. Male contamination is easily avoided when using large nematodes such as A. lumbricoides. However, we urge caution for studies using DNA isolated from small invertebrates that store sperm or fertilized eggs or both.
Animals↗
Real-time quantitative PCR assay for analysis of platelet glycoprotein IIIa gene expression.
A quantitative detection assay for analysis of platelet glycoprotein GPIIIa gene expression is presented. The assay uses two fluorescently labeled TaqMan MGB probes to detect the polymorphic site in GPIIIa nucleotide sequence, leading to antigens HPA-1a and HPA-1b. In order to avoid the influence of DNA contamination on RNA quantification, a forward primer was constructed to span an exon-exon junction. The assay is therefore applicable to expression studies also in samples containing only a small amount of contaminating DNA. To standardize the amount of sample cDNA added to the reaction, amplification of endogenous control 18SrRNA was included in a separate well. The amplification validation experiment showed a high real-time PCR efficiency for HPA-1a, HPA-1b and 18SrRNA. Relative quantification was therefore performed using the comparative C(T) method. The assay was optimized on a reversely transcribed total RNA from platelets, and the specificity rate was determined by sequencing. The amount of cDNA at which amplification was still clearly detectable was 5 ng. This newly developed real-time quantitative PCR assay is a sensitive, reproducible and reliable method. It is suitable for studying different stages of megakaryopoiesis, monitoring molecular alteration in defective platelets and determining differences in the GPIIIa expression level between normal and pathological megakaryocytic differentiation pathways.
Antigens, Human Platelet↗
Rapid method for isolation of total RNA from eukaryotic cell lines and leukocytes.
Total RNA was isolated from human leukocytes (monocytes, granulocytes), various cell lines (COS-7, Mono-Mac-6, L-132, HaCaT, EA.hy926, HL-60), and fungal mycelium by a rapid two-step method. Cells were lysed with NaDodSO4 in a citric acid-containing buffer. This procedure was succeeded by salt precipitation to remove contaminating DNA and protein and a final alcohol precipitation of RNA. Isolated RNA was of high quality, with a reasonable yield and little or no protein or DNA contamination. We present here a fast method for preparing RNA particularly from cell lines, which limits the use of toxic compounds.
Animals↗
Risk assessment on the carcinogenic potential of hybridoma cell DNA: implications for residual contaminating cellular DNA in biological products.
The aim of this study was to evaluate the possible carcinogenic potential of residual DNA derived from immortalized and possibly tumorigenic cell lines due to activated oncogenic sequences (oncogenes). These cell lines have been used for the production of biologicals, i.e. monoclonal antibodies, lymphokines and vaccines. The authors used hybridoma DNA as a first model. For this reason experiments in two species were performed, namely in 3-4 week-old female Balb/c mice and newborn Riv:TOX rats. Doses of 250 micrograms DNA, derived from Balb/c hybridoma cells, were injected subcutaneously (s.c.) in 200 mice. These mice also received a s.c. injection of the solvent only (TE buffer) at another site of the back skin (negative control for local tumour development). An additional group of 50 mice was treated intraperitoneally (i.p.) with the solvent only to serve as a negative control group for possible systemic tumorigenic effects. Doses of 5 micrograms plasmid pPy1 DNA, containing the entire Polyoma virus genome, served as positive control and were injected s.c. and i.p. in 20 and 50 mice, respectively. Doses of 50 micrograms hybridoma DNA or 5 micrograms pPy1 DNA were injected s.c. in rats too, using nine animals per group. During the experiment, animals were observed weekly, especially for the occurrence of subcutaneous tumours at the injection sites. The mouse study was terminated after more than 2 years, the rat study after 1 year. Gross necropsy was performed on all animals and histopathological examination of grossly suspected neoplastic lesions was performed. In the mouse experiment, tumour development at the s.c. injection site of the DNA was observed in one out of 20 animals in the pPy1-treated positive control group (neurofibrosarcoma) and one out of 200 animals in the hybridoma DNA-treated group (haemangioma-like lesion). Tumour development at or near the s.c. injection site of the solvent only was observed in two out of 200 animals. In the rat study none out of nine hybridoma DNA-treated rats developed tumours at the injection site, while three out of nine rats of the positive control group, injected with the pPy1 DNA, showed local tumour development (benign and malignant soft tissue tumours.) It is concluded that, at the high dose and numbers of animals tested, parenteral administration of hybridoma DNA does not induce local tumour development. Furthermore, no indications were found for systemic carcinogenic potential of the hybridoma DNA used. Based on a worst case approach of our data, the oncogenic risk of 100 pg residual DNA was estimated to be 2 x 10(-9), a value intermediate of the estimations of the WHO (1987) and the Dutch Health Council (1988) 5 x 10(-11) and 2 x 10(-7), respectively. Therefore, it is unlikely that the risk of 100 pg of DNA derived from other immortalized cell lines will exceed the level of generally accepted cancer risk of 10(-6).
Animals↗
A rare and atypical case of long-distance indirect DNA transfer: Contamination from an investigator never present at the scene.
To maximize the usefulness of DNA obtained from biological samples in forensic genetics, it is crucial to avoid DNA contamination throughout all procedures, from sample collection at crime scenes to STR profile generation in DNA laboratories. This study reports a rare and atypical case of DNA contamination in a forensic setting. During the analysis of biological evidence from a cold case preserved for 18 years, the STR profile obtained from the surface of a plastic bag matched that of an investigator, identified through the DNA elimination database. Case reconstruction confirmed that the investigator-who was located 80 km from the DNA laboratory and had never entered the crime scene or the sample storage room-was not a suspect and that the obtained STR profile originated from contamination. The most plausible explanation for the contamination was indirect transfer: investigator's DNA had adhered to a colleague's clothing and was subsequently dislodged and deposited onto the surface of the plastic bag as the colleague approached the sample pretreatment area. This study integrates trace DNA profiling of challenged samples with rapid contamination investigation and proposes prevention and control measures. This case underscores that, although DNA is widely regarded as the "gold standard" in forensic genetics, its interpretation must be considered within the context of the entire case. Conclusions should not be drawn based solely on a single DNA result.
Humans↗
Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA.
We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen.
Bone and Bones↗
Sensitive and specific cytokeratin 18 reverse transcription-polymerase chain reaction that excludes amplification of processed pseudogenes from contaminating genomic DNA.
Processed pseudogenes of residual contaminating genomic DNA interfere with a sensitive detection of cytokeratin 18 (CK18) mRNA by reverse transcription and polymerase chain reaction (RT-PCR). This may cause false-positive results when CK18 mRNA is used as a marker for ectopic tumor cells in specimens from cancer patients. To establish a sensitive CK18 RT-PCR by excluding the amplification of processed pseudogenes, the following strategy was chosen: (a) CK18 pseudogene sequences were cloned from genomic DNA by PCR; (b) cDNA-specific primers were designed on the basis of mismatches between pseudogenes and cDNA; (c) PCR conditions were adjusted to reach maximum sensitivity and specificity. Epithelial cells (1-10) could be detected in 1 mL of blood. Among the numerous CK18 genes homologous to the transcribed gene, at least two different processed pseudogenes exist that are highly homologous to each other and to the exons of the transcribed CK18 gene.
Biomarkers, Tumor↗
Exclusive amplification of cDNA template (EXACT) RT-PCR to avoid amplifying contaminating genomic pseudogenes.
Genomic DNA contamination within RNA samples has important implications for RT-PCR, particularly if there is a pseudogene related to the gene under investigation, because amplification from pseudogenes and reverse-transcribed cDNA can be very difficult to distinguish. Methods to remove DNA contamination cannot guarantee the absolute absence of DNA from the sample without a loss of RNA quantity or quality, which can be crucial for small amounts of RNA or for the investigation of transcripts with a low level of expression. Here, we describe a general technique for RT-PCR that applies a sequence to the 5' tail of reverse-transcribed cDNA that is not present in genomic DNA and uses this for annealing the reverse PCR primer to exclude genomic DNA amplification in unmodified RNA samples.
Base Sequence↗
Methods and reagents. Better competent cells and DNA polymerase contaminants.
Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methods-reagents, available on the Internet. This month's column discusses a new method for harvesting Escherichia coli cells for transformation, and contaminants found in DNA polymerase stocks used for the polymerase chain reaction. For details on how to partake in the newsgroup, see the accompanying box.
DNA-Directed DNA Polymerase↗
Transabdominal placental biopsy in the second and third trimesters of pregnancy: what is the risk of maternal contamination in DNA diagnosis?
We investigated the risk of maternal contamination in antenatal DNA diagnosis after second- and third-trimester transabdominal placental biopsy. For this purpose, we compared the restriction fragment length polymorphism (RFLP) patterns of 11 chorionic villus DNA samples after late chorionic villus sampling (CVS) with those of the corresponding maternal DNA. Ten of 11 aspirated tissue samples were not separated from maternal contamination before DNA extraction. All 11 mother-embryo pairs were informative for analysis of maternal contamination, ie, the mother showed one RFLP allele not present in the embryo. In none of the 11 cases did the fetal DNA show maternal contamination after molecular hybridization, although ten samples were contaminated with maternal tissue macroscopically and microscopically. Despite some maternal tissue admixture, the risk of contamination seems to be lower in the second- and third-trimester CVS than in first-trimester CVS, based on previous reports and our own experiences. This is most likely due to the anatomically closer contact of villi and decidua in the first trimester of pregnancy.
Alleles↗
Hypersensitive PCR, ancient human mtDNA, and contamination.
When highly efficient polymerase was used with high cycle numbers (50-60), strong amplifications were observed, but negative controls were also unexpectedly amplified in a study of ancient human mtDNA from 2000-year-old skeletons. The results of a series of tests revealed that the hypersensitive polymerase chain reaction (PCR) generated by higher cycles and the presence of contaminant DNA (though at extremely low levels) should be responsible for the amplification of negative controls. We suggest that PCR sensitivity be optimized to take advantage of highly efficient polymerase and at the same time prevent "background DNA" from becoming "contaminant DNA" and obscuring the analysis of authentic ancient DNA. We propose the use of multiple positive controls when amplifying ancient human mtDNA samples to indicate the sensitivity of individual PCR amplifications and to monitor the contamination levels of modern human DNA. This study provides some suggestions as to how to amplify and analyze ancient human mtDNA when unavoidable and extremely tiny amounts of modern human DNA exist.
Archaeology↗
Single-cell cDNA-PCR: removal of contaminating genomic DNA from total RNA using immobilized DNase I.
A procedure utilizing immobilized DNase I that allows the efficient amplification of cDNA by PCR from a single cell in the absence of contaminating genomic DNA is described. DNase I treated, total RNA derived from single cells was reverse transcribed into cDNA followed by PCR using beta-actin and c-fos specific primers that recognize different exons of the respective genes. Amplification products corresponding to cDNA, but not to genomic sequences, were detected after treatment with immobilized DNase I in samples previously shown to be contaminated with genomic DNA. This method allows the efficient removal of DNA contaminating total RNA derived from a single cell.
Artifacts↗
Improved method for the removal of endotoxin from DNA.
Contaminating endotoxin in solutions used in gene therapy and genetic immunization can result in various deleterious effects both in vitro and in vivo. In order to avoid such complications, attempts were made to characterize the extent of the problem of endotoxin contamination and develop a solution to this problem. After screening for endotoxin in plasmid DNA preparations using the Limulus Amoebocyte Lysate (LAL) assay, nearly half of all samples displayed high endotoxin levels. Therefore, a simple one-step procedure was developed for the removal of endotoxin using a polymyxin B resin.
Animals↗