SEARCH · PubMed Health

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 883 records · Page 49Linked to original sources

PubMed2005

Comparison of six RNA extraction methods for the detection of classical swine fever virus by real-time and conventional reverse transcription-PCR.

Six RNA extraction methods, i.e., RNAqueous kit, Micro-to-midi total RNA purification system, NucleoSpin RNA II, GenElute mammalian total RNA kit, RNeasy mini kit, and TRIzol LS reagent, were evaluated on blood and 7 tissues from pig infected with classical swine fever virus (CSFV). Each of the 6 extraction methods yielded sufficient RNA for positive results in a real-time reverse transcription-PCR (RT-PCR) for CSFV, and all RNA, except the one extracted from blood by TRIzol LS reagent, yielded positive results in both a conventional RT-PCR for CSFV and a conventional RT-PCR for an endogenous gene encoding beta-actin. The RNA extracted from blood by TRIzol LS reagent became positive in both conventional RT-PCR assays when it was diluted to 1:2, 1:4, or up to 1:64 in nuclease-free water. It is concluded that all 6 methods are more or less useful for the detection of CSFV by real-time and conventional RT-PCR in swine blood and tissues. However, some of the 6 reagents offer certain advantages not common to all 6 extraction procedures. For example, RNA extracted by the TRIzol LS reagent constantly had the highest yield; that by the RNAqueous kit had the highest A260/A280 ratio for almost all samples; and that by the NucleoSpin RNA II and the GenElute mammalian total RNA kit was most likely to be free of contaminations with genomic DNA.

Animals↗

PubMed2006

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

BACKGROUND: Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. RESULTS: Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (rho0) cells (control) with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences. CONCLUSION: These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.

Base Sequence↗

PubMed2003

[Chronic Chagas' disease: from xenodiagnosis and hemoculture to polymerase chain reaction].

Although there has been an improvement in the diagnosis of chronic Chagas' disease, the low sensitivity of indirect parasitological tests is a drawback to its application in diagnosis and post-therapeutic control. Polymerase chain reaction (PCR) has limited use in routine diagnosis due to the need of specific laboratory facilities, common DNA cross-contamination, and high costs. At the same time, the high variability of PCR results found in different regions of Brazil raises some questions concerning its applicability for diagnosis. PCR's high specificity is indicative that it can be used as a confirmation method in inconclusive serology diagnosis as well as an auxiliary method in pos-therapeutic control of chronic Chagas' disease when comparing to serology and parasitological techniques. It is discussed here the applicability of molecular and indirect parasitological methods in the diagnosis and post-therapeutic control of chronic Chagas' disease based on the literature published from 1954 to 2001.

Animals↗

PubMed2004

Molecular epidemiology of tuberculosis.

Molecular epidemiology (ME), a blend of molecular biology and epidemiology, is very useful to study the spread of tubercle bacilli in mini epidemics, outbreaks, to analyse the transmission dynamics of tuberculosis (TB) and to determine the risk factors for TB transmission in a community. ME has a great role in distinguishing between exogenous reinfection and endogenous reactivation. In the laboratory, molecular epidemiology can be used to identify cross contamination. Many new DNA typing methods have been introduced after the initial introduction of restriction fragment length polymorphism (RFLP) in 1993. An internationally accepted, standardized protocol for RFLP typing of the Mycobacterium tuberculosis complex using IS6110 was published in 1993 and is still used today. Most of the newer DNA typing methods are PCR based and microarray based methods are also available. This will enable individual strains of M. tuberculosis or clonal groups to be identified by specific phenotypic traits. ME will continue to be a useful tool in future to measure the impact of any public health intervention strategy for control of tuberculosis in the community.

Disease Outbreaks↗

PubMed1992

Lack of transmission of deleted mtDNA from a woman with Kearns-Sayre syndrome to her child.

We have investigated the daughter of a woman with Kearns-Sayre syndrome. The woman had a high percentage of deleted mtDNA in muscle, but no deleted mtDNA was detected in fibroblasts, bone marrow, and peripheral blood cells by Southern blot analysis. With PCR, analytical sensitivity was significantly increased, and deleted mtDNA was detected in all examined tissues from this patient. The patient had healthy parents and nine healthy siblings. No deleted mtDNA was detected in blood from the mother of the patient. The patient had an uneventful pregnancy and delivered at term. Deleted mtDNA could not be detected in placenta by Southern blot analysis. With PCR, deleted mtDNA was detected in the majority of placental specimens. This finding may, however, be due to contamination with maternal DNA. The patient's daughter was healthy at age 5 mo, and morphologic examination of muscle was normal. No transmission of deleted mtDNA to the daughter could be detected by Southern blot and PCR analysis of peripheral blood cells, bone marrow, fibroblasts, and muscle. The presence of deleted mtDNA was excluded at a fractional level of less than 1:100,000 in all examined tissues from the daughter.

Adolescent↗

PubMedDate not supplied

[The method of isolation of Sau 6782-type methylases].

Heterogeneous profile of methylases was found in S. aureus 6782 strain. A procedure was developed for isolation of individual methylases from Sau 6782 free of Sau 6782 restrictases and unspecific nucleases by means of hydrophobic chromatography on phenyl-Sepharose. Ion exchange, affinity chromatographies and gel filtration were also used for isolation of the Sau 6782 methylases. But this technique was of limited suitability for isolation of individual methylating enzymes of the Sau 6782 type because it did not allow to separate completely these methylases from contaminating enzymes of DNA degradation. Effects of salts, glycerol and Triton X-100 on activity of total preparation of methylases Sau 6782 were studied. Na+ and K+ chlorides, ammonium sulfate at concentrations 0.4 M and highen as well as Triton X-100 inhibited reversibly the methylase activity followed by complete reduction up to initial level after dialysis. Glycerol at concentration 60% activated Sau 6782 methylases by 50% and stabilized the enzyme.

Chromatography, Affinity↗

PubMed1994

Multipoint mapping calculations for sperm-typing data.

This paper explains how multipoint likelihoods can be computed for sperm-typing data. Experimental errors such as multiple sperm per tube, inadequate amplification, and contamination by exogenous DNA are explicitly taken into account. By limiting the number of sperm theoretically possible per tube to a predetermined maximum and by assuming no chiasma interference, maximum-likelihood estimation can be carried out rapidly using the theory of hidden Markov chains.

Algorithms↗

PubMed1985

[Population of murine rhabdomyosarcoma MKh-53 clones under different proliferation conditions studied by flow cytometry].

Clones of rhabdomyosarcoma cells were obtained due to implantation of the tumor cells in the eye anterior chamber, in subcutaneous connective tissue and in lungs of mice. The DNA contents in the clone cells were measured using flow cytometry. Diploid indices of clones were calculated from the ratio of the modal content of DNA in G1-cells to the DNA content in lymphocytes contaminating these clones. The diploid indices of various clones varied from 1.4 to 2.3. The mean diploid index calculated for clones that grew under given conditions of proliferation varied within 1.85-1.88. Only one of the 66 clones examined displayed a two-peak distribution of cell according to their DNA content in phase G1, which may suggest a karyotypic instability of the progeny of the tumor clonogenic cell. No correlation was revealed between the diploid indices of clones and the following parameters, such as: the portion of tumor cells being at different phases of cell cycle; the number of normal (stromal) cells contaminating the clones, coefficients of variation of DNA contents in tumor cell clones. A positive correlation was observed between the coefficients of variation of DNA contents in the normal (stromal) cells contaminating the clones and those of tumor clone cells being in phase G1. It is concluded that the variability of results of the flow cytometric measurement of DNA in G1-cells may reflect the variability of cells in respect not only to their DNA contents but also to their capacity of dye sorbtion.

Animals↗

PubMed1993

Mutagenic activity of drinking water in Wroclaw, Poland.

The Salmonella mutagenicity test was applied to the evaluation of mutagenic activity of Wroclaw drinking water. Contaminants of water samples were concentrated by adsorption on XAD-2 resin. After while they were eluted sequentially with acetone, dichloromethane/methanol (1:1, v/v) and methanol, and then obtained organic extracts were evaporated to dryness. The extracts were then dissolved in DMSO and examined by using the Ames test. The results proved significant contamination of drinking water with mutagenic substances. Hydroxyapatite column chromatography performed after direct incubation of standard DNA probes with tested water extracts showed that drinking water was contaminated with DNA interstrand cross-linking substances. Filtration of tap water through carbon filters markedly reduced mutagenic activity of tested water extracts, whereas ceramic filters were more efficient in depleting of DNA interstrand cross-linking contaminants.

Animals↗

PubMed2004

Detection of bacterial DNA in blood samples from febrile patients: underestimated infection or emerging contamination?

We applied real-time broad-range polymerase chain reaction (PCR) to detect bacteraemia in blood from febrile patients. Interpretation of amplification results in relation to clinical data and blood culture outcome was complex, although the reproducibility of the PCR results was good. Sequencing analysis of the PCR products revealed the presence of Burkholderia species DNA while no Burkholderia species grew in culture. The source of this contamination was shown to be the commercial DNA isolation kit used in the automated MagNA Pure Isolation Robot. A high degree of suspicion is required when uncommon or unexpected pathogens are diagnosed by molecular methods as clinical consequences can be serious.

Bacteremia↗

PubMed1983

Synthesis of full-length, virus genomic DNA by nuclei of vaccinia-infected HeLa cells.

It is well established that vaccinia virus infection induces the synthesis of virus-specific DNA in cytoplasmic 'factories', which are sites of virus-specific transcription. The present study demonstrates that vaccinia virus-specific DNA is synthesized also in the nuclei of infected cells with a similar time course. Direct observation and radiolabelling confirm the integrity of isolated nuclei. Reconstitution experiments and inhibitor studies demonstrate that virus-induced DNA is synthesized de novo within nuclei and does not result from cytoplasmic contamination. Cell-specific DNA synthesis is inhibited completely after infection and nuclei of infected cells then synthesize DNA which co-sediments with virus genomic DNA in denaturing gradients. Restriction endonuclease cleavage and hybridization with a virus-specific probe indicate that this is full-length, virus genomic DNA. The biological implications of this are discussed.

Cell Fractionation↗

PubMed1983

Rapid preparation of vector-free hybridization probes suitable for screening recombinant libraries.

A procedure is described to rapidly prepare radioactively labeled DNA inserts from crude recombinant plasmid DNA preparations. These probes can subsequently be used to identify homologous nucleotide sequences in bacteria containing recombinant plasmids by colony hybridization. In a single procedure, crude recombinant plasmid DNA is both 32P-labeled and fragmented by nick-translation in the presence of sufficient pancreatic DNase I to produce radioactive DNA of about 0.2-0.3-kb single-strand length. At this DNA fragment length the majority of the vector and insert sequences are on different DNA fragments. The insert DNA can then be separated from vector and contaminating Escherichia coli host chromosomal DNA by the following method. The DNA fragment population is first denatured and renatured under conditions such that the recombinant plasmid DNA reassociates but host DNA does not. The renatured plasmid DNA fragments are separated from the denatured host DNA by hydroxylapatite chromatography. The plasmid DNA fragments are then denatured and renatured with an excess of insert-free vector DNA. Conditions are chosen such that the insert DNA remains single-stranded while the vector DNA becomes double-stranded. The single-stranded insert DNA can be separated from the double-stranded vector DNA on hydroxylapatite and used directly for colony hybridization.

DNA, Recombinant↗

PubMed1978

Replication of nondefective parvoviruses: lack of a virion-associated DNA polymerase.

We have examined four of the nondefective parvoviruses for an associated DNA polymerase. Virions were purified from neuraminidase-treated infected-cell lysates by isopycnic centrifugation in CsCl or from infected cell material by CaCl(2) precipitation and centrifugation through sucrose into CsCl. Preparations of bovine parvovirus or Kilham rat virus obtained by the former procedure contained DNA polymerase activity but were not free of contaminating cellular proteins. The latter method produced viral preparations free of contaminating cellular proteins, and no DNA polymerase activity was detected in light infectious particles of H-1, LuIII, bovine parvovirus, or Kilham rat virus. Examination of levels of each cellular DNA polymerase in these preparations from each step of both purification procedures revealed that DNA polymerase beta had a greater tendency to copurify with bovine parvovirus and Kilham rat virus than did DNA polymerases alpha or gamma. Disruption of infectious virions obtained by the second purification method with detergents and sonic treatment did not result in the detection of a DNA polymerase activity. The biological activity and purity of each of the four different viruses obtained by the latter procedure were determined by hemagglutination and infectivity assays, polyacrylamide gel electrophoresis, and electron microscopy. In each case, the virions banding at a density of 1.39 to 1.41 g/cm(2) in CsCl were infectious and contained only the virion structural proteins. DNA polymerase activity was not detected in any of these preparations, and we have concluded that a virion-associated DNA polymerase is not required for productive infection with the nondefective parvoviruses.

Animals↗

PubMed1988

High-performance liquid chromatographic analysis of DNA composition and DNA modification by chloroacetaldehyde.

The separation of common and modified deoxyribonucleosides derived from DNA hydrolyzates was examined under different chromatographic conditions on silica-based octadecyl (C18) columns, involving hydrophobic interactions with the matrix. A novel method for the analysis of the DNA composition is described. It involves the removal of RNA contaminants and enzymatic hydrolysis of DNA, first to deoxyribonucleoside monophosphates and then dephosphorylation of the latter to deoxyribonucleosides. Hydrolysis conditions were sought to avoid deamination of dA and dC residues to dI and dU contaminants, respectively. Elution of these contaminants and the artifacts (ribonucleosides derived from RNA) is described in relation to the elution of deoxyribonucleosides. Chromatographic separation of the hydrolyzate derived from a 15-micrograms sample of DNA under selected separation conditions and on one high-performance liquid chromatographic column is achieved in 18 min at room temperature. Detection of modified components (and contaminants) present in minute amounts is enhanced with the use of a diode-array detector. The power of this technique lies in its ability to characterize and quantitate accurately the amount of modified species present in the DNA structure (less than 2% of all the other residues). Examples of the composition analysis of DNA derived from a prokaryote (Escherichia coli B) and a eukaryote (salmon sperm) are described. Details of quantitation (calibration graphs) of different nucleosides are furnished for peak-area integration by commercially available software, and spectral properties of the nucleoside in the elution buffer are described for quantitation by other means. Application of the composition analysis is shown here for probing the DNA conformation in solution by chemical means, while using chloroacetaldehyde as the modifying agent.

Acetaldehyde↗

PubMed1984

Alkaline transfer of DNA to plastic membrane.

DNA forms a stable complex with Gene Screen Plus membrane at alkaline pH. Based on this, a method of alkaline transfer of DNA from agarose gel to Gene Screen Plus membrane was elaborated. The procedure entails the use of 0.4 M NaOH for both, the DNA denaturation and DNA transfer steps. The alkaline transfer offers a higher hybridization efficiency and simplifies the transfer procedure as compared with the standard method of DNA transfer at neutral pH. In addition, it can be used to remove RNA contamination from the transferred DNA.

Animals↗

PubMed1977

Interaction of polyoma and mouse DNAs. IV. Time course and extent of integration of polyoma DNA into mouse DNA during lytic infection.

The time course of covalent binding of polyoma viral DNA to mouse DNA was followed in mouse embryo cells that had been grown prior to infection in the presence of 5-bromodeoxyuridine. Density-labeled (HL) mouse DNA was separated from free polyoma DNA by CsCl isopycnic centrifugation. Polyoma DNA sequences present in HL mouse DNA were detected by hybridization with radioactive cRNA synthesized in vitro. In reconstruction experiments, the limit of detection was found to be, on the average, about 0.5 genome equivalent (g.e.) of polyoma DNA per cell. To find conditions for the isolation of HL mouse DNA and for its complete separation from free polyoma DNA, cultures infected at 4 degrees C were used. HL mouse DNA extracted with sodium dodecyl sulfate and high salt concentrations (5 to 6 M CsCl) and then purified by three consecutive CsCl density gradient centrifugations was free from detectable amounts of polyoma DNA, whereas HL mouse DNA extracted with chloroform and phenol and purified in the same way always contained contaminating, noncovalently bound polyoma DNA. In lytically infected bromodeoxyuridine-prelabeled mouse embryo cultures, polyoma DNA bound to HL mouse DNA that had been extracted by the sodium dodecyl sulfate-CsCl procedure was first detected in small amounts (1 to 2 g.e. per cell) at 10 h after infection. In cultures incubated with medium containing thymidine (5 mug/ml), 4 to 6 g.e. of polyoma DNA per cell was detected at 14 and 18 h after infection. In these samples, practically all viral DNA was bound to high-molecular-weight HL mouse DNA. In cultures incubated with normal medium (no additions) and extracted between 17 and 20 h after infection, 20 to 350 g.e. of polyoma DNA per cell banded with HL mouse DNA. However, when DNA of one of these samples was subfractionated by sodium dodecyl sulfate-salt precipitation prior to isolation of HL mouse DNA, about 80% of the viral DNA banding at increased density was present in the low-molecular-weight DNA fraction. This observation suggests that in normal medium some progeny viral DNA of increased density was synthesized. Covalent binding of polyoma DNA to density-labeled mouse DNA was demonstrated by alkaline CsCl density gradient centrifugation: nearly equal amounts of polyoma DNA were found in the H and L strands, respectively, as is expected for linear integration of viral DNA. The results lead to the conclusions that (i) early polyoma mRNA is transcribed from free parental viral DNA; (ii) covalent linear integration is first detectable at the time when tumor (T)-antigen is synthesized; and (iii) only few copies (<10 g.e./cell) become integrated between 10 and 18 h after infection, i.e., during the period when cellular and viral DNA replication starts in individual cells.

Animals↗

PubMed1991

Stimulation of in vitro murine lymphocyte proliferation by bacterial DNA.

Although DNA is generally considered to be a poor immunogen, recent evidence suggests that DNA from various species differ in their immunologic activity and that bacterial DNA, unlike mammalian DNA, can induce significant antibody responses in mice. To explore further the immunologic activities of bacterial DNA, its ability to stimulate in vitro proliferation of murine lymphocytes was tested. The stimulation of lymphocytes with highly purified ssDNA from Escherichia coli resulted in a dose-dependent response that was maximal at 48 h. Several lines of evidence indicate that DNA, rather than endotoxin contamination, induced this response: 1) LPS at doses equivalent to those detected in the DNA preparation caused significantly less proliferation than the DNA; 2) the response to DNA was insensitive to polymyxin B; 3) pretreatment of DNA with DNase completely abrogated the response; and 4) DNA induced the proliferation of cells from endotoxin-resistant C3H/HeJ mice. Furthermore, although DNA from three different bacterial species induced proliferation, mammalian DNA from three species were nonmitogenic. Depletion of T cells from lymphocytes did not reduce proliferation, suggesting that bacterial DNA directly triggered B cell proliferation. These studies provide further evidence that DNA are not uniform in their immunologic activities likely because of their content of nonconserved structural determinants.

Animals↗

PubMed1993

A hot alkaline plasmid DNA miniprep method for automated DNA sequencing protocols.

A hot alkaline lysis procedure for plasmid DNA isolation is described for the preparation of high-quality substrates for automated DNA sequence analysis. This miniprep procedure employs routine laboratory chemicals while avoiding the use of enzymes and organic solvents to produce plasmid DNA free of RNA contamination. The method is inexpensive, relatively quick and can yield over 20 micrograms plasmid DNA from a 5-ml overnight culture. Automated sequencing has a success rate of > or = 96% with plasmid substrates prepared by this method. In addition, the plasmid DNAs can be used successfully in all types of molecular biology manipulations.

DNA, Bacterial↗