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PubMed1983

Rapid purification of plasmid DNA by a single centrifugation in a two-step cesium chloride-ethidium bromide gradient.

A procedure for rapid, preparative purification of plasmid DNA is described and compared with a conventional equilibrium centrifugation method. A discontinuous, two-step CsCl-ethidium bromide gradient is used, with the starting position of the plasmid-containing extract being at the bottom of the tube. During centrifugation in a fixed angle rotor, covalently closed circular plasmid DNA is separated from contaminating protein, RNA, and chromosomal DNA in 5 hr. Plasmids purified by this method are considerably less contaminated with RNA than when purified by a 48-hr equilibrium run in a homogeneous gradient, as determined by agarose gel electrophoresis and 5'-end-labeling studies. Plasmid DNA purified in two-step gradients can be used directly for restriction endonuclease analysis and DNA sequencing.

Autoradiography↗

PubMed2002

Protein-mediated isolation of plasmid DNA by a zinc finger-glutathione S-transferase affinity linker.

The sequence-specific affinity chromatographic isolation of plasmid DNA from crude lysates of E. coli DH5alpha fermentations is addressed. A zinc finger-GST fusion protein that binds a synthetic oligonucleotide cassette containing the appropriate DNA recognition sequence is described. This cassette was inserted into the SmaI site of pUC19 to enable the affinity isolation of the plasmid. It is shown that zinc finger-GST fusion proteins can bind both their DNA recognition sequence and a glutathione-derivatized solid support simultaneously. Furthermore, a simple procedure for the isolation of such plasmids from clarified cell lysates is demonstrated. Cell lysates were clarified by cross-flow Dean vortex microfiltration, and the permeate was incubated with zinc finger-GST fusion protein. The resulting complex was adsorbed directly onto glutathione-Sepharose. Analysis of the glutathione-eluted complex showed that plasmid DNA had been recovered, largely free from contamination by genomic DNA or bacterial cell proteins.

Chromatography, Affinity↗

PubMedDate not supplied

Absence of p16 gene (CDKN2) deletions in microdissected primary breast carcinoma specimens.

BACKGROUND: The p16 gene (CDKN2), a tumor suppressor gene located on chromosome 9p21, has been demonstrated to be mutated or deleted with high frequency in a variety of tumor cell lines, including breast. While previous studies have not demonstrated CDKN2 mutations in primary breast carcinomas, it is possible that gene deletion in neoplastic DNA was marked by the presence of contaminating normal stromal DNA in breast carcinoma specimens. METHODS: We investigated the incidence of homozygous deletion of CDKN2 by analyzing 20 microdissected pure populations of primary breast carcinoma cells. Using polymerase chain reaction (PCR) techniques, the entire coding region and intervening introns of CDKN2 were amplified. The PCR products were resolved by agarose gel electrophoresis and single-strand conformation polymorphism (SSCP) analysis. RESULTS: We detected no deletions or mutations of the p16 gene. CONCLUSIONS: CDKN2 is not deleted with high frequency in primary breast carcinomas, and the p16 gene does not play a role in breast carcinogenesis via this mechanism.

Breast Neoplasms↗

PubMed1991

Flow cytometric DNA analysis of ducks accumulating 137Cs on a reactor reservoir.

The objective of this study was to detect red blood cell (rbc) DNA abnormalities in male, game-farm mallard ducks as they ranged freely and accumulated 137Cs (radiocesium) from an abandoned nuclear reactor cooling reservoir. Prior to release, the ducks were tamed to enable recapture at will. Flow cytometric measurements conducted at intervals during the first year of exposure yielded cell cycle percentages of DNA (G0/G1, S, G2 + M phases) of rbc, as well as coefficients of variation (CV) in the G0/G1 phase. DNA histograms of exposed ducks were compared with two sets of controls which were maintained 30 and 150 miles from the study site. 137Cs live wholebody burdens were also measured in these animals in a parallel kinetics study, and an approximate steady-state equilibrium was attained after about 8 months. DNA histograms from 2 of the 14 contaminated ducks revealed DNA aneuploid-like patterns after 9 months exposure. These two ducks were removed from the experiment at this time, and when sampled again 1 month later, one continued to exhibit DNA aneuploidy. None of the control DNA histograms demonstrated DNA aneuploid-like patterns. There were no significant differences in cell cycle percentages at any time point between control and exposed animals. A significant increase in CV was observed at 9 months exposure, but after removal of the two ducks with DNA aneuploidy, no significant difference was detected in the group monitored after 12 months exposure. An increased variation in the DNA and DNA aneuploidy could, therefore, be detected in duck rbc using flow cytometric analysis, with the onset of these effects being related to the attainment of maximal levels of 137Cs body burdens in the exposed animals.

Animals↗

PubMed1993

Development and validation of laboratory procedures for preimplantation diagnosis of Duchenne muscular dystrophy.

In order to develop and validate methods for the preimplantation diagnosis of Duchenne muscular dystrophy (DMD), we have established and evaluated PCR assays for the analysis of four loci within the DMD gene and for two Y chromosome sequences in single cells. A model system using buccal cells picked from mouthwash samples has been used for an extensive evaluation of the sensitivity and specificity of the assays, and each assay has been tested in samples containing single cells, two cells, and three cells per tube. The four DMD and two Y assays have been combined in duplex and triplex reactions to enable simultaneous diagnosis of DMD and of fetal sex. One of the DMD markers is a highly polymorphic simple tandem repeat locus which produces a basic DNA profile, and provides a control for contamination by foreign DNA. Amplification of DMD or Y sequences was observed in 78 to 92% of single male cells, rising to 96% and 97% in tubes containing two or three male cells respectively. Coamplification of both a DMD and a Y sequence together occurred with a mean success of 74% in single male cells, increasing to 93% with two, and 95% with three cells per tube. With appropriate precautions, we believe that it is now possible to proceed to clinical application of these procedures.

Base Sequence↗

PubMed1994

[Detection of Aspergillus fumigatus DNA by polymerase chain reaction in the clinical samples from individuals with pulmonary aspergillosis].

Aspergillosis is a disastrous cause of mortality and morbidity in patients in an immunocompromised state and old lung tuberculosis. However, the diagnosis of aspergillosis remains unsettled. In the present study, we developed a test to detect the Aspergillus fumigatus DNA using polymerase chain reaction (PCR) in clinical samples including sputum and bronchial aspirations from the patients with aspergillosis. We selected 2 pairs of oligonucleotide primers and the DNA for the small subunit ribosomal RNA of aspergillus fumigatus and they were significantly amplified. Although isolation of Aspergillus DNA may reflect contamination and colonization without infection, no aspergillus DNA was found in sputum or bronchial aspirations from the patients with lung cancer or interstitial lung diseases except a case of pulmonary fibrosis associated with rheumatoid arthritis chronically received 20 mg of corticosteroid. There was a 100% correlation between the culture results and the nested PCR results in the patients with pulmonary aspergillosis. These findings indicate that PCR detection of aspergillus fumigatus might be valuable for the diagnosis of aspergillosis.

Aged↗

PubMedDate not supplied

Molecular detection of cell line cross-contaminations using amplified fragment length polymorphism DNA fingerprinting technology.

We have tested amplified fragment length polymorphism (AFLP) technology, in comparison with isoenzyme analysis, for the simultaneous detection of inter- and intraspecific cell line cross-contaminations (CCCs) in the cell line collection held at the Istituto Zooprofilattico della Lombardia e dell'Emilia Romagna. Isoenzyme analysis identified four cases of interspecific CCCs. In a single experiment, AFLP was able to identify the species of origin of all cell lines for which a reference genomic deoxyribonucleic acid was available and to detect five interspecific contaminations. Four CCCs confirmed data on isoenzymes, whereas the fifth CCC was detected in a species for which isoenzyme analysis was noninformative. In addition, AFLP was able to identify the putative source of the contaminations detected. The utility of the technology in the detection of intraspecific cell line contaminations depends on the number of cell lines that have to be distinguished in a specific species and on the availability of highly informative fingerprinting systems. In mice, a single AFLP primer pair produced 16 polymorphisms and distinguished all the 15 strains of mouse cell lines analyzed. In humans, 18 AFLPs identified 83 different profiles in the 159 cell lines analyzed. Amplified fragment length polymorphism can conveniently be applied for cell line fingerprinting in species for which hypervariable markers are not available. In species for which a highly informative multiplex of microsatellite markers is available, AFLP can still provide a useful and cheap tool for simultaneously testing inter- and intraspecific contaminations.

Animals↗

PubMed2004

Influence of template DNA degradation on the genotyping of SNPs and STR polymorphisms from forensic materials by PCR.

Detection of single nucleotide polymorphisms (SNPs) and short tandem repeat (STR) polymorphisms by PCR is widely used to analyze degraded DNAs in forensic science. The success of DNA analysis from human remains largely depends on the quality of the template DNA. We examined two SNPs (HLA-DQA1 and ABO) and two STR polymorphisms (VWA and CD4) by SSCP gel or denaturing gel electrophoresis, using two kinds of degraded DNA samples (165 teeth and blood stains contaminated with saliva) derived from the same person and investigated the influence of template DNA degradation on genotyping. As the degradation of DNA proceeds, unbalanced amplification of alleles occurred in the analysis of both SNPs and STRs, followed by allele drop, and further by loss of amplification. Non-target allelic products of STRs were amplified from highly degraded DNA samples; however, false allelic products of SNPs were not amplified from them. Amplification efficiency increased in proportion to the decrease of PCR target size, but reduction of the PCR target sizes also increased the chances of amplifying contaminating DNA, especially in highly degraded DNA specimens. The present results will help investigators to evaluate the genotyping of highly degraded DNA samples in forensic casework.

ABO Blood-Group System↗

PubMed2005

Synthesis, characterization, and 32p-postlabeling analysis of DNA adducts derived from the environmental contaminant 3-nitrobenzanthrone.

3-Nitrobenzanthrone (3-NBA) is a potent mutagen and potential human carcinogen identified in diesel exhaust and ambient air particulate matter. 3-NBA forms DNA adducts in rodent tissues that arise principally through reduction to N-hydroxy-3-aminobenzanthrone (N-OH-ABA), esterification to its acetate or sulfate ester, and reaction of this activated ester with DNA. We detected 3-NBA-derived DNA adducts in rodent tissues by (32)P-postlabeling and generated them chemically by acid-catalyzed reaction of N-OH-ABA with DNA, but their structural identification has not yet been reported. We have now prepared 3-NBA-derived adducts by reaction of a possible reactive metabolite, N-acetoxy-N-acetyl-3-aminobenzanthrone (N-Aco-N-Ac-ABA), with purine nucleosides and nucleotides, characterized them, and have shown that they are present in DNA treated with this 3-NBA derivative. Three of these adducts have been characterized as the C-C adduct N-acetyl-3-amino-2-(2'-deoxyguanosin-8-yl)benzanthrone, the C-N adduct N-acetyl-N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone, and an unusual 3-acetylaminobenzanthrone adduct of deoxyadenosine, which involves a double linkage between adenine and benzanthrone (N1 to C1, N(6) to C11b), creating a five-membered imidazo type ring system. According to IUPAC fused ring conventions, we propose the following systematic name for this adduct: (9'-(2' '-deoxyribofuranosyl))purino[6',1':2,3]imidazo[5,4-p](1,11b-dihydro-(N-acetyl-3-amino))benzanthrone. The 3'-phosphates of these novel adducts could be 5'-postlabeled using [gamma-(32)P]ATP, although the efficiency of labeling was found to be low (less than 20%). However, none of these adducts could be detected in DNA from 3-NBA-treated rats by (32)P-postlabeling. Two of these synthetic adducts were treated with alkali to generate nonacetylated adducts, and these were also shown by HPLC to differ from those adducts found in rat DNA. Therefore, a different approach to the synthesis of authentic standards is needed for the structural characterization of 3-NBA-derived DNA adducts formed in vivo.

Animals↗

PubMed1996

HIV-1 proviral DNA polymerase chain reaction detection in chorionic villi after exclusion of maternal contamination by variable number of tandem repeats analysis.

OBJECTIVE: The study of the placental HIV infection in cases of seropositive pregnant women after exclusion of maternal contamination of chorionic villi samples by variable number of tandem repeats (VNTR) analysis. METHODS: We studied 30 HIV-positive women: 17 terminated their pregnancy (11 in the first trimester and six in the second) and 13 delivered at term (one was a twin gestation). We selected chorionic villi and ruled out maternal contamination by VNTR analysis. DNA from chorionic villi and cord and maternal blood were tested for HIV by PCR. All infants underwent a paediatric follow-up. RESULTS: All maternal blood samples tested positive for HIV-1 by polymerase chain reaction. No maternal contamination was revealed and HIV was found in six out of 11 first trimester placentas, in all second trimester samples, and in 10 out of 14 at term. Cord blood tested positive in all second trimester cases and in seven out of 14 liveborns. In no case was HIV found in cord blood without infection of the corresponding placenta; conversely, three placentas tested positive but cord blood was negative. Two infants were HIV-positive, 11 were uninfected (one case was lost to follow-up). CONCLUSION: Our study indicates that HIV-1 can infect the placenta from first trimester onwards. HIV was found in two-thirds of our cord blood samples but it is possible that some viral DNA in cord blood may have come from infected placental cells. Additional studies are needed to assess the source of HIV in cord blood and the possible contribution of placental or maternal cells infected with HIV to vertical transmission of the virus.

Blotting, Southern↗

PubMed1986

A simple procedure for the preparation of pure kinetoplast DNA network free of nuclear DNA from the kinetoplast hemoflagellate Leishmania donovani.

A simple, inexpensive procedure for preparing pure kinetoplast DNA network from Leishmania donovani is described. L. donovani promastigotes were lysed by incubating with pronase in presence of sodium dodecylsulfate. Crude kinetoplast DNA networks were obtained by centrifugation of the lysate through a 20% sucrose solution. The pellet containing kinetoplast DNA was deproteinized by phenol extraction. Contaminating nuclear DNAs were removed by denaturation with alkali, neutralization, and addition of polyethylene glycol-8000 to a concentration of 10% to facilitate precipitation of kinetoplast DNA. kDNA isolated after centrifugation was deproteinized several times with phenol and finally precipitated with ethanol. The average yield by this procedure is 30-50 micrograms of kDNA per gram of wet cells. By slot-blot hybridization with a nuclear DNA probe, no nuclear DNA contamination of the kDNA networks could be detected.

Animals↗

PubMed1990

32P-postlabeling detection of DNA adducts in fish from chemically contaminated waterways.

Fish were collected from sites in the chemically-contaminated Buffalo River, New York, and the Detroit River, Michigan. The sediments of these rivers have high levels of chemical contaminants, including polycyclic aromatic hydrocarbons (PAHs), and fish from these locations have high prevalences of liver cancer. To determine chemical-DNA interactions and a possible role for chemicals as a cause of the observed tumors, DNA was isolated from livers and was enzymatically digested to normal and adducted nucleotides. The DNA digests were enriched for hydrophobic, bulky adducts, either by preparative reverse phase high pressure liquid chromatography, or by selective nuclease P1 dephosphorylation of normal nucleotides. DNA-chemical adducts were then quantitated by 32P-postlabeling analysis. Regardless of the adduct enrichment procedure, the chromatograms derived from DNA of fish from polluted areas showed a diffuse, diagonal radioactive zone consisting, at least in part, of multiple overlapping discrete adduct spots. The behavior of the adducts in the diagonal radioactive zone and of their unlabeled precursors is consistent with their identification as nucleotide adducts of a variety of bulky, hydrophobic, aromatic genotoxic compounds. Analysis of bile demonstrated recent exposure to multi-ringed aromatic compounds.

Animals↗

PubMed1983

A papillomavirus DNA from a cervical carcinoma and its prevalence in cancer biopsy samples from different geographic regions.

DNA from one biopsy sample of invasive cancer of the cervix contained sequences hybridizing with human papillomavirus (HPV) type 11 DNA only under nonstringent conditions. This DNA was molecularly cloned in lambda phage. Under stringent conditions of hybridization it cross-hybridized to a minor extent (less than 0.1%) with HPV types 10, 14, and 15 and showed no homology with DNA of other human HPV types. We therefore propose to designate it tentatively as HPV 16. HPV 16 DNA was used as a probe to test additional cancer biopsy samples from cervical, vulval, and penile cancer, as well as benign genital warts (condylomata acuminata) and cervical dysplasias for the presence of homologous sequences. In 61.1% (11/18) of cervical cancer samples from German patients sequences were found hybridizing with HPV 16 DNA under conditions of high stringency. In contrast, only 34.8% (8/23) of cancer biopsy samples from Kenya and Brazil revealed this DNA. Vulval and penile cancer biopsy samples hybridized to 28.6% (2/7) or 25% (1/4), respectively. Only 2 out of 33 condylomata acuminata contained HPV 16 DNA. Both positive tumors harbored in addition HPV 6 or HPV 11 DNA. The data thus indicate that HPV 16 DNA prevails in malignant tumors, rendering an accidental contamination with papillomavirus DNA from adjacent papillomas rather unlikely. The rare presence in benign genital papillomas in addition to common genital papillomaviruses suggests a dependence of HPV 16 replication on helper virus.

Bacteriophage lambda↗

PubMed2002

An investigation into the transference and survivability of human DNA following simulated manual strangulation with consideration of the problem of third party contamination.

Amplification was performed on human DNA material transferred during a model of manual strangulation. A total of 29 separate experiments were performed using a single male offender-female victim combination to observe whether DNA was transferred both from the offender's fingers to the victim's neck and vice versa and to consider the period of time after the event during which the material could potentially be recovered and amplified. DNA was amplified from either the victim's neck or the offender's fingers for at least 10 days after the contact although it is discussed whether this is potentially due to primary contact or a secondary/tertiary transfer event. The study highlights the problem of contamination of the offender's hands and victim's neck with third party DNA, the presence of which could have a significant outcome for both the investigating authority and the third party.

Asphyxia↗

PubMed1993

[Problems in DNA ploidy analysis using flow cytometry--influences from contaminant mononuclear cells].

The present study was undertaken to examine the influences of excessive contamination by lymphocytes on the flow cytometric analysis of DNA ploidy of head and neck cancers. Although lymphocytes which contaminate test cells can serve as an internal control (2C), an excess of these lymphocytes can mask the aneuploid peak of cancers. This tendency was particularly prevalent in well-differentiated squamous cell carcinoma. In some cases, most of the cells isolated from tumor-positive HE-stained tissue samples were lymphocytes. This is probably because lymphocytes are likely to survive the cell-isolating procedure, whereas keratocytes are likely to be destroyed during it. If samples excessively contaminated by lymphocytes are subjected to flow cytometry, the aneuploid peak of cancer cells is low relative to the 2C peak, possibly causing an erroneous judgment of diploid. Cytofluorometry, in which a smear of test cells is observed directly to quantify the DNA of cancer cells alone, was useful in detecting lymphocyte-masked aneuploid cells.

Carcinoma, Squamous Cell↗

PubMedDate not supplied

Identification and enumeration of beta-hemolytic Listeria monocytogenes in naturally contaminated dairy products.

A DNA probe was used to identify hemolytic Listeria monocytogenes in naturally contaminated dairy products: unpasteurized milk, ricotta cheese, and imported semisoft cheeses. Of 34 milk samples, 12 were suspected to contain hemolytic L. monocytogenes; 1 contained greater than 6000 viable organisms/g. The ricotta cheese, although temperature-abused, had a titer of 3.6 x 10(6) beta-hemolytic L. monocytogenes cells/g, whereas the semisoft cheeses reached a maximum of 5.6 x 10(6) cells/g. Pure cultures of L. monocytogenes isolated from both types of cheese were found positive by the CAMP test and the DNA probe.

Animals↗

PubMed1977

Evaluation of a standardised assay for the measurement of antibodies to double-stranded (native) DNA.

A standardised commercially available radioimmunoassay kit for the detection of antibodies to native DNA (N-DNA) has been evaluated in clinical practice. This test system is shown to be a reliably reproducible method of detecting these antibodies. In addition, evaluation of the purity of the radiolabelled test antigen in this assay has shown it to be almost entirely double stranded (native) DNA with virtually no contamination with single stranded (denatured) DNA, and with few areas of single stranded breaks or ends in the duplex molecule. The inclusion of known standards and precise characterisation of the DNA has partially overcome variability in results and provides for interlaboratory standardisation which is lacking in the techniques used at present.

Antibodies, Antinuclear↗

PubMed1997

Presence of RNase A causes aberrant DNA band shifts.

RNase A, which is routinely added during DNA purification to reduce contaminating RNA, causes shifting of DNA bands in agarose gels. DNA band sizes on agarose gels increase as much as 10%-20% when RNase A is present. The low concentrations of RNase A typically used to purify DNA cause shifting of select DNA bands, in contrast to higher concentrations of RNase A where all band are shifted and smeared. The binding of RNase A to the DNA is specific and the degree of the shift varies; not all DNA bands are retarded, and the deviation is more pronounced in certain buffers. Other proteins, such as bovine serum albumin or proteinase K, do not induce DNA band shift, suggesting the interaction is specific. The binding of RNase A to DNA is reversible. The formation of RNase:DNA complexes may affect experiments involving DNA:protein interactions such as gel shift, footprinting and filter binding assays. Researchers performing DNA characterization from miniprep protocols should be aware that RNase may cause the apparent sizes of DNA fragments to be altered and obscure the presence of very small cloned fragments.

Buffers↗