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UV irradiation is widely used to inactivate contaminating DNA in PCR. Highly UV-absorbent deoxyribonucleoside triphosphates in PCR mixtures reduce the efficiency of UV decontamination. Optimal decontamination may be achieved by irradiating the PCR mixture without the deoxyribonucleoside triphosphates.
DNase I can be used to remove contaminating DNA from RNA samples. Heat treatment has been recommended as a method to inactivate DNase I enzymatic activity, thereby allowing subsequent reverse transcription and PCR amplification of DNase I treated RNA. We have found that inactivation of DNase I by heat treatment is strongly dependent on Mg2+ concentration. In addition, deoxyribonucleolytic activity of "inactivated" enzyme may be restored by changes in Mg2+ concentration following heat treatment. Caution should be exercised when using heat treatment alone as a method of DNase I inactivation.
BACKGROUND: The stage-specific expression of genes is one of the most characteristics of parasites. It has been found that a lot of genes of Spriometra erinaceieuropaei are specifically expressed in pleroceroid in large amount, but not expressed when the plerocercoid development into adult worm. The study is to screen other stage-specific ecpression genes of plerocercoid of Spirtmetra erinceieuropaei. METHODS: RNA was separately extracted by acid guanidinium thiocyanate-phenol-chloroform from plerocercoids and adult worms of Spirometra erinaceieuropaei, DNA contaminated in the RNA was digested by RNase-free DNase. After the RNA was reverse transcripted to cDNA using T12MA, T12MC, T12MG and T12MT anchor-primers, PCR was done using the same T12MN and one random primer with alpha 35S-dATP in the system. The PCR products were fractionated on an 8% denatured polyacrylamide gel. Differential bands of the plerocercoid found in the gel were cut out, amplified by PCR and sequenced. Northern hybridization was used to identify the stage-specific expression genes. RESULTS: Eleven differential bands were selected from the gel and classified into 3 kinds of gene fragments by hybridization, after they were amplified by PCR. Fragments 1 (238 bp) and 2 (383 bp), were confirmed by Northern hybridization, as being expressed in the plerocercoid. However, fragment 3 (433 bp), was expressed in both the plerocercoid and the adult worm. Data from the 3 gene fragments underwent homological analysis in GenBank. The sequence which was homologous with fragments 1 and 2 was not found, but fragment 3 had high homology with many kinds of 28S rRNA. CONCLUSIONS: The gene expressions of plerocercoids are different from adult worms because they live in different hosts. Two types of different gene fragments from the plerocercoid were found by mRNA differential display technique.
RNA isolation from yeast is complicated by the need to initially break the cell wall. While this can be accomplished by glass bead disruption or enzyme treatment, these approaches result in DNA contamination and/or the need for incubation periods. We have developed a protocol for the isolation of RNA samples from yeast that minimizes degradation by RNases and incorporates two purification steps: acid phenol extraction and binding to a silica matrix. The procedure requires no precipitation steps, facilitating automation, and can be completed in less than 90 min. The RNA quality is ideal for microarray analysis.
A new and efficient method for isolation of plant RNAs was developed by adding bentonite into extraction buffer in order to get rid of protein and restrain Rnase. The electrophoretic patterns of nucleic acids and absorbance at 230 nm, 260 nm and 280 nm in a UV-Vis spectrophotometer revealed the extraction with this method can obtain RNAs with good integrity and purity without any apparent DNA contamination from the plant materials rich in with polysaccharide and polyphenol like Jatropha curcas leaves, to which TRIZOL reagent, SDS-KAc solution and Guanidine isothiocyanate solution failed. Furthermore, the result of nuclear gene (18 S rRNA gene) amplified by RT-PCR indicated that the RNAs prepared with this method can meet the needs of most molecular biological experiments including gene cloning and expression analysis.
The isolation of total RNA from primary culture of human splenocytes and its physico-chemical and biological properties are described. Human splenocytes are characterized by a high content of mRNA of human immune interferon, low content of total RNA and an extremely high activity of RNAases. Therefore it was necessary to elaborate conditions for the isolation of mRNA without DNA contaminants in the presence of extensive inhibitors of the RNAase activity. These include cell homogenization, separation of cytoplasm at -10 degrees C and treatment by RNAase inhibitors--ribonucleoside-vanadyl complexes or a combination of aurin-tricarboxylic acid with dithiothreitol. The resulting preparations of total RNA were purified by chromatography on oligo (dT)-cellulose and translated in a cell-free system from rabbit reticulocytes. These preparations were free of nonspecific translation inhibitors which are normally present in the lymphoid cells mRNA. In a cell-free system mRNA of human splenocytes induced with staphylococcal enterotoxin A code the synthesis of biologically active interferon which was identified as immune (gamma) human interferon, using a serological analysis. The preparations of immune interferon mRNA obtained under the conditions described above can further be used for cloning of the corresponding gene in bacterial cells.
We identified skeletal remains of a highly decomposed body by amplifying the COL2A1 3' variable region. We extracted degraded and contaminated DNA from teeth and bone fragments and amplified the hyper variable regions of COL2A1 by nested PCR. This method is 2,000 times more sensitive than the 27 cycle standard PCR. The sensitivity and specificity of the amplification was extremely improved using nested primer pairs. Using 47 cycles of total amplification by nested PCR, we were able to effectively amplify the target fragment. A total 47 cycles of dual PCR using one pair of primers was not as sensitive as nested PCR, which enabled us to amplify and detect the fragment from 5 pg of template DNA by agarose gel electrophoresis with ethidium bromide staining. We found that the hypersensitive nested PCR was suitable for the forensic identification of old, unidentifiable skeletal remains.
The molecular mechanism that in human bladder tumors leads to the loss of blood group ABO glycosyltransferase activity and, thereby, the loss of ABO antigens was investigated. In 15 tumors and 3 normal biopsies from blood group AB individuals and 7 tumors and 3 normal biopsies from blood group O individuals, mRNA was detected by a reverse transcription PCR (RT-PCR) assay, and the ABO blood group structure was determined by immunohistology. The RT-PCR spanned several introns in the ABO gene to exclude DNA contamination, and the RT-PCR product was shown to reflect the ABO gene message by dideoxy sequencing. The ABO mRNA was present in normal urothelium and low-grade tumors but disappeared from high grade tumors. This correlation to tumor grade was significant (P<0.04). Immunohistochemistry with monoclonal anti-blood group antibodies showed a complete correlation between the presence of mRNA and the presence of AB carbohydrate structures on cell surfaces. In two urothelial cell lines, genotyped as A/- and A/A, growth stimulation with the cholera toxin B subunit led to a total loss of ABO mRNA, and epidermal growth factor stimulation had an identical effect on one of the cell lines. We conclude that the ABO glycosylation in normal and malignant urothelium is regulated at the mRNA level, and that a mechanism associated with cell proliferation may trigger down-regulation of ABO mRNA.
Recombinant IFN-alpha2b (Intron A, Schering-Plough Corp, Kenilworth, NJ), derived from Escherichia coli, is currently approved worldwide for the therapy of various cancers and chronic hepatitis B and C. We describe here the purity and identity tests for both physicochemical properties and bioactivity that have been developed for the characterization of highly purified IFN-alpha2b with a specific activity of 2.5 x 10(8) IU/mg protein. The data indicate that a product of high purity can be consistently produced without DNA contamination. The antiviral bioassay chosen to measure potency is based on the ability of IFN-alpha2b to protect human foreskin fibroblast FS-71 cells from the cytopathic effects of encephalomyocarditis virus. Various immunoassays are described that have been used to quantitate the presence of binding and neutralizing antibodies in patients treated with IFN-alpha2b. Overall, the available data indicate a very low incidence of neutralizing antibody formation. We also summarize the current state of knowledge with respect to IFN reference standards for the biologic assay as well as recommendations for the calculation of antibody neutralization titers.
Two patients with an HIV-I infection, a man aged 47 with confusion, aphasia and diarrhoea, and a man aged 32 with dysphagia, a non-productive cough and diarrhoea, were diagnosed as having a disseminated Mycobacterium genavense infection. Both had low counts of CD4+ T lymphocytes. They responded to antimycobacterial treatment. M. genavense was recognized in Geneva in the early nineties as a causative agent of disseminated mycobacterial infections in HIV-seropositive patients with poor cellular immunity. The clinical picture resembles that of a generalized infection with M. avium-intracellulare. M. genavense is a slowly growing mycobacterium which can be isolated and identified using enriched nutrient media and molecular-biological techniques. The infection probably begins in the gastrointestinal tract after oral contamination. DNA of M. genavense can be demonstrated in 25% of the intestinal biopsy samples of non-HIV-seropositive patients.
The production of rabies vaccine on baby hamster kidney (BHK-21) cells for human use is discussed. Long term experience in application of this vaccine in animals, without any noticeable complications and findings of inactivation of contaminated DNA from the cell substrate by beta-propiolactone have justified its recommendation for human use. Preliminary results of applying this simple, adjuvant vaccine in volunteers, confirmed its good tolerability and immunogenicity.
We have studied the effect of in vivo treatment with trioxsalen on DNA replication in mammalian cells. In vitro cultured bovine liver cells were exposed to two or four cycles of treatment with 45 microM trioxsalen followed by irradiation with long-wave ultraviolet light. Thymidine incorporation was reduced by about 95% during the first hour after a double treatment. A large proportion of the label was released in alkaline sucrose gradients as a low molecular weight fraction (average length about 500 nucleotides) which was supposed to consist of replication origins containing DNA fragments. From the relative quantities of this DNA obtained at different times of the S phase we concluded that it contains a considerable but not precisely determinable proportion of non-origin DNA. We also find that the fraction is contaminated by a large excess of non-replicating bulk DNA.
A new modification of DNA purification has been developed. It includes: 1) standard treatment of biological material with proteinase K followed by phenol-chlorophorm extraction; 2) subsequent sample purification using micro-columns packed with Dowex-50 and Sephadex G-50. Oligonucleotide primers often used for DNA typing in man by means of polymerase chain reaction have also been modified. These are VNTR (variable number of tandem repeats) loci of apoB and D17S5. The increase of stability and specificity of amplification of VNTR loci of apoB and D17S5 was achieved by increase of primer length and amplification cycle. The sensitivity of this mode of amplification is 2-4 ng DNA-template. Employment of the nested amplification for apoB locus increased sensitivity of this method up to a few copies of DNA.
Using fluorescence resonance energy transfer technology and Lightcycler analysis, we developed a real-time PCR assay with primers and probes designed by using IS900 which allowed rapid detection of Mycobacterium avium subsp. paratuberculosis DNA in artificially contaminated milk. Initially, the PCR parameters (including primer and probe levels, assay volume, Mg(2+) concentration, and annealing temperature) were optimized. Subsequently, the quantitative ability of the assay was tested and was found to be accurate over a broad linear range (3 x 10(6) to 3 x 10(1) copies). The assay sensitivity when purified DNA was used was determined to be as low as five copies, with excellent reproducibility. A range of DNA isolation strategies was developed for isolating M. avium subsp. paratuberculosis DNA from spiked milk, the most effective of which involved the use of 50 mM Tris HCl, 10 mM EDTA, 2% Triton X-100, 4 M guanidinium isothiocyante, and 0.3 M sodium acetate combined with boiling, physical grinding, and nucleic acid spin columns. When this technique was used in conjunction with the real-time PCR assay, it was possible to consistently detect <100 organisms per ml of milk (equivalent to 2,000 organisms per 25 ml). Furthermore, the entire procedure (extraction and PCR) was performed in less than 3 h and was successfully adapted to quantify M. avium subsp. paratuberculosis in spiked milk from heavily and mildly contaminated samples.
Administration in vivo of monoclonal antibodies to humans is challenged by considerations regarding their safety. Contamination with viruses, potentially oncogenic nucleic acids and biologically active components like growth factors and hormones forms a serious point of concern in this respect. We have investigated the potential risk of viral contamination by measuring the reduction of 12 different viruses (after spiking) in the standard downstream purification process of ascitic fluid. Depending on the type of virus added and the purification step employed, the reduction of infectious virus particles varies considerably. The overall reduction ranges from about 10(3), observed for a member of the family of Papovaviridae, to more than 10(12) for members of the families of Herpesviridae and Orthomyxoviridae. Using hybridization analysis with a mouse (genomic) DNA probe, we show that the amount of residual DNA in ascitic fluids may also vary considerably, ranging from 75 ng/ml to 1 microgram/ml. In crude preparations produced in cell culture, much lower DNA concentrations are found (0.3 ng/ml). When standard downstream purification procedures are applied to ascitic fluid, a significant reduction of residual DNA levels is observed in the purified monoclonal antibody preparations and in intermediate fractions. The overall reduction factors vary from about 10(3) to 10(4), which is also confirmed by spiking experiments with either purified DNA or crude chromatin-like DNA. Using in-vitro cellular assays, we further show that peptide growth factors like PDGF and TGF beta are present in considerable amounts in ascitic fluids. The observed biological activities, however, are completely eliminated during the purification steps applied.
The subcloning of large inserts (>50 kbp) from P1-derived artificial chromosomes (PACs) was found to be hindered by the presence of contaminating Escherichia coli chromosomal fragments which, because of their smaller median size, are recovered preferentially as unwanted subclones. A significant fraction of contaminating DNA was seen to persist after conventional plasmid purification methods. We describe a rigorous protocol for eliminating the bulk of contamination that involves plasmid isolation on commercially available silica-based columns followed by three pulsed field gel electrophoresis steps. Using this, we were able to subclone 55, 85 and 90 kbp PAC inserts but failed to subclone a 195 kbp PAC insert. After surveying a range of DNA purification methods, we devised an optimised protocol that allowed us to subclone the 195 kbp insert. The optimised protocol, which reliably yields DNA with essentially no contaminating material, consists of plasmid isolation on silica-based columns followed by treatment with highly purified DNaseI and retrieval by electroelution of restriction-digested DNA electrophoresed on a single pulsed field gel. By inference it is applicable to the purification of large inserts from other single-copy plasmid vectors such as bacterial artificial chromosomes (BACs).
BACKGROUND: Preparation of RNA free from DNA is a critical step before performing RT-PCR assay. Total RNA isolated from several sources, including those obtained from Saccharomyces cerevisiae, using routine methodologies are frequently contaminated with DNA, which can give rise to amplification products that mimic the amplicons expected from the RNA target. RESULTS: We investigated the efficiency of two DNase I based protocols for eliminating DNA contaminations from RNA samples obtained from yeast cells. Both procedures are very efficient in eliminating DNA contamination from RNA samples and entail three main steps, which involve treating of RNA samples with DNase I, inhibition of the enzyme by EDTA and its subsequent inactivation at 65 degrees C. The DNase I treated samples were further purified with phenol: chloroform followed by precipitation with ice-cold ethanol (protocol I) or, alternatively, they were directly used in RT-PCR reactions (protocol II). Transcripts from ACT1, PDA1, CNA1, CNA2, TPS1 and TPS2 analyzed after each treatment showed that all mRNAs tested can be amplified if total RNA was extracted and purified after DNase I treatment, however, only TPS1, TPS2 and ACT1 mRNAs were amplified without extraction/purification step. CONCLUSION: Although more laborious and requiring a higher initial amount of material, the inclusion of an extraction and purification step allows to prepare RNA samples that are free from DNA and from low molecular contaminants and can be applied to amplify any Saccharomyces cerevisiae mRNA by RT-PCR.
Paleogenetic investigations of ancient DNA extracted from fossil material is for many reasons susceptible to falsification by the presence of more recent contamination from several sources. Gelatine-based bone glue that has been used extensively for nearly two centuries by curators to preserve hard tissues contributes nonauthentic DNA to paleontological material. This fact has been frequently neglected and is barely mentioned in the literature. Now paleogeneticists, curators, and conservators are faced with the problem that treatment of samples with adhesives and consolidants for conservatory purposes has seldom been recorded. Here, we show that racemization of amino acids, and in particular serine, is an excellent indicator for the treatment of paleontological samples with glue.