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PubMed1999

Optical PCR: genomic analysis by long-range PCR and optical mapping.

Optical mapping is an approach for the rapid, automated, non-electrophoretic construction of ordered restriction maps of DNA from ensembles of single molecules. Previously, we used optical mapping to make high-resolution maps of large insert clones such as bacterial artificial chromosomes (BAC) and large genomic DNA molecules. Here, we describe a combination of optical mapping and long-range polymerase chain reaction (PCR), in a process we term optical PCR, which enables automated construction of ordered restriction maps of long-range PCR products spanning human genomic loci. Specifically, we amplified three long PCR products, each averaging 14.6 kb in length, which span the 37-kb human tissue plasminogen activator (TPA) gene. PCR products were surface mounted in gridded arrays, and samples were mapped in parallel with either ScaI, XmnI, HpaI, ClaI, or BglII. A contig of overlapping high-resolution maps was generated, which agreed closely with maps predicted from sequence data. The data demonstrate an approach to construct physical maps of genomic loci where very little prior sequence information exists, since the only sequence needed is that required to anchor PCR primers. Large segments of genomic DNA (within the practical limits imposed by long-range PCR) can be mapped quickly and to high resolution without the use of cloning vectors.

DNA Restriction Enzymes↗

PubMed2002

Allele-specific PCR amplification due to sequence identity between a PCR primer and an amplicon: is direct sequencing so reliable?

PCR-direct sequencing (DS) is thought to be a very reliable method of determining DNA sequence and genotyping. Under certain conditions, however, DS can generate inaccurate results. Here we report a case of erroneous DS, in which a single nucleotide polymorphism (SNP) in the human PAX9 gene was mistyped due to allele-dependent PCR amplification. Examination of the amplified region showed that the 5' eight bases of one of the PCR primers were identical to the eight bases of the reverse strand downstream of the SNP, and the ninth base matched one of the alleles. Altering the primer so that it matched the other allele reversed the allele-specific inhibition. Reducing the base-pairing abolished the inhibition. Thus, the SNP was responsible for the difference in annealing efficacy of the primer and was therefore critical for the allele dependency. The allele-specific inhibition presented here can occur with any PCR primer sequence that encompasses a site that is polymorphic in the gene sequence. This phenomenon needs to be considered as a possibility when interpreting results from all PCR-based experiments. Sequence similarity between PCR primers and internal amplified regions should be considered for all methods for mutation detection and genotyping using PCR.

Alleles↗

PubMed1995

Low-stringency single specific primer PCR, DNA sequencing and single-strand conformation polymorphism of PCR products for identification of genetic variants of human papillomavirus type 16.

Two fragments from within the long control region of the genome of human papillomavirus type 16 (HPV16) were amplified using the polymerase chain reaction (PCR). Putative genetic variation among the parent viruses was assessed by complete sequence analysis and single-strand conformation polymorphism (SSCP) analysis of one of the fragments and by application of the recently described low-stringency single specific primer (LSSP) PCR to both PCR products. The study comprised 34 HPV16 positive samples, derived from seventeen different individuals. It is demonstrated that under experimentally standardised conditions the LSSP PCR-, sequencing- and SSCP-data display differing degrees of resolution. Based on combined LSSP PCR analyses, 33 out of 34 samples can be discriminated, whereas SSCP and direct sequencing identify 4 and 8 types, respectively. Although the variability observed among LSSP PCR patterns may be the consequence of small quantities of mutated viral amplimers, no concordant grouping of strains, identical by sequencing and SSCP analysis, can be established by either of the four theoretically possible LSSP PCR assays. Results are discussed in the context of experimental variability of the procedures or genetic heterogeneity of HPV16 pools derived from cervical swabs.

Base Sequence↗

PubMed1994

The impact of the PCR plateau phase on quantitative PCR.

The quantitative use of the polymerase chain reaction (PCR) is often compromised by the variability of the amplification. The most useful system for quantitation by PCR involves the use of controls which are almost identical to the target and which can be amplified using the same primers as the sequences of interest. In this paper, we use a model system consisting of differently sized targets amplifiable with varying primers to demonstrate the effects of the plateau phase of PCR on quantitation by PCR. This model confirms two commonly observed results: (i) when varying amounts of a single target are amplified, a constant maximum level of product is obtained and (ii) coamplification of different concentrations of different targets results in retention of the initial proportions. The inherent contradiction in these results is examined by replacement of the key elements of the reaction including enzyme, dNTPs or primers, none of which have an effect on the plateau. Pyrophosphate is found to exert no inhibitory effect on the reaction, nor does the exonuclease action of the enzyme cause the plateau. Levels of amplification attained during amplification are both theoretically and empirically defined as being insufficient to lead to the plateau due to competition between self-annealing of product DNAs and primer binding. We conclude that, pending further biochemical enquiry into the enzyme(s) used in the PCR, none of reasons conventionally proposed for the plateau phase of the PCR are sufficient to explain the phenomenon. This being so, we define the plateau as being a feature of the reaction as a whole and, since the onset of this phase is simultaneous for all amplicons, quantitation using the internal control system need not require exponential amplification. This therefore greatly simplifies the quantitative application of PCR.

Animals↗

PubMed1994

Rapid and sensitive detection of the femA gene in staphylococci by enzymatic detection of polymerase chain reaction (ED-PCR): comparison with standard PCR analysis.

Despite its recent cloning and characterization, the physiological role of FemA remains unclear. To easily and reliably identify femA in staphylococci, we analysed 45 blood isolates of staphylococci using enzymatic detection of polymerase chain reaction (ED-PCR). ED-PCR is a new method that detects amplified PCR products using biotin-streptavidin affinity and an enzyme-linked antibody. Of 45 samples, 34 strains contained the femA gene as detected by ED-PCR. Phenotyping analysis showed that these 34 strains (femA-positive) were Staphylococcus aureus and that the other 11 (femA-negative) were S. epidermidis. These results were completely consistent with the results of femA detection using standard PCR and subsequent Southern blot hybridization. The ED-PCR procedure was complete within 4 h and could be done in one tube. We conclude that ED-PCR is a rapid, simple and reliable method for detecting the femA gene and that it provides an important means of classifying staphylococcal strains in the clinical field.

Base Sequence↗

PubMed1995

Evaluation and comparison of the Amplicor HIV-1 PCR kit with an 'in-house' nested PCR.

BACKGROUND: The polymerase chain reaction (PCR), a powerful gene amplification technique, is moving rapidly from the research laboratory into routine clinical use. OBJECTIVES: To evaluate the specificity and sensitivity of a commercially available PCR kit, the Amplicor HIV-1 PCR kit (AMP) and to compare it with an in-house nested PCR, which amplified part of the POL gene (POL(n)). STUDY DESIGN: A total of 517 samples were tested by AMP, including 159 fresh whole blood specimens from HIV-1 antibody positive Europeans and 358 archival samples (338 seropositive and 20 seronegative individuals) originating from 35 different countries in Africa and Europe. We compared the performance of AMP on the archival samples with POL(n). RESULTS: The overall sensitivity and specificity as compared to HIV-1 serology were 93% and 100%, and 96% and 100%, for AMP and the in-house PCR, respectively. Repeat testing on co-cultured lymphocytes increased the sensitivity of AMP to 95%. CONCLUSIONS: AMP is a rapid, and easy to use commercially available PCR kit, since only one amplification of the test sample is required. Moreover, the use of radioactivity is omitted, and reading of the test can be done with a spectrophotometer. The use of at least one additional primer pair may increase confidence in distinguishing a positive and negative sample by both PCR techniques.

Journal Article↗

PubMed1995

Assessment of amplicons in the DNA from boiled tissue by PCR and AP-PCR amplification.

Polymerase chain reaction (PCR) is a technique sensitive enough to amplify small DNA fragments a billion-fold. The generation of amplicons either by PCR with a set of oligo primers or by arbitrarily primed AP-PCR with a single oligonucleotide primer is based on the availability of intact template and priming sites. With these approaches, it is possible to generate specific and random amplicons to assess the extent of damage to DNA caused by any of the physical, chemical, or environmental factors. We report the amplification of sex chromosome and autosome specific loci in the buffalo (Bubalus bubalis) genome by symmetrical and AP-PCR performed on DNA samples isolated from the muscle tissues that were boiled (treated) for different lengths of time. No difference was noticed in the amplification profile of DNA cooked for various lengths of time. However, after HinfI treatment, AP-PCR amplification of these DNAs revealed more bands on agarose gel than unrestricted samples. The successful amplification of the DNA samples isolated from the boiled tissues is attributed to the intactness of the amplicons. This suggests that despite storage for more than a year and subsequent heat treatment to the muscle tissues, the DNA remains a good substrate for PCR and AP-PCR amplification. Relevance of this work in the context of DNA probe technology is discussed.

Animals↗

PubMed2004

Detection and differentiation of herpes simplex virus types 1 and 2 by a duplex LightCycler PCR that incorporates an internal control PCR reaction.

BACKGROUND: In recent years polymerase chain reaction (PCR) has proven to be a highly sensitive and specific method for the diagnosis of herpes simplex virus (HSV) infections. The advent of real-time HSV PCR protocols now enables rapid result turnaround times with minimal hands-on time. OBJECTIVES: In this study, we developed a real-time duplex PCR assay (HSVgD-dPCR) comprising of HSV and internal control PCR reactions. STUDY DESIGN: Using the LightCycler, the HSVgD-dPCR targeted the HSV glycoprotein D gene and HSV typing was performed by melting curve analysis. The internal control PCR reaction targeted sequences of the DNA of the human endogenous retrovirus (ERV-3). In total, 300 swab specimens, from patients with suspected HSV infection, were tested by the HSVgD-dPCR assay. The results were then compared to the results obtained by another HSV LightCycler assay, which utilized published primer and probe sequences targeting the HSV DNA polymerase gene (Dpol-HSV-LCPCR). RESULTS: Overall, 91 (30.3%) specimens were positive and 204 (68.0%) specimens were negative for HSV by both LightCycler assays. In addition, four (1.3%) specimens were positive by Dpol-HSV-LCPCR and negative by HSVgD-dPCR, whereas one (0.3%) specimen was positive by HSVgD-dPCR and negative by Dpol-HSV-LCPCR. The presence of HSV in these five specimens was confirmed by conventional PCR. Melting curve analysis by the HSVgD-dPCR assay enabled all HSV positive specimens to be typed, whereas sequence variation prevented three HSV positive specimens from being typed by the Dpol-HSV-LCPCR. Using the ERV-3 PCR, 5% specimens were found to contain inhibitory substances. CONCLUSIONS: By developing the HSVgD-dPCR we have enhanced the diagnostic utility of real-time detection of HSV by incorporating an internal control reaction and by accurately typing a greater proportion of HSV positive specimens.

Adolescent↗

PubMed2005

Application of a spotting sample preparation technique for the detection of pathogens in woody plants by RT-PCR and real-time PCR (TaqMan).

An extraction technique for reverse transcription-PCR (RT-PCR) detection of plant pathogens including viruses, bacteria and phytoplasma is described. The total nucleic acid of these plant pathogens was obtained by direct spotting of crude sap derived from infected leaf, petiole or cambial tissue onto two different types of membranes, positively charged Hybond N(+) Nylon and FTA membranes, and processed for use in PCR. Thirteen different plant viruses, Xylella fastidiosa (causal agent of Pierce's disease) and phytoplasmas were included in the experiment. A thermal treatment (95 degrees C for 10 min) of the Hybond N(+) Nylon discs in a buffered solution improved the detection, but for FTA membrane discs the thermal treatment was not required and the discs were directly placed in the PCR reaction cocktail. Specific amplification of genomic or ribosomal RNA fragments of these pathogens was obtained by one-step RT-PCR except for X. fastidiosa in which a fragment of the genomic DNA was used for amplification. The same sample preparation methods also worked well for real-time RT-PCR (TaqMan). The sample preparation techniques reported here could be used to store samples for future PCR test or for long distance shipment to a detection laboratory.

Edetic Acid↗

PubMed2006

Comparative evaluation of RT-PCR, nucleic acid sequence-based amplification (NASBA) and real-time RT-PCR for detection of noroviruses in faecal material.

Using different primer and probe sets, RT-PCR, NASBA and TaqMan RT-PCR molecular methods were compared to detect NoV GII in 13 clinical stool samples. The RT-PCR results observed by gel electrophoresis (Ando, Kageyama and Anderson amplification and probe systems), dot blot hybridization (Ando and Kageyama) and real-time TaqMan assay (Ando and Kageyama) were shown to be consistent and reproducible for the detection of NoV GII. Whereas, the NASBA assay using Ando primers showed some reproducibility discrepancies. Detection limits of the NoV GII/Kageyama system were found to be equal or significantly higher than the Ando system. Real-time TaqMan RT-PCR assay showed similar detection limits to that of NASBA with the Kageyama amplification and detection system, while it was 1log less sensitive than the Ando system. In a clinical context, RT-PCR, NASBA and real-time TaqMan RT-PCR methods using undiluted samples were all suitable for the detection of NoV GII, however the NASBA assay provided less consistent signals. The NoV GII Kageyama real-time TaqMan RT-PCR assay was reliable with a high analytical sensitivity and has shown the capability of detecting one genomic equivalent copy.

Base Sequence↗

PubMed2000

RT-PCR from eosinophil-depleted leukocytes without RNA extraction: cell selection using streptavidin PCR tubes.

OBJECTIVES: The major RNase activity of leukocytes has been attributed to eosinophil-derived neurotoxin EDN. Depletion of eosinophils enables RT-PCR from 10(5) leukocytes without RNA extraction. In this study we introduced streptavidin-coated PCR tube strips for the selection of eosinophil-free leukocytes for RT-PCR analysis. DESIGN AND METHODS: Polypropylene 0.2 ml PCR tube strips were coated with streptavidin and biotinylated antibodies against cell surface antigens were attached to the tubes. CD7-positive T-lymphocytes, CD19-positive B-lymphocytes and CD16-positive cells (mainly neutrophils and monocytes) were positively selected by incubating of 1-2 x 10(5) leukocytes in the antibody-coated PCR tubes for 30 min at 23 degrees C. RESULTS: The mean amount of cells bound into a tube was 31,500 (CV25%) T-cells and 8,600 (CV61%) B-cells from 12 blood samples, and 23,600 (CV22%) CD16+ cells from 17 samples. The influence of selected cell lysate on the RT-PCR analysis of Philadelphia chromosome (bcr/abl translocation) from 100 K562 cells was small: 78% (CV28%) of the leukocyte-free signal was obtained in the presence of CD16+ cells or 89% (CV15%) and 99% (CV11%) and in the presence of T-cells and B-cells, respectively. CONCLUSIONS: These results suggest that through the introduction of eosinophil-free cell population into RT-PCR a reproducible method with reasonable leukocyte yield and avoiding RNA extraction was developed.

Adolescent↗

PubMed2002

Comparison and verification of quantitative competitive reverse transcription polymerase chain reaction (QC-RT-PCR) and real time RT-PCR for avian leukosis virus subgroup J.

Avian leukosis virus subgroup J (ALV-J) infections cause significant economic losses because of increased mortality, tumor production, decreased production, and cost for eradication. Current quantification methods for ALV-J expressed by TCID(50) are difficult to determine because of the lack of cytopathic effect in cell cultures and non-specificity of currently available antigen-capture ELISA tests. In this study, a one-tube fluorescent probe based real time RT-PCR method was developed for quantification of ALV-J and compared with available quantification methods. Cell lysates with different TCID(50)s determined by cell culture and antigen capture ELISA (ag-ELISA) were used for one-tube real time RT-PCR using fluorogenic probe and quantitative competitive RT-PCR (QC-RT-PCR). The results of QC-RT-PCR and real time RT-PCR were highly correlated to the TCID(50)s determined by conventional culture methods. They were also very specific, sensitive, easy to perform, reproducible, and rapid compared with conventional methods. These RT-PCR based quantification methods of ALV-J viral RNA will be useful for virological and pathogenesis studies.

Animals↗

PubMed2002

Differential amplifying RT-PCR: a novel RT-PCR method to differentiate mRNA from its DNA lacking intron.

A major problem with reverse transcription-polymerase chain reaction (RT-PCR) is that the products amplified from RNA and DNA are not distinguishable. The use of a primer set targeted for an intron-containing sequence or RNA extract without contaminating DNA has been established to overcome this problem. However, an intron sequence does not always exist in the target region and complete removal of DNA during RNA extraction is not practical. For these reasons, we developed differential amplifying RT-PCR (DART-PCR) based on differences in reaction temperatures between RT and PCR, as well as in architectures between RNA and DNA. DART-PCR was designed to differentiate products amplified from RNA and DNA regardless of the presence of introns. DART-PCR can be readily applied for diagnosis of active infection of human cytomegalovirus by detection of glycoprotein B mRNA, which gene lacks introns. Other advantages of DART-PCR were as follows: there is no need for separation of RNA from DNA, simultaneous/differential detection in a single tube and possibility of determination of relative amounts of RNA and DNA.

Cell Line↗

PubMed2002

Detection and differentiation of serologically cross-reacting tobamoviruses of economical importance by RT-PCR and RT-PCR-RFLP.

A procedure involving reverse transcription followed by the polymerase chain reaction (RT-PCR) using a single primer pair was developed for the detection of five tobamovirus species which are related serologically. Either with a subsequent restriction enzyme analysis (RT-PCR-RFLP) or with a RT-PCR using species specific primers the five species can be differentiated. To differentiate those species by serological means is time consuming and might give ambiguous results. With the example of the isolate OHIO V, which is known to break the resistance in a selection of Lycopersicon peruvianum, the suitability of the RT-PCR-RFLP technique to detect variability at the species level was shown. In sequence analysis 47 codons of the coat protein gene of this isolate were found to be mutated compared to a tobacco mosaic virus (TMV) coat protein gene sequence. Forty of these mutations were silent and did not change the amino acid sequence. Both procedures are suitable to detect mixed infections. In addition, the RT-PCR-RFLP give information on the relative amounts of the viruses that are present in a doubly infected plant. The RT-PCR-RFLP using general primers as well as the RT-PCR using species specific primers were proven to be useful for the diagnosis and control of the disease and will be helpful for resistance breeding, epidemiological investigations and plant virus collections.

Amino Acid Sequence↗

PubMed2001

Application of polymerase chain reaction (PCR) and TaqMan PCR techniques to the detection and identification of Rhodococcus coprophilus in faecal samples.

Rhodococcus coprophilus, a natural inhabitant of herbivore faeces, has been suggested as a good indicator of animal (as opposed to human) faecal contamination of aquatic environments. However, conventional detection methods limit its use for this as they require up to 21 days to obtain a result. In this paper an optimised method for extracting R. coprophilus DNA from faecal samples is described. PCR and 5'-nuclease (TaqMan) PCR methods were developed to allow the detection and enumeration of R. coprophilus in faecal samples within 2-3 days. Both PCR methods targeted the 16S rRNA gene, producing an amplicon of 443 bp which was specific for R. coprophilus. Sixty cells were required to produce an amplification product by conventional PCR, while as little as one cell was required for the TaqMan PCR method. The latter approach gave a linear quantitative response over at least four log units with both bacterial cells and DNA. Successful amplification by PCR was achieved using DNA extracted from cow, sheep, horse and deer faeces but was negative for samples from humans, pig, possum, duck and rabbit. These PCR methods enhance the feasibility of using R. coprophilus to distinguish faecal pollution of farmed herbivores from human pollution.

Animals↗

PubMed1999

Antiserum generated by DNA vaccine binds to hepatitis E virus (HEV) as determined by PCR and immune electron microscopy (IEM): application for HEV detection by affinity-capture RT-PCR.

Previously, we have described that injection of an expression vector containing hepatitis E virus (HEV) open reading frame 2 (HEV-ORF-2) generated a strong antibody response in mice. To characterize the reaction of this antiserum with native HEV and to evaluate its potential diagnostic application, we tested the antiserum's ability to bind HEV using immune electron microscope (IEM) and affinity-capture reverse transcription polymerase chain reaction (RT-PCR) amplification. Antiserum to ORF-2 aggregated HEV virions as seen by electron microscopy, providing direct evidence that ORF-2 encodes a structural protein. Antiserum also captured HEV for RT-PCR amplification. This antiserum bound HEV from diverse origins (Asia, Africa, Mexico) at virus concentrations found in patient fecal specimens and bile from inoculated non-human primates. The specificity of the affinity binding was demonstrated when pre-immune sera or sera collected from mice injected with control DNA vector (lacking the HEV ORF-2 gene) failed to bind HEV for RT-PCR amplification and IEM. Specific RT-PCR amplification was confirmed by restriction enzyme digestion of PCR products. The sensitivity of the binding was evaluated by RT-PCR amplification of serially diluted bile containing a genetically divergent HEV, Mexico'86. HEV was detected in a 10(-8) dilution of this bile. This is the first report that antibodies elicited by a DNA vaccine recognize native HEV. Our results indicate that ORF-2 encodes a structural protein and that antiserum to this protein enables simple, sensitive, and specific HEV detection by affinity-capture RT-PCR.

Animals↗

PubMed2001

DNA profiling of disputed chilli samples (Capsicum annum) using ISSR-PCR and FISSR-PCR marker assays.

A case of marketing of spurious seeds of chilli, Capsicum annum in the brand name of an elite variety referred to us from an Indian court of law, for identification is described here. The highly reproducible molecular marker assays, inter simple sequence repeat polymerase chain reaction [ISSR-PCR] and FISSR-PCR (for fluorescent ISSR-PCR) were used for differentiating the four disputed chilli samples. A total number of 17 ISSR anchored primers, which included nine di-, and eight tri-nucleotide primers were used for the analysis. The ISSR-PCR products were separated on a 2% agarose gel. A total of 212 and 288 bands were resolved by seven di- and eight tri-nucleotide primers, respectively, with an average of 30 bands per primer. Five out of nine dinucleotide primers and four out of eight trinucleotide primers could unambiguously differentiate all the four disputed chilli samples. The sensitivity and informativeness of the ISSR-PCR assay were further enhanced by the use of FISSR-PCR technique. The FISSR-PCR assay revealed a total number of 566 bands using three tri- and one di-nucleotide primers with an average of 141 bands per primer. These four primers could reliably distinguish all the four disputed samples unambiguously. In developing countries like India, violation of Plant Breeder's Rights is a major concern of law. The present report is, therefore, a step to protect the Plant Breeder's Rights by making use of reliable and modern DNA technologies.

Breeding↗

PubMed1999

Single PCR and nested PCR with a mimic molecule for detection of Mycobacterium avium subsp. paratuberculosis.

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. The current methods for detection of M. avium subsp. paratuberculosis are slow and insensitive. We report the use of a polymerase chain reaction (PCR) based on IS900 to confirm growth of M. avium subsp. paratuberculosis in primary bacterial cultures from bovine tissue and fecal samples. The use of PCR on single colonies reduced the time for analysis by 2 months compared with conventional methods. We also report the development of a nested PCR based on IS900 and the development of a positive internal control molecule, a so-called mimic. The system was tested with spiked tissue samples, and the sensitivity was estimated to 10 CFU per sample. Seventeen tissue samples, previously found M. avium subsp. paratuberculosis positive by microbiological culture, were analyzed by nested PCR and the efficiency of the PCR was checked by co-amplification of the mimic. Absence of the mimic amplicon indicated inhibition of the amplification. Ten of the samples were positive and five were negative, as judged from the presence or absence of the IS900 PCR product. Two negative samples could not be judged because of inhibition revealed by mimic molecules. It was concluded that the nested PCR, together with the mimic, could be a useful tool in screening tissue materials.

Animals↗