Rapid plasmid insert amplification with polymerase chain reaction

Unusual phosphorylation sequence in the gpIV (gI) component of the varicella-zoster virus gpI-gpIV glycoprotein complex (VZV gE-gI complex)

Varicella-zoster virus (VZV) glycoprotein gpIV, to be renamed VZV gI, forms a heterodimer with glycoprotein gpI (gE) which functions as an Fc receptor in virus-infected cells. Like VZV gpI (gE), this viral glycoprotein is phosphorylated in cell culture during biosynthesis. In this report, we investigated the nature and specificity of the phosphorylation event involving VZV gpIV (gI). Phosphoamino acid analysis indicated that gpIV (gI) was modified mainly on serine residues. To identify the precise location of the phosphorylation site on the 64-kDa protein, a step-by-step mutagenesis procedures was followed. Initially a tailless mutant was generated, and this truncated product was no longer phosphorylated. Thereafter, point mutations were made within the cytoplasmic tail of gpIV (gI) at potential phosphorylation sites. The phosphorylation site was localized to the following sequence: Ser-Pro-Pro (amino acids 343 to 345). Examination of the point mutants established that serine 343 in the cytoplasmic tail was the major phosphoacceptor. In addition, we found that the prolines located immediately to the C terminus of serine 343 were an integral part of the kinase recognition sequence. This site was located immediately N terminal to a predicted beta-turn secondary structure. By comparison with known substrate consensus sequences for various protein kinases, these data suggested that the phosphorylation of VZV gpIV (gI) was catalyzed by a proline-directed protein kinase. Computer homology analysis of other alphaherpesviruses demonstrated that a similar potential phosphorylation site was highly conserved in the cytoplasmic tails of herpes simplex virus type 1 gI, equine herpesvirus type 1 gI, and pseudorabies virus gp63.

The polymerase chain reaction: a new tool for the understanding and diagnosis of HIV-1 infection at the molecular level

The polymerase chain reaction (PCR) is at present the most powerful analytical tool for detection of specific nucleic acid sequences. The method is based on the in vitro amplification of DNA segments before detection with conventional hybridization techniques or visualization following electrophoresis and staining. The current diagnostic methods for HIV-1 do not allow easy identification of subgroups of infected patients including infants born to seropositive mothers, individuals with delayed serological responses to the virus, infected patients with indeterminate serology results, and patients with dual retroviral infections. Furthermore, response to antiviral therapy cannot be evaluated with serological assays. The rationale for applying PCR in those situations is elaborated here. The applications of this technique for HIV-1 as a diagnostic test and for the understanding of the pathogenesis of this retrovirus are described. Potential limitations of this technique for diagnostic purposes include mainly the possibility of false-positive results due to contamination and false-negative reactions caused by Taq polymerase inhibition. Non-isotopic means for detection of amplified products have been described and should allow for a wider application of this technology. Modifications of PCR which make use of internal standards seem promising for quantitative analysis of nucleic acids. PCR has great potential for viral diagnosis but still requires further studies and better characterization.

The use of polymerase chain reaction in generation of biotinylated human papillomavirus DNA probes for in situ hybridization

The polymerase chain reaction (PCR) was used to produce biotin-labelled human papillomavirus (HPV) 16- and 18-specific DNA probes for in situ hybridization (ISH). PCR was performed by using Amplitaq DNA amplification reagent kit according to the manufacturer's instructions, except that dTTP was substituted by different concentrations of biotinylated dUTP (bio-11-UTP). As template DNA, DNA extracted either from CaSki or HeLa cells was used. The reaction mixture was taken through up to 40 cycles of amplification in a Perkin-Elmer Cetus Thermal Cycler. The highest yield was achieved when the concentrations of dTTP and biotinylated dUTP were 150 and 50 microM, respectively. ISH results compatible with those obtained with biotinylated whole genomic HPV DNA probes were demonstrated when primers from E7 and E6 ORF of the HPV-18 genome were used to produce the biotinylated probe by PCR. With HPV-16, several areas of the genome had to be amplified to generate a PCR probe with equal sensitivity as the whole genomic probe. The background staining was always stronger with the PCR probes than with the whole genomic probes. The sensitivity of the PCR probes does not seem to bear a clear-cut correlation with the size or nucleotide content of the probe, but it might rather depend on the three dimensional structure of the probe and the availability of biotin for the detection system by ISH.

Using the polymerase chain reaction to maintain DNA probe inventories in clinical and diagnostic laboratories

Clinical and diagnostic DNA laboratories must maintain a large inventory of DNA probes for use in hybridization studies. The preparation of plasmid DNA and isolation of DNA fragments for use as probes in both expensive and time consuming. We present here a rapid and relatively inexpensive method of producing large amounts of DNA fragments from stocks, using the polymerase chain reaction (PCR). Our experience over the past year using this technique has been very positive and we believe many laboratories could benefit by employing such a labor-saving approach to maintaining DNA probes. The technique uses the bacteriophage M13 DNA sequencing primers to amplify cloned inserts contained in commonly used plasmid vectors. As examples, we illustrate the use of DNA produced in this manner as probes for linkage analysis of the fragile X syndrome and for detection of deletions in the Duchenne muscular dystrophy gene. We have also found that at least two probes can be amplified in the same PCR reaction, allowing the detection of two different restriction fragment length polymorphisms (RFLP) simultaneously. It should be possible for laboratories to devise strategies particular to their individual needs using more than one DNA probe produced in the same PCR reaction to detect RFLP's. Such strategies would need only to consider that the predicted alleles of the multiple polymorphisms do not migrate to the same position during electrophoresis. Stocks of single or multiple probes produced by the PCR could then be maintained for more rapid Southern analyses.

The polymerase chain reaction: miracle or mirage? A critical review of its uses and limitations in diagnosis and research

Since publication of the polymerase chain reaction (PCR) technique in 1985 (Saiki et al. Science 1985; 230: 1350-1354), there has been an explosion of reports on its use in medicine and science. We critically review its use both as a diagnostic technique and as a research tool, and show the pathologist how to evaluate PCR data and how to avoid the pitfalls of overinterpretation. We discuss the value of PCR in the characterization of genetic defects, prenatal diagnosis, carrier testing, HLA typing, detecting micro-organisms, identifying activated oncogenes, and in the characterization of leukaemias and lymphomas, and summarize the main applications in biomedical research.

Detection of plasmid DNA from all Chlamydia trachomatis serovars with a two-step polymerase chain reaction

A polymerase chain reaction was used to amplify a 137-base-pair sequence of DNA from a Chlamydia trachomatis plasmid. Various parameters of the polymerase chain reaction were explored, and it was found that two short steps per reaction cycle were sufficient to achieve 10(12)-fold amplification in less than 1 h. By use of this procedure, 10(-18) g of a sequence of plasmid DNA, representing the amount of that sequence found in one C. trachomatis bacterium, was amplified to the point where it was clearly visible on an ethidium bromide-stained polyacrylamide gel under UV light. DNA from intact cells from each of the 15 serovars of C. trachomatis could also be amplified for visualization. With this procedure, the presence or absence of C. trachomatis DNA in a sample could be established in less than 1.5 h. The speed and extreme sensitivity of this detection procedure may make it a useful method for the detection of C. trachomatis, and similar techniques should be possible for any type of bacteria.

Clinical applications of the polymerase chain reaction

The polymerase chain reaction (PCR) is a technique that allows a million-fold, or greater, amplification of defined regions of DNA or RNA. It is potentially capable of detecting a single copy of a gene, present only once in 105 eukaryotic cells. This remarkable level of sensitivity has allowed the development of many diagnostic assays for human pathogens and disease states. These include: the detection of viral, bacterial and protozoal agents; diagnosis and genetic analysis of inherited diseases such as β-thalassaemia, sickle cell disease, haemophilia, Tay-Sachs disease and many others; diagnosis and analysis of neoplastic disorders such as, chronic myelogenous leukaemia (CML), acute lymphocytic lymphoma (ALL), follicular lymphomas and various other cancers, including the detection of activated oncogenes; prenatal and pre-implantation diagnosis; and the development of genetic risk prediction.

The PCR can greatly simplify diagnostic processes that were previously difficult to perform, particularly where the initial amounts of biological material were very limited. In other cases, PCR provides the only method available for detection and diagnosis. However, although simple in theory, the PCR technique remains, for routine clinical diagnostic purposes, currently in the domain of the specialist laboratory. This is because of its sensitivity to nucleic acid contamination from other sources that can cause misleading results. Procedures and precautions are being developed to minimize this problem and there is little doubt that, in many instances, the PCR will be the diagnostic method of choice within the next few years.

Porcine tumor necrosis factor alpha: cloning with the polymerase chain reaction and determination of the nucleotide sequence

We have cloned the gene for the porcine tumor necrosis factor alpha (TNF-alpha) utilizing the polymerase chain reaction (PCR). Total RNA from stimulated monocytes was used to generate TNF-alpha-specific single-stranded cDNA, with reverse transcriptase and a conserved consensus primer, starting at the TNF-alpha translation stop codon. After adding a second conserved consensus primer to the propeptide region, we amplified the cDNA between the two primers. The isolated fragment was cloned and sequenced. Comparison of the nucleotide sequence indicated an 85% sequence similarity to the human TNF-alpha gene. Eighteen amino acids of the deduced mature peptide sequence of porcine TNF-alpha were different from those in the sequence of man. The technique used in this work allows rapid cloning of specific genes from total RNA, and, additionally, screens for full-length transcripts during the amplification procedure.

The polymerase chain reaction: an improved method for the analysis of nucleic acids

The polymerase chain reaction (PCR) is a method for the selective amplification of DNA or RNA segments of up to 2 kilobase-pairs (kb) or more in length. Synthetic oligonucleotides flanking sequences of interest are used in repeated cycles of enzymatic primer extension in opposite and overlapping directions. The essential steps in each cycle are thermal denaturation of double-stranded target molecules, primer annealing to both strands and enzymatic synthesis of DNA. The use of the heat-stable DNA polymerase from the archebacterium Thermus aquaticus (Taq polymerase) makes the reaction amenable to automation. Since both strands of a given DNA segment are used as templates, the number of target sequences increases exponentially. The reaction is simple, fast and extremely sensitive. The DNA or RNA content of a single cell is sufficient to detect a specific sequence. This method greatly facilitates the diagnosis of mutations or sequence polymorphisms of various types in human genetics, and the detection of pathogenic components and conditions in the context of clinical research and diagnostics; it is also useful in simplifying complex analytical or synthetic protocols in basic molecular biology. This article describes the principles of the reaction and discusses the applications in different areas of biomedical research.

New prospects for the diagnosis of viral infections

The diagnosis of viral infections is important for the accurate management of patients with infectious diseases and for the monitoring of the course of epidemics in susceptible populations. The utility of traditional viral diagnostic assays is limited by the time, expense, and expertise required for the performance of tissue culture techniques. Similarly, the application of immunoassay techniques has been inhibited by the limited degrees of sensitivity and specificity which can be attained by most immunoassay methods. Recently, techniques for the identification of DNA and RNA have been applied to the detection of viral nucleic acids in clinical samples. Such assays have a number of potential advantages over corresponding immunoassays directed at the detection of viral antigens. In order to be generally applicable to clinical diagnosis, however, formats for the detection of viral nucleic acids have to be devised which allow for the reproducible quantitation of target DNA or RNA in human body fluids. Furthermore, formats need to be devised which allow enhanced assay sensitivity while maintaining high degrees of specificity and reproducibility. The use of non-isotopic labeling, liquid-phase hybridization, and target amplification techniques offers partial solutions to these problems. The development of practical assays for the detection of viral nucleic acids under a broad range of clinical and laboratory conditions would represent a major advance in the ability of physicians to care for patients with suspected infections.