Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions

DNA polymerases amplify DNA fragments through primer extension reactions. However, polymerization behavior of short primers in the primer extension process has not been systematically explored. In this study, we examined the minimal primer length required for primer extension, and the effect of primer length, mismatches and other conditions on DNA polymerization using a non-radioactive method. Under the condition we conducted, the shortest primers polymerized by Klenow fragment (KF) and Taq DNA polymerase in our experiments were respectively heptamer and octamer. The extension efficiency was also affected by the up-stream overhanging structure of the primer-template complex. We hypothesized a simple model to interpret these observations based on the polymerase structures. Furthermore, it was found that the longer the primer, the more efficient is the primer extension. These polymerization behavior of short primers lay foundation about DNA polymerization mechanism and development of novel nucleic acid detection assays.

Taqman real-time PCR detects Avipoxvirus DNA in blood of Hawai'i 'amakihi (Hemignathus virens)

Background

Avipoxvirus sp. is a significant threat to endemic bird populations on several groups of islands worldwide, including Hawaìi, the Galapagos Islands, and the Canary Islands. Accurate identification and genotyping of Avipoxvirus is critical to the study of this disease and how it interacts with other pathogens, but currently available methods rely on invasive sampling of pox-like lesions and may be especially harmful in smaller birds.

Methodology/Principal Findings

Here, we present a nested TaqMan Real-Time PCR for the detection of the Avipoxvirus 4b core protein gene in archived blood samples from Hawaiian birds. The method was successful in amplifying Avipoxvirus DNA from packed blood cells of one of seven Hawaiian honeycreepers with confirmed Avipoxvirus infections and 13 of 28 Hawaìi `amakihi (Hemignathus virens) with suspected Avipoxvirus infections based on the presence of pox-like lesions. Mixed genotype infections have not previously been documented in Hawaìi but were observed in two individuals in this study.

Conclusions/Significance

We anticipate that this method will be applicable to other closely related strains of Avipoxvirus and will become an important and useful tool in global studies of the epidemiology of Avipoxvirus.

[Development of the real-time reverse transcription-polymerase chain reaction assay for the rapid detection of rubella virus]

OBJECTIVE

A new TaqMan probe based real-time assay was developed to rapid detection of rubella virus.

METHODS

The specific primer pair and probe were designed within the conserved P150 gene of rubella virus and the PCR reactive condition was optimized to improve the sensitivity and specificity of the assay. Clinical specimens collected from two outbreaks were detected by the developed assay.

RESULTS

The assay is specific to detect rubella virus. There is no cross-reactions to measles, mumps, influenza and other respiratory viruses. It could detect 0.01 TCID50/tube of rubella RNA and took only three hours to finish a detection. In addition, the assay is simple, accurate and repeatable.

CONCLUSION

The TaqMan based real-time PCR developed in this study provides a fast, sensitive and specific tool for molecular diagnosis on rubella virus.

Interaction of aurintricarboxylic acid (ATA) with four nucleic acid binding proteins DNase I, RNase A, reverse transcriptase and Taq polymerase

In the investigation of interaction of aurintricarboxylic acid (ATA) with four biologically important proteins we observed inhibition of enzymatic activity of DNase I, RNase A, M-MLV reverse transcriptase and Taq polymerase by ATA in vitro assay. As the telomerase reverse transcriptase (TERT) is the main catalytic subunit of telomerase holoenzyme, we also monitored effect of ATA on telomerase activity in vivo and observed dose-dependent inhibition of telomerase activity in Chinese hamster V79 cells treated with ATA. Direct association of ATA with DNase I (K(d)=9.019 microM)), RNase A (K(d)=2.33 microM) reverse transcriptase (K(d)=0.255 microM) and Taq polymerase (K(d)=81.97 microM) was further shown by tryptophan fluorescence quenching studies. Such association altered the three-dimensional conformation of DNase I, RNase A and Taq polymerase as detected by circular dichroism. We propose ATA inhibits enzymatic activity of the four proteins through interfering with DNA or RNA binding to the respective proteins either competitively or allosterically, i.e. by perturbing three-dimensional structure of enzymes.

Substitution of Ile(707) for Leu in Klentaq DNA polymerase reduces the amplification capacity of the enzyme

The high yield and specificity of PCR amplifications are affected by DNA polymerase activity at room temperature. One way of preventing this unwanted activity is by genetic modifications of the DNA polymerase. For Taq DNA polymerase, mutations in the gene (Glu626Lys, Trp706Arg, Ile707Leu and Glu708Asp), when introduced individually or in certain combinations, were found to contribute to a significant decrease of the enzyme activity at room temperature. The aim of this study was to evaluate the usefulness of the Ile707Leu cold-sensitive mutation in the N-terminal deletional variant of Taq DNA polymerase in PCR reaction. The Ile(707) to Leu substitution was introduced to Klentaq278 by site-directed mutagenesis. Normal and mutant DNA polymerases were expressed under a tac promoter and purified to homogeneity. The mutant polymerase showed reduced polymerase activity at room temperature by up to 12 times and no significant change in thermostability, compared to Klentaq278 DNA polymerase. The major effect of the amino acid substitution was the reduction of the amplification capacity of the polymerase. Mutant polymerase could not amplify fragments over 1 kb. In conclusion, the substitution of Ile707Leu in Klentaq278 DNA polymerase reduces the overall processivity of the enzyme and therefore limits the application of this DNA polymerase in PCR.

Experimental and simulation studies of a real-time polymerase chain reaction in the presence of a fullerene derivative

The real-time polymerase chain reaction of the plant gene heat shock transcription factor was fully inhibited in the presence of a fullerene derivative C(60)(OH)(20) at a concentration of 4 x 10(-4) mM. This inhibition was attributed to the interaction between the nanoparticle and Taq DNA polymerase in the reaction. Atomistic molecular dynamics simulations showed a clear tendency for hydrogen bonding between C(60)(OH)(20) and both the dNTPs and ssDNA components of the polymerase chain reaction. These studies facilitate our understanding of the fate of nanoparticles in biomolecular systems, a topic of tremendous importance for addressing the biological and environmental implications of nanomaterials.

Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria

Background

PCR in principle can detect a single target molecule in a reaction mixture. Contaminating bacterial DNA in reagents creates a practical limit on the use of PCR to detect dilute bacterial DNA in environmental or public health samples. The most pernicious source of contamination is microbial DNA in DNA polymerase preparations. Importantly, all commercial Taq polymerase preparations inevitably contain contaminating microbial DNA. Removal of DNA from an enzyme preparation is problematical.

Methodology/Principal Findings

This report demonstrates that the background of contaminating DNA detected by quantitative PCR with broad host range primers can be decreased greater than 10-fold through the simple expedient of Taq enzyme dilution, without altering detection of target microbes in samples. The general method is: For any thermostable polymerase used for high-sensitivity detection, do a dilution series of the polymerase crossed with a dilution series of DNA or bacteria that work well with the test primers. For further work use the concentration of polymerase that gave the least signal in its negative control (H₂O) while also not changing the threshold cycle for dilutions of spiked DNA or bacteria compared to higher concentrations of Taq polymerase.

Conclusions/Significance

It is clear from the studies shown in this report that a straightforward procedure of optimizing the Taq polymerase concentration achieved “treatment-free” attenuation of interference by contaminating bacterial DNA in Taq polymerase preparations. This procedure should facilitate detection and quantification with broad host range primers of a small number of bona fide bacteria (as few as one) in a sample.

[Rapid detection of Vibrio parahaemolyticus by TaqMan-based real-time PCR assay targeting the toxR gene]

We designed a pair of specific primers and a TaqMan fluorescent probe targeting the toxR gene of Vibrio parahaemolyticus (VP). After optimizing the conditions, the specialty, sensitivity and reproducibility of the detection method were evaluated.

RESULTS

(1) the developed real-time PCR assay protocol detected only VP and was not affected by other normal food pathogens such as Staphylococcus aureus, Salmonela, Listeria monocytogenes. (2) the limit of detection was 25 copies of toxR gene in the detected samples, and the sensitivity of pure cultures and simulated food samples was 21 cfu/mL and 210 cfu/g. (3) the developed protocol of real-time PCR assay had a high reproducibility, and the sample's variation was 0.9% and 1.3% within the same sample and between tests. (4) the standard curve had a good linearity when the gene quantity was between 2.5x10(1) and 2.5x10(6) copies. The developed detection assay targeting the toxR gene can quantitatively detect VP in only 3 hours, and thus is an efficacious method for the detection of Vibrio parahaemolyticus.

Molecular cloning and characterization of buffalo alpha(s1)-casein gene

Buffaloes in Indian subcontinent play an important role as the producer of milk and milk products. The alpha(s1)-casein constitutes 38% of the total milk proteins. The present study was carried out to characterize the gene in Murrah breed of Riverine buffalo. Buffalo alpha(s1)-casein cDNA was synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of alpha(s1)-casein cDNA was of 645 bp with GC content of 45.58%. The alpha(s1)-casein gene coded 214 amino acids precursor with a signal peptide of 15 amino acid residues. The similarity of buffalo alpha(s1)-casein mRNA sequence with that of cattle, goat, sheep, pig, camel, equine and human were estimated as 97.2, 93, 92.3, 57.2, 59.5, 55.9 and 46.6%, respectively. A similar trend was observed when compared amino acid sequences of these species. In the phylogenetic trees, constructed from the data of the alpha(s1)-casein mRNA as well as protein sequences, it has been observed that buffalo, cattle, goat and sheep formed a cluster with a closer relationship between cattle and buffalo followed by goat and sheep.

Suppression by glutamate of proliferative activity through glutathione depletion mediated by the cystine/glutamate antiporter in mesenchymal C3H10T1/2 stem cells

Although previous studies including ours have demonstrated the functional expression of different glutamate (Glu) signaling machineries such as Glu receptors (GluRs) and transporters in osteoblasts and chondrocytes, little attention has been paid to the role of Glu in their ancestral mesenchymal stem cells to date. In the present study, we have evaluated the possible functionality of Glu in cultured mouse mesenchymal stem cell line C3H10T1/2 cells endowed to proliferate for the self-renewal and to differentiate toward osteoblast, chondrocyte, adipocyte, and myocyte lineages. Expression of mRNA was for the first time shown with the cystine/Glu antiporter composed of xCT and 4F2hc subunits, in addition to particular excitatory amino acid transporter (EAAT) isoforms and ionotropic GluRs, in undifferentiated C3H10T1/2 cells. Glu significantly suppressed the proliferation activity at a concentration over 500 microM without inducing cell death or differentiation, while the suppression occurred in a manner sensitive to the prevention by cystine and reduced glutathione (GSH), but not by EAAT inhibitors. A significant decrease was seen in intracellular GSH levels in C3H10T1/2 cells cultured with Glu, whereas the cellular proliferation activity was drastically decreased by the addition of the GSH depleter cyclohexene-1-one and the GSH biosynthesis inhibitor L-buthionine-[S,R]-sulfoximine, respectively. Transient overexpression of both xCT and 4F2hc subunits led to an increased basal proliferative activity in C3H10T1/2 cells. These results suggest that Glu could suppress the cellular proliferation toward self-renewal through a mechanism associated with the depletion of intracellular GSH after promoting the retrograde operation of the cystine/Glu antiporter in C3H10T1/2 cells.

Development of TaqMan-based real-time PCR assays for diagnostic detection of Babesia bovis and Babesia bigemina

Two TaqMan-based real-time polymerase chain reaction (PCR) assays devised for the detection of two bovine Babesia parasites, Babesia bovis and B. bigemina, were evaluated for their diagnostic utility using cultured parasites and 92 field bovine blood samples collected from cattle living in Brazil. The real-time PCR assays were compared with previously established nested-PCR assays. The detection limits of both B. bovis- and B. bigemina-real-time PCR assays were identical at the value of 2.5 parasites/microL of the infected blood. When 92 field bovine blood samples were tested using the real-time assays, B. bovis-positive signals were observed in 30 samples among 31 B. bovis-positive blood samples in the nested-PCR assay (96.9% sensitivity and 100% specificity), whereas the B. bigemina-real-time PCR assay could detect the parasite from all of 45 B. bigemina-positive blood samples in the nested-PCR assay (100% sensitivity and specificity). The real-time assays using the TaqMan-system can therefore be practically implemented in the epidemiologic survey for bovine babesiosis. Further studies will be necessary to investigate the clinical value of this technique, especially for the quantitative detections of the parasites.

Detection of the Escherichia coli pathogenic gene eae with three real-time polymerase chain reaction methods

Several real-time polymerase chain reaction (PCR) methods are currently available to rapidly detect the presence of a specific DNA sequence. When used for detection of pathogenic organisms, the turnaround time for PCR-based methods is much lower than for traditional culture techniques. This study compared the sensitivity of three real-time PCR methods when detecting the Escherichia coli pathogenic gene eae to determine which method is most effective in identifying very low levels of the organism. The three methods were used to detect the eae gene over a range of DNA concentrations. The differences in sensitivity were statistically significant (p<0.05), and SYBR Green I PCR was found to have the lowest detection limit of the three; LUX primers had the highest detection limit. Therefore, using a defined DNA concentration for detecting the eae gene, SYBR Green I is the best alternative.

Development of a TaqMan minor groove binding protein assay for the detection and quantification of Crimean-Congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus of the genus Nairovirus and the family Bunyaviridae. It is a negative-strand RNA virus comprised of small (S), medium (M), and large (L) genome segments. The S segment encodes for nucleocapsid protein, the M segment codes for envelope glycoproteins (Gn and Gc), and the L segment codes for the RNA-dependent RNA polymerase. Currently, there are a limited number of methods for rapidly diagnosing CCHFV infections. We developed a real-time, reverse transcription-polymerase chain reaction assay for the rapid detection of CCHFV by using the TaqMan((R))-minor groove binding protein probe technology. The primers and probes were designed to amplify and detect a region in the S segment of CCHFV that is conserved across multiple strains. The limit of detection of the assay was 10 genome copies of RNA. This primer and probe set was specific to 18 strains of CCHFV tested and did not cross-react with either a DNA panel of 78 organisms or a panel of 28 diverse RNA viruses. This will rapidly and specifically detect CCHFV, and it has been used to detect CCHFV infection in samples from humans, animals, and ticks.

Nucleotide insertion opposite a cyclobutane pyrimidine dimer analogue caused from photoligation by a replicative DNA polymerase

We previously reported an efficient and reversible template-directed photoligation using 5-carboxyvinyl-2'-deoxyuridine ((CV)U)-containing ODN at the 5'-terminal. This method forms d(T-(CV)U) as a cyclobutane pyrimidine dimer (CPD) analogue between 3'-terminal thymidine and 5'-terminal (CV)U of two oligodeoxynucleotides (ODNs). In this study, we performed PCR using a DNA template containing d(T-(CV)U). And then, we disclosed that two adenines were incorporated opposite the d(T-(CV)U).

Cloning, sequence analysis and identification of a nonsense mutation-mediated mRNA decay of porcine GSTM2 gene

The glutathione S-transferase mu 2 gene (GSTM2) encodes a GST functioning in the elimination of electrophilic compounds and the regulation of cell growth. In this study, the sequence of porcine GSTM2 gene that contains the complete sequence encoding a protein of 218 amino acids was cloned. The deduced amino acid sequence shared 76%, 78% and 76% identity with that of human, mouse and rat, respectively. mRNA expression analysis showed that the porcine GSTM2 gene was expressed at a high level in liver and testis, at a medium level in longissimus dorsi muscle, adipose tissue, spleen and lung, at a low level in kidney, and at a very low level in heart and embryo. A nonsense mutation (CGA-->TGA) resulted from C27T substitution in the fifth exon to produce a premature translation termination codon was identified, and it was discovered that nonsense-mediated mRNA decay might have an effect on the regulation of porcine GSTM2 gene expression. This polymorphism was analyzed in Large White, Landrace, Meishan and Qingping pig populations using the Taq I-polymerase chain reaction-restriction fragment length polymorphism method. The result showed that allele C had a higher frequency than allele T in each population.

Analyses of PCR products using DNA templates containing a consecutive deoxyinosine sequence

We determined nucleotide incorporation specificity of four thermostable DNA polymerases opposite deoxyinosine in order to evaluate the mutagenic effect of the presence of a consecutive deoxyinosine sequence during PCR amplification. Deoxycytosine was the only incorporated nucleotide opposite deoxyinosine during PCR amplification, irrespective of origin of DNA polymerase.

Molecular diagnosis and analysis of Chikungunya virus

BACKGROUND

In March 2005 a Chikungunya fever outbreak began on the islands of the Indian Ocean. The number of cases of this disease dramatically rose amongst these islands before affecting over a million people in India. Travellers to these regions have returned to the UK with the disease leading to a greater than 15-fold increase in the annual number of Chikungunya virus (CHIKV) sero-positive samples in 2006.

OBJECTIVES

A real-time RT-PCR test was developed for CHIKV and designed to detect currently circulating strains of virus as well as other genotypes. Its sensitivity was compared with an existing standard RT-PCR assay and a previously published real-time assay.

STUDY DESIGN

A real-time RT-PCR assay was optimised and evaluated using a panel of 55 clinical serum samples and a synthetic RNA transcript as a positive control. Nucleotide sequencing of part of the E1 gene of CHIKV was used to investigate the relatedness of the samples.

RESULTS

The real-time RT-PCR was 10-fold more sensitive than a conventional block-based RT-PCR and could detect as low as 20 copies of RNA transcript. The assay also had 10-fold improved sensitivity in detecting the outbreak strain of virus when compared to another published TaqMan assay. Analysis of sequences from patients that had travelled to India, Mauritius or the Seychelles showed high similarity with published sequences from the Indian Ocean island of Réunion.

CONCLUSIONS

A sensitive and rapid real-time RT-PCR assay has been developed for CHIKV and tested against current isolates.

Use of TaqMan gene probe for real-time monitoring of acidophilic hydrogen-producing bacteria

Using a TaqMan gene probe targeting the 16S rDNA of acidophilic hydrogen-producing bacteria (HPB), the abundance of this HPB in the biomass was found to increase from 0.02 to 72% in a single batch treating rice slurry waste at pH 4.5 over 130 h. The corresponding abundances were 4.4% in the batch operated at pH 5.0 and 0.01-0.02% at pH 5.5-6.5. During the growth phase, the generation time for the acidophilic HPB at pH 4.5 averaged 3.5 h.

A multiplexed TaqMan assay for the detection of arthropod-borne flaviviruses

Arboviruses in the genus Flavivirus are major causes of human disease worldwide, and yet they are widely under reported. This is partially due to the classical methods of detection, using virologic or immunologic techniques, which typically lack sensitivity and specificity or require biological containment facilities in order to manipulate infectious cultures. Molecular detection assays based on broadly reactive (degenerate) primers also tend to have differential and lower sensitivity for many flaviviruses. In this study, an assay was designed to test for many flaviviruses using species-specific and group-specific primers in a single reaction. This real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay combines flavivirus species-specific and group-specific TaqMan primers and probes (some previously described) into a single tube and subjected it to a standardized thermocycling conditions. The multiplex assay contains specific detection for St. Louis encephalitis virus, West Nile virus, and consensus sequences for tick-borne encephalitis complex groups: Russian Spring-Summer encephalitis and Central European encephalitis viruses. The assay also contained group-specific primers for Dengue I, II, III and IV viruses. Viral RNA was extracted from infected cell-culture derived stock viruses, field samples, or was synthesized as subgenomic target RNA molecules. All flavivirus species and sample types were detected by the multiplex assay. A sensitivity analysis of the assay suggested that the multiplex was no less able to detect low virus titer samples than the single-virus assay. This technique allows for a collection of specific assays to be used to screen for the presence of many flaviviruses of interest while saving labor and reagents, and without sacrificing sensitivity. The results demonstrated that these viruses can be screened for specifically in multiplex reactions using the rapid and sensitive method of real time qRT-PCR.

Identification of four novel MHC-C alleles in chimpanzees

Sequence-based typing strategy is used to identify polymorphism of Patr-C. Four new Patr-C alleles are described.

Evaluation of 5'-nuclease and hybridization probe assays for the detection of shiga toxin-producing Escherichia coli in human stools

5'-Nuclease and a hybridization probe assays for the detection of shiga toxin-producing Escherichia coli were validated with regard to selectivity, analytical sensitivity, reproducibility and clinical performance. Both assays were capable of detecting the classical stx(1) and stx(2) genes when challenged with reference strains of E. coli (n=40), although 1 to 4 minority sequence variants, whose clinical relevance is limited (stx(1c), stx(1d), and stx(2f)), were detected less efficiently or not at all by one or both assays. No cross reaction was observed for both assays with 37 strains representing other gastrointestinal pathogens, or normal gastrointestinal flora. Analytical sensitivity ranged from 3.07 to 3.52 log(10) and 3.42 to 4.63 log(10) CFU/g of stool for 5'-nuclease and hybridization probe assay, respectively. Reproducibility was high with coefficients of variation of </=5% for both inter- and intra-assay variation. Clinical performance was identical with a panel of archived positive specimens (n=19) and a prospective panel of stools associated with bloody diarrhea (n=115). In conclusion, both assays proved to be sensitive and reproducible.

Tissue-specific mRNA expression profiles of human carbohydrate sulfotransferase and tyrosylprotein sulfotransferase

Pairs of forward and reverse primers and TaqMan probes specific to each of 15 human sulfotransferases were prepared. The mRNA expression level of each target enzyme was analyzed in total RNA from single and pooled specimens of various human tissues (adrenal gland, bone marrow, brain, colon, heart, kidney, liver, lung, pancreas, peripheral leukocytes, placenta, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testis, thymus, thyroid gland, trachea, and uterus) by real-time reverse transcription PCR using an ABI PRISM 7700 Sequence Detection System. The mRNA expression profiles of the sulfotransferases in these 23 different human tissues were used to identify the tissues exhibiting high transcriptional activity for these enzymes. These results provide valuable information for studies concerning the human carbohydrate sulfotransferase and tyrosylprotein sulfotransferase genes in various tissues.

Autonomous microfluidic multi-channel chip for real-time PCR with integrated liquid handling

We report on a novel, polymer-based, multi-channel device for polymerase chain reaction that combines, for the first time, rapid sample processing in less than 5 min with high throughput at low costs. This is achieved by sample shuttling, during which submicroliter sample plugs (approximately 100 nl) are oscillated rapidly over three constant-temperature zones by pneumatic actuation with integrated system. The accuracy and the speed of the liquid handling have been significantly increased, while the design of the device can be kept very simple and allows for mass production using conventional low-cost polymer fabrication processes. Massive parallelization can lead to a throughput up to 100 samples in 10 min including the preparation time. The amplification can be optically monitored by means of online fluorescence detection. Successful real-time PCR and the determination of the threshold cycle, Ct, using the developed device were demonstrated with plasmid DNA in a fluorescent real-time format.