Genomes and Genes
Summary: A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.
- Sutlovic D, Definis Gojanovic M, Andelinovic S, Gugic D, Primorac D. Taq polymerase reverses inhibition of quantitative real time polymerase chain reaction by humic acid. Croat Med J. 2005;46:556-62 pubmed..acid (HA) on the quantitative real time polymerase chain reaction (QRT-PCR) inhibition and the efficiency of Taq polymerase increment in preventing inhibition by HA in DNA extracted from ancient bones...
- Ong J, Loakes D, Jaroslawski S, Too K, Holliger P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J Mol Biol. 2006;361:537-50 pubmed..Our results suggest that spCSR will be a powerful strategy for the generation of polymerases with altered substrate specificity for applications in nano- and biotechnology and in the enzymatic synthesis of antisense and RNAi probes. ..
- Koncan R, Valverde A, Morosini M, García Castillo M, Canton R, Cornaglia G, et al. Learning from mistakes: Taq polymerase contaminated with beta-lactamase sequences results in false emergence of Streptococcus pneumoniae containing TEM. J Antimicrob Chemother. 2007;60:702-3 pubmed
- Bu Z, Biehl R, Monkenbusch M, Richter D, Callaway D. Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. Proc Natl Acad Sci U S A. 2005;102:17646-51 pubmed..framework, we reveal overdamped, coupled domain motion within DNA polymerase I from Thermus aquaticus (Taq polymerase)...
- Spangler R, Goddard N, Thaler D. Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria. PLoS ONE. 2009;4:e7010 pubmed publisher..Importantly, all commercial Taq polymerase preparations inevitably contain contaminating microbial DNA...
- Bass C, Williamson M, Wilding C, Donnelly M, Field L. Identification of the main malaria vectors in the Anopheles gambiae species complex using a TaqMan real-time PCR assay. Malar J. 2007;6:155 pubmed..merus/melas/bwambae, vectors with restricted distributions, are not present it can be used alone to discriminate vector from non-vector or in combination with the Walker TaqMan assay to distinguish An. arabiensis and An. gambiae s.s. ..
- Ho D, Byrnes W, Ma W, Shi Y, Callaway D, Bu Z. Structure-specific DNA-induced conformational changes in Taq polymerase revealed by small angle neutron scattering. J Biol Chem. 2004;279:39146-54 pubmedThe DNA polymerase I from Thermus aquaticus (Taq polymerase) performs lagging-strand DNA synthesis and DNA repair...
- Kermekchiev M, Tzekov A, Barnes W. Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic Acids Res. 2003;31:6139-47 pubmed..We show that the novel cold-sensitive mutants can provide a hot start for PCR and exhibit slightly improved fidelity. ..
- Yang S, Lin S, Kelen G, Quinn T, Dick J, Gaydos C, et al. Quantitative multiprobe PCR assay for simultaneous detection and identification to species level of bacterial pathogens. J Clin Microbiol. 2002;40:3449-54 pubmed..This assay has broad potential in the clinical arena for rapid and specific diagnosis of infectious diseases. ..
- Miyazaki K, Takenouchi M. Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques. 2002;33:1033-4, 1036-8 pubmed..The present method, which we designated MEGAWHOP (megaprimer PCR of whole plasmid), is thus ideal for creating random mutagenesis megalibraries. ..
- Heininger A, Binder M, Ellinger A, Botzenhart K, Unertl K, Doring G. DNase pretreatment of master mix reagents improves the validity of universal 16S rRNA gene PCR results. J Clin Microbiol. 2003;41:1763-5 pubmed..The DNase I requirement for the elimination of false-positive results varied between 0.1 and 70 IU per master mix depending on the applied Taq polymerase. PCR sensitivity was mostly maintained when 0.1 IU of DNase I was used.
- Mohammadi T, Reesink H, Vandenbroucke Grauls C, Savelkoul P. Optimization of real-time PCR assay for rapid and sensitive detection of eubacterial 16S ribosomal DNA in platelet concentrates. J Clin Microbiol. 2003;41:4796-8 pubmed..Digestion of the PCR reagents with Sau3AI prior to PCR amplification was effective in eliminating this contaminating DNA without affecting the sensitivity of the assay. ..
- Ghadessy F, Ramsay N, Boudsocq F, Loakes D, Brown A, Iwai S, et al. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol. 2004;22:755-9 pubmed..Such 'unfussy' polymerases have immediate utility, as we demonstrate by the generation of microarray probes with up to 20-fold brighter fluorescence. ..
- Boekholdt S, Sacks F, Jukema J, Shepherd J, Freeman D, McMahon A, et al. Cholesteryl ester transfer protein TaqIB variant, high-density lipoprotein cholesterol levels, cardiovascular risk, and efficacy of pravastatin treatment: individual patient meta-analysis of 13,677 subjects. Circulation. 2005;111:278-87 pubmed..The CETP TaqIB variant is firmly associated with HDL-C plasma levels and as a result, with the risk of CAD. Importantly, this CETP variant does not influence the response to pravastatin therapy. ..
- Spiess A, Mueller N, Ivell R. Trehalose is a potent PCR enhancer: lowering of DNA melting temperature and thermal stabilization of taq polymerase by the disaccharide trehalose. Clin Chem. 2004;50:1256-9 pubmed
- Hamasuna R, Osada Y, Jensen J. Antibiotic susceptibility testing of Mycoplasma genitalium by TaqMan 5' nuclease real-time PCR. Antimicrob Agents Chemother. 2005;49:4993-8 pubmed..MICs for tetracycline ranged from 0.125 to 4 mg/liter. This new method could increase the number of M. genitalium strains available for antibiotic susceptibility testing and significantly shorten the time from sampling to MIC results...
- Achmüller C, Köhler A, Bösch S, Schneider R. A-overhang-dependent repeat expansion determination (ADRED). Biotechniques. 2008;45:577-80 pubmed publisher..Because ADRED includes a sequencing step, disease-relevant polymorphisms (e.g., CAA interruptions in spinocerebellar ataxia type 2) can simultaneously be detected. ..
- Skidmore S, Kaye M, Bayliss D, Devendra S. Validation of COBAS Taqman CT for the detection of Chlamydia trachomatis in vulvo-vaginal swabs. Sex Transm Infect. 2008;84:277-8; discussion 278-9 pubmed publisher..12/267 (4.5%) VVSs were invalid/inhibitory and so no result was available for these samples. This compared with 2/267 (0.7%) for endocervical swabs. VVS are suitable samples for detecting C trachomatis. ..
- Huang Z, Buckwold V. A TaqMan PCR assay using degenerate primers for the quantitative detection of woodchuck hepatitis virus DNA of multiple genotypes. Mol Cell Probes. 2005;19:282-9 pubmed
- Friedrichs E, Simmel F. Controlling DNA polymerization with a switchable aptamer. Chembiochem. 2007;8:1662-6 pubmed
- Elsammak M, Al Sharkaweey R, Fahmy M, Reda A, Farid W, Emara A, et al. Taq1B polymorphism of cholesteryl ester transfer protein (CETP) in Egyptian patients with metabolic syndrome. Diabetes Metab Syndr. 2011;5:61-5 pubmed publisher..Egyptian patients affected with metabolic syndrome have a higher prevalence of B1B1 genotype that is associated with lower serum HDL-C levels. ..
- Sikorsky J, Primerano D, Fenger T, Denvir J. DNA damage reduces Taq DNA polymerase fidelity and PCR amplification efficiency. Biochem Biophys Res Commun. 2007;355:431-7 pubmed..Because the MME method can detect small reductions in amplification efficiency, it may be useful in comparing the extent of damage in environmentally degraded or archival DNA specimens. ..
- Garcia E, Dowding L, Stanton L, Slepnev V. Scalable transcriptional analysis routine--multiplexed quantitative real-time polymerase chain reaction platform for gene expression analysis and molecular diagnostics. J Mol Diagn. 2005;7:444-54 pubmed..Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics. ..
- Derrick K, Norbury K, Kieswetter K, Skaf J, McNulty A. Comparative analysis of global gene expression profiles between diabetic rat wounds treated with vacuum-assisted closure therapy, moist wound healing or gauze under suction. Int Wound J. 2008;5:615-24 pubmed publisher..A.C. Therapy. This study is the first to assess wound healing by whole genome interrogation in a diabetic rat model treated with different healing modalities. ..
- Bragin A, Glushkov S, Ivanov M, Krasnov A, Dymshits G. Determination of DNA polymerase and nuclease activities of DNA-dependent polymerases using fluorescence detection under real-time conditions. Biochemistry (Mosc). 2008;73:1007-17 pubmed..The method can be also used for estimation of endonuclease activities of DNA polymerases. ..
- Willi B, Meli M, Luthy R, Honegger H, Wengi N, Hoelzle L, et al. Development and application of a universal Hemoplasma screening assay based on the SYBR green PCR principle. J Clin Microbiol. 2009;47:4049-54 pubmed publisher..The SYBR green PCR assay described here is a suitable tool to screen for known and so-far-undiscovered hemoplasma species. Positive results should be confirmed by specific TaqMan PCR or sequencing...
- Nieddu M, Pichiri G, Manconi S, Mezzanotte R. Some remarks on the use of TaqI to detect highly repetitive DNA sequences in human chromosomes. Eur J Histochem. 2006;50:281-3 pubmed..These results permitted us to draw some conclusions on the highly repetitive DNA composition of these regions, in terms of alphoid and classical satellite DNAs. ..
- Cabrera Artiles Y, Martínez García D, Pérez Cruz E, Márquez Perera G, Feble M. Osmoregulated TAQ polymerase gene expression in Escherichia coli. Rev Latinoam Microbiol. 2002;44:14-8 pubmed
- Sugita T, Shiraki Y, Hiruma M. Real-time PCR TaqMan assay for detecting Trichophyton tonsurans, a causative agent of tinea capitis, from hairbrushes. Med Mycol. 2006;44:579-81 pubmed..We recently developed a real-time PCR TaqMan assay as a culture-independent method for the rapid detection of T. tonsurans from hairbrushes. ..
- Song J, Lee J, Lee J, Jeong B, Lee W, Lee S. Removal of contaminating TEM-la beta-lactamase gene from commercial Taq DNA polymerase. J Microbiol. 2006;44:126-8 pubmed
- Gelderblom H, Menting S, Beld M. Clinical performance of the new rRoche COBAS TaqMan HCV Test and High Pure System for extraction, detection and quantitation of HCV RNA in plasma and serum. Antivir Ther. 2006;11:95-103 pubmed..This is clinically relevant because underestimation of HCV RNA levels during therapy may lead physicians into making incorrect treatment decisions. ..
- Hochberger S, Althof D, Gallegos de Schrott R, Nachbaur N, Rock H, Leying H. Fully automated quantitation of hepatitis B virus (HBV) DNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol. 2006;35:373-80 pubmed..The results obtained with the new test show a good correlation to titers obtained with other platforms. ..
- Horn D. Directional enrichment of directly cloned PCR products. Biotechniques. 2005;39:40, 42, 44, 46 pubmed
- Zivkovic M, Stankovic A, Dincic E, Popovic M, Popović S, Raicevic R, et al. The tag SNP for HLA-DRB1*1501, rs3135388, is significantly associated with multiple sclerosis susceptibility: cost-effective high-throughput detection by real-time PCR. Clin Chim Acta. 2009;406:27-30 pubmed publisher..41-3.09, p<0.001) for MS susceptibility. We assessed significant association of rs3135388 A allele carriership with MS in patients from Serbia. This HLA-DRB1*1501 "surrogate" marker is useful in association studies in MS. ..
- Slatko B, Albright L, Tabor S, Ju J. DNA sequencing by the dideoxy method. Curr Protoc Mol Biol. 2001;Chapter 7:Unit7.4A pubmed publisher..The use of automated fluorescent sequencers for four-color dideoxy DNA sequencing is also described in detail. ..
- Wang P, Ren L, He H, Liang F, Zhou X, Tan Z. A phenol quaternary ammonium porphyrin as a potent telomerase inhibitor by selective interaction with quadruplex DNA. Chembiochem. 2006;7:1155-9 pubmed
- Enouf V, Dos Reis G, Guthmann J, Guerin P, Caron M, Marechal V, et al. Validation of single real-time TaqMan PCR assay for the detection and quantitation of four major genotypes of hepatitis E virus in clinical specimens. J Med Virol. 2006;78:1076-82 pubmed..The real-time RT-PCR assay was 10- to 100-fold sensitive than for conventional RT-PCR assays used in this study with a range quantitation from 1.8 x 10(1) to 7.2 x 10(3) RNA copies/microl in clinical samples (serum and stools). ..
- Ortu S, Molicotti P, Sechi L, Pirina P, Saba F, Vertuccio C, et al. Rapid detection and identification of Mycobacterium tuberculosis by Real Time PCR and Bactec 960 MIGT. New Microbiol. 2006;29:75-80 pubmed..The sensitivity and specificity of this assay, 10% and 100%, respectively, were compared to those of conventional microbiological methods. ..
- Rueckert A, Morgan H. Removal of contaminating DNA from polymerase chain reaction using ethidium monoazide. J Microbiol Methods. 2007;68:596-600 pubmed..The methodology presented is straightforward and can be accomplished within 10 min...
- Rasmussen J, Barbez P, Burgoyne L, Saint C. Rapid preparation of cyanobacterial DNA for real-time PCR analysis. Lett Appl Microbiol. 2008;46:14-9 pubmed
- Lu Y, Yan J, Feng Y, Xu C, Shi W, Mao H. Rapid detection of H5 avian influenza virus by TaqMan-MGB real-time RT-PCR. Lett Appl Microbiol. 2008;46:20-5 pubmed..Real-time RT-PCR assay with MGB probe was an effective means for quick and quantitative laboratory detection and monitoring of H5 avian influenza viruses. ..
- McCrea J, Liu C, Ng L, Wang G. Detection of the Escherichia coli pathogenic gene eae with three real-time polymerase chain reaction methods. Can J Microbiol. 2007;53:398-403 pubmed..Therefore, using a defined DNA concentration for detecting the eae gene, SYBR Green I is the best alternative. ..
- Renberg B, Shiroyama I, Engfeldt T, Nygren P, Karlström A. Affibody protein capture microarrays: synthesis and evaluation of random and directed immobilization of affibody molecules. Anal Biochem. 2005;341:334-43 pubmed..For the best slides, the limit of detection was 3 pM for IgA and 30 pM for Taq DNA polymerase. ..
- Engle R, Russell R, Purcell R, Bukh J. Development of a TaqMan assay for the six major genotypes of hepatitis C virus: comparison with commercial assays. J Med Virol. 2008;80:72-9 pubmed..TaqMan assays have become an essential tool to follow viral load in clinical samples and cell culture-based experiments and this technology offers significant advantages in linear dynamic range, sensitivity and customization. ..
- Reina G, Orlando C, Rebora P, Ambrogi F, Casini Raggi C, Verderio P, et al. Bivariate statistical approach to evaluate laboratory performance by analysis of standard curves in an External Quality Assurance program for quantitative assays based on real-time PCR with Taq-Man probes. Clin Chem Lab Med. 2006;44:18-22 pubmed..Furthermore, specific indexes to evaluate the impact of these two features on the determination of the initial number of molecules are given to help to improve the assay procedure. ..
- Bossard C, Bieche I, Le Doussal V, Lidereau R, Sabourin J. Real-time RT-PCR: a complementary method to detect HER-2 status in breast carcinoma. Anticancer Res. 2005;25:4679-83 pubmed..These results show a high concordance rate (84%) between Q-RT-PCR and IHC (p < 10(-4)). We conclude that Q-RT-PCR is a useful complementary method for determination of the HER-2 status. ..
- Easterday W, Van Ert M, Simonson T, Wagner D, Kenefic L, Allender C, et al. Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis. J Clin Microbiol. 2005;43:1995-7 pubmed..cereus, and B. thuringiensis isolates. The assay differentiated B. anthracis from these genetic near-neighbors and determined that the nonsense mutation is ubiquitous across 89 globally and genetically diverse B. anthracis strains. ..
- van der Sluis R, van Montfort T, Centlivre M, Schopman N, Cornelissen M, Sanders R, et al. Quantitation of HIV-1 DNA with a sensitive TaqMan assay that has broad subtype specificity. J Virol Methods. 2013;187:94-102 pubmed publisher..Execution of the pre-amplification step with a second primer set enables for the exclusive quantitation of the 2-LTR circular HIV-1 DNA form. ..
- Kosch T, Summers K. Techniques for minimizing the effects of PCR inhibitors in the chytridiomycosis assay. Mol Ecol Resour. 2013;13:230-6 pubmed publisher..and four PCR methods (Amplitaq Gold, bovine serum albumin, PowerClean DNA Clean-up and inhibitor resistant Taq Polymerase)...
- Qiu F, Zheng H, Yi Y, Jia Z, Cao J, Bi S. Comparative evaluation of a novel TaqMan real-time reverse transcription-polymerase chain reaction assay for hepatitis A virus detection. J Int Med Res. 2013;41:427-34 pubmed publisher..To develop and evaluate a novel system for detecting and quantifying hepatitis A virus (HAV) nucleic acid...