Novel properties of recombinant Sso7d-Taq DNA polymerase purified using aqueous two-phase extraction: Utilities of the enzyme in viral diagnosis

Kermekchiev, 2009, Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples, Nucleic Acids Res., 37, e40, 10.1093/nar/gkn1055 Miura, 2013, Comparison of six commercially available DNA polymerases for direct PCR, Rev. Inst. Med. Trop. Sao Paulo, 55, 401, 10.1590/S0036-46652013000600005 Cursons, 1999, The use of polymerase chain reaction to detect septicemia in critically ill patients, Crit. Care Med., 27, 937, 10.1097/00003246-199905000-00029 Espy, 2006, Real-time PCR in clinical microbiology: applications for routine laboratory testing, Clin. Microbiol. Rev., 19, 165, 10.1128/CMR.19.1.165-256.2006 Rautenberg, 1999, Evaluation of the AmpliSensor PCR and the SHARP signal detection system for the early prediction of symptomatic CMV infection in solid transplant recipients, J. Clin. Virol., 13, 81, 10.1016/S1386-6532(99)00013-X Bussani, 2007, Prenatal diagnosis of common aneuploidies in transcervical samples using quantitative fluorescent-PCR analysis, Mol. Diagn. Ther., 11, 117, 10.1007/BF03256231 Deng, 2006, Noninvasive genotyping of 9 Y-chromosome specific STR loci using circulatory fetal DNA in maternal plasma by multiplex PCR, Prenat. Diagn., 26, 362, 10.1002/pd.1422 Al-Soud, 2001, Purification and characterization of PCR-inhibitory components in blood cells, J. Clin. Microbiol., 39, 485, 10.1128/JCM.39.2.485-493.2001 Zhang, 2010, Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq, J. Mol. Diagn., 12, 152, 10.2353/jmoldx.2010.090070 Hall, 2013, Evaluation of inhibitor-resistant real-time PCR methods for diagnostics in clinical and environmental samples, PLoS One, 8, e73845, 10.1371/journal.pone.0073845 Al-Soud, 1998, Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples, Appl. Environ. Microbiol., 64, 3748, 10.1128/AEM.64.10.3748-3753.1998 Panaccio, 1993, FoLT PCR: a simple PCR protocol for amplifying DNA directly from whole blood, Biotechniques, 14, 238 Chien, 1976, Deoxyribonucleic acid polymerase from the extreme thermophile Thermusaquaticus, J. Bacteriol., 127, 1550, 10.1128/JB.127.3.1550-1557.1976 Lawyer, 1989, Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus, J. Biol. Chem., 264, 6427, 10.1016/S0021-9258(18)83367-1 Ding, 2011, Preparation of Taq DNA polymerase by thermal purification, Agri. Biotechnol., 12, 375 Meier, 1993, Elimination of contaminating DNA within polymerase chain reaction reagents: implications for a general approach to detection of uncultured pathogens, J ClinMicrobiol, 31, 646 Pluthero, 1993, Rapid purification of high-activity Taq DNA polymerase, Nucleic Acids Res., 21, 4850, 10.1093/nar/21.20.4850 Chen, 2015, A simple and efficient method for extraction of Taq DNA polymerase, Electron. J. Biotechnol., 18, 355, 10.1016/j.ejbt.2015.08.001 Carroll, 1999, Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion, J. Clin. Microbiol., 37, 3402, 10.1128/JCM.37.10.3402-3404.1999 Wang, 2004, A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro, Nucleic Acids Res., 32, 1197, 10.1093/nar/gkh271 Goja, 2013, Aqueous two-phase extraction advances for bioseparation, J. Bioproces. Biotechniq., 4, 1 Das, 2010, An alternate method for purification of recombinant Taq DNA polymerase using an aqueous two-phase system, Ind. Biotechnol., 6, 295, 10.1089/ind.2010.6.295 Das, 2011, Cloning, soluble expression and purification of high yield recombinant hGMCSF in Escherichia coli, Int. J. Mol. Sci., 12, 2064, 10.3390/ijms12032064 Kirk, 1995, Optimising the recovery of recombinant thermostable proteins expressed in mesophilic hosts, J. Biotechnol., 42, 177, 10.1016/0168-1656(95)00078-5 Nesterenko, 1994, A simple modification of Blum’s silver stain method allows for 30 minute detection of proteins in polyacrylamide gels, J. Biochem. Biophys. Methods, 28, 239, 10.1016/0165-022X(94)90020-5 Bradford, 1976, Rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem., 72, 248, 10.1016/0003-2697(76)90527-3 Eckert, 1990, High fidelity DNA synthesis by the Thermusaquaticus DNA polymerase, Nucleic Acids Res., 18, 3739, 10.1093/nar/18.13.3739 Williams, 1989, Optimization strategies for the polymerase chain reaction, Biotechniques, 7, 762 Ellsworth, 1993, Artifactual variation in randomly amplified polymorphic DNA banding patterns, Biotechniques, 14, 214 Lee, 2008, Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli, Appl. Microbiol. Biotechnol., 78, 371, 10.1007/s00253-007-1300-6 Itoh, 2005, High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by A PCR–SSOP–Luminex method in the Japanese population, Immunogenetics, 57, 717, 10.1007/s00251-005-0048-3 Lange, 2014, Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing, BMC Genomics, 63, 10.1186/1471-2164-15-63 Pelt-Verkuil, 2008 Varadaraj, 1994, Denaturants or co-solvents improve the specificity of PCR amplification of a G+C-rich DNA using genetically engineered DNA polymerases, Gene, 140, 1, 10.1016/0378-1119(94)90723-4 Bickley, 1999, Ionic and non-ionic detergents inhibiting PCR Maiwald, 1994, Characterization of contaminating DNA in Taq polymerase which occurs during amplification with a primer set for Legionella 5S ribosomal RNA, Mol. Cell Probes, 8, 11, 10.1006/mcpr.1994.1002 Větrovský, 2013, The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses, PLoS One, 8, e57923, 10.1371/journal.pone.0057923 Spangler, 2009, Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria, PloS One, 4, e7010, 10.1371/journal.pone.0007010 Melissis, 2007, One-step purification of Taq DNA polymerase using nucleotide-mimetic affinity chromatography, Biotechnol. J., 2, 121, 10.1002/biot.200600191 Sun, 2006, Purification of recombinant Pfu DNA polymerase using a new JK110 resin, Korean J. Chem. Eng., 23, 607, 10.1007/BF02706802 Oppermann, 1998, Isolation and structure of repressor-like proteins from the archaeon Sulfolobus solfataricus, FEBS Lett., 432, 141, 10.1016/S0014-5793(98)00848-5 Guagliardi, 1997, Annealing of complementary DNA strands above the melting point of the duplex promoted by an archaeal protein, J. Mol. Biol., 267, 841, 10.1006/jmbi.1996.0873 López-García, 1998, In vitro DNA binding of the archaeal protein Sso7d induces negative supercoiling at temperatures typical for thermophilic growth, Nucleic Acids Res., 26, 2322, 10.1093/nar/26.10.2322 Guagliardi, 2000, The chromosomal protein sso7d of the Crenarchae on Sulfolobus solfataricus rescues aggregated proteins in an ATP hydrolysis-dependent manner, J. Biol. Chem., 275, 31813, 10.1074/jbc.M002122200 Corless, 2000, Contamination and sensitivity issues with a real-time universal 16S rRNA PCR, J. Clin. Microbiol., 38, 1747, 10.1128/JCM.38.5.1747-1752.2000 Andersson, 1991, Bioconversion in aqueous two-phase systems, Enzyme Microb. Technol., 12, 242, 10.1016/0141-0229(90)90095-8 Tjerneld, 1985, Enzymatic hydrolysis of cellulose in aqueous two-phase systems.I. Partition of cellulases from Trichoderma reesei, Biotechnol. Bioeng., 27, 1036, 10.1002/bit.260270715 Tjerneld, 1986, New aqueous two-phase system based on hydroxyl propyl starch useful in enzyme purification, Enzyme Microb. Technol., 8, 417, 10.1016/0141-0229(86)90149-3 Walter, 1991, Partitioning in aqueous two-phase systems: recent results, Anal. Biochem., 197, 1, 10.1016/0003-2697(91)90348-W Guan, 1996, Use of aqueous two-phase systems in the purification of human interferon-α1 from recombinant Escherichia coli, Enzyme Microb. Technol., 19, 446, 10.1016/S0141-0229(96)00051-8 Bradoo, 1999, Partitioning and resolution of mixture of two lipases from Bacillus stearothermophilus SB-1 in aqueous two-phase system, Process Biochem., 35, 57, 10.1016/S0032-9592(99)00032-1 S. Somani, S. Padmanabhan, Process for purification of recombinant human granulocyte colony stimulating factor. US 20120093765 A1, 2010. Nebbia, 2012, Hepatitis B infection: current concepts and future challenges, QJM., 105, 109, 10.1093/qjmed/hcr270 Biazar, 2015, Relationship between hepatitis B DNA viral load in the liver and its histology in patients with chronic hepatitis B, Casp. J. Intern. Med., 6, 209 Nuovo, 1993, Importance of different variables for enhancing in-situ detection of PCR-amplified DNA, PCR Methods Appl., 2, 305, 10.1101/gr.2.4.305 Thaker, 1999 Hu, 1992, Effect of freezing of the PCR buffer on the amplification specificity: allelic exclusion and preferential amplification of contaminating molecules, PCR Methods Appl., 2, 182, 10.1101/gr.2.2.182 Monis, 2005, Comparison of SYTO9 and SYBR Green I for real time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis, Anal. Biochem., 340, 24, 10.1016/j.ab.2005.01.046 Gudnason, 2007, Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature, Nucleic Acids Res., 35, e127, 10.1093/nar/gkm671