Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples

Nucleic Acids Research

Volumn 37, Issue 5, 2009, Pages

  Kermekchiev, Milko B ^a   Kirilova, Lyubka I ^a   Vail, Erika E ^a   Barnes, Wayne M ^a,b  

^a DNA Polymerase Technology Inc   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEMIN; HEMOGLOBIN; HUMIC ACID; IMMUNOGLOBULIN G; KLENTAQ1 POLYMERASE; LACTOFERRIN; TAQ POLYMERASE; UNCLASSIFIED DRUG; DNA; ENZYME INHIBITOR; FLUORESCENT DYE; ORGANIC COMPOUND; SYBR GREEN I;

AMINO TERMINAL SEQUENCE; ARTICLE; BLOOD SAMPLING; CODON; CONTROLLED STUDY; DNA PURIFICATION; ENZYME ACTIVITY; GENE AMPLIFICATION; GENE DELETION; GENE NUMBER; GENE TARGETING; HUMAN; MOLECULAR CLONING; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SOIL; WILD TYPE; BLOOD; DRUG ANTAGONISM; EVALUATION; GENETICS; METABOLISM; METHODOLOGY; MICROBIOLOGY; MUTATION; POLYMERASE CHAIN REACTION; TIME;

DNA; ENZYME INHIBITORS; FLUORESCENT DYES; HUMANS; MUTATION; ORGANIC CHEMICALS; POLYMERASE CHAIN REACTION; SEQUENCE DELETION; SOIL MICROBIOLOGY; TAQ POLYMERASE; TIME FACTORS;

EID: 63249099357     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn1055     Document Type: Article

References (53)

1. Radstrom,P., Knutsson,R., Wolffs,P., Lövenklev,M. and Löfström,C. (2004) Pre-PCR processing: Strategies to generate PCR-compatible samples. Mol. Biotechnol., 26, 133-146.
2. Lantz,P.-G., Al-Soud,W.A., Knutsson,R., Hahn-Haegerald,B. and Radstrom,P. (2000) Biotechnical use of the polymerase chain reaction for microbial analysis of biological samples. Biotechnol. Annu. Rev., 5, 87-130.
3. Altwegg,M. and Verhoef,J. (1995) Amplification methods in diagnostic microbiology. J. Microbiol. Methods, 23, 1-2.
4. Al-Soud,W.A. and Radstrom,P. (2000) Effect of amplification facilitators on diagnostic PCR in the presence of blood, feces and meat. J. Clin. Microbiol., 38, 4463-4470.
5. Al-Soud,A.W. and Radstrom,P. (1998) Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol., 64, 3748-3753.
6. Frackman,S., Kobs,G., Simpson,D. and Storts,D. (1998) Betaine and DMSO: enhancing agents for PCR. Promega Notes, 65, 27.
7. Topal,M.D. and Sinha,N.K. (1983) Products of bacteriophage T4 genes 32 and 45 improve the accuracy of DNA replication in vitro. J. Biol. Chem., 258, 12274-12279.
8. Kreader,C.A. (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol. 62, 1102-1106.
9. Al-Soud,A.W., Jönsson,L.J. and Radstrom,P. (2000) Identification and characterization of immunoglobulin G in blood as a major inhibitor of diagnostic PCR. J. Clin. Microbiol., 38, 345-350.
10. de Franchis,R., Cross,N.C., Foulkes,N.S. and Cox,T.M. (1988) A potent inhibitor of Taq polymerase copurifies with human genomic DNA. Nucleic Acids Res., 16, 10355-10366.
11. Al-Soud,W.A. and Radstrom,P. (2001) Purification ands characterization of PCR-inhibitory components in blood cells. J. Clin. Microbiol., 39, 485-493.
12. Akane,A., Matsubara,K., Nakamura,H., Takahashi,S. and Kimura,K. (1994) Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J. Forensic Sci., 39, 362-372.
13. Kuske,C.R., Banton,K.L., Adorada,D.L., Stark,P.C., Hill,K.K. and Jackson,P.J. (1998) Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl. Environ. Microbiol., 64, 2463-2472.
14. Poussier,S., Cheron,J., Couteau,A. and Luisetti,J. (2002) Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates. J. Microbiol. Methods., 51, 349-359.
15. Tsai,Y.-L. and Olson,B.H. (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol., 58, 2292-2295.
16. Watson,R.J. and Blackwell,B. (2000) Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Can. J. Microbiol., 46, 633-642.
17. Yeates,C., Gillings,M.R., Davison,A.D., Altavilla,N. and Veal,D.A. (1998) Methods for microbial DNA extraction from soil for PCR amplification. Biol. Proceed. Online, 1, 40-47.
18. LaMontagne,M.G., Michel,F.C. Jr., Holden,P.A. and Reddy,C.A. (2001) Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis. J. Microbiol. Methods, 49, 255-264.
19. Watson,R.J. and Blackwell,B. (2000) Purification and characterization of a common soil component which inhibits the polymerase chain reaction. Can. J. Microbiol., 46, 633-642.
20. Forbes,B.A. and Hicks,K.E (1996) Substance interfering with direct detection of mycobacterium tuberculosis in clinical specimens by PCR: effects of bovine serum albumin. J. Clin. Microbiol., 34, 2125-2128.
21. Kreader,C.A. (1996) Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol. 62, 1102-1106.
22. Wilson,I.G. (1997) Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol., 63, 3741-3751.
23. Morata,P., Queipo-Ortuno,I. and Colmenero,J. (1998) Strategy for optimizing DNA amplification in a peripheral blood PCR assay used for diagnosis of human brucellosis. J. Clin. Microbiol., 36, 2443-2446.
24. Al-Soud,A.W., Lantz,P.-G., Bäckman,A., Olcen,P. and Radstrom,P. (1998) A sample preparation method which facilitates detection of bacteria in blood cultures by the polymerase chain reaction. J. Microbiol. Methods, 32, 217-224.
25. Klein,A., Barsuk,R., Dagan,S., Nusbaum,O., Shouval,D. and Galun,E. (1997) Comparison of methods for extraction of nucleic acid from hemolytic serum for PCR amplification of hepatitis B virus DNA sequences. J. Clin. Microbiol., 35, 1897-1899.
26. Cattaneo,C., Graig,O.E., James,N.T. and Bolton,H. (1997). Comparison of three DNA extraction methods on bone and blood stains up to 43 years old and amplification of three different gene sequences. J. Forensic Sci. 42, 1126-1135.
27. Bourke,M.T., Scherczinger,C.A., Ladd,C. and Lee,H.C. (1999) NaOH treatment to neutralize inhibitors of Taq polymerase. J. Forensic Sci., 44, 1046-1050.
28. Harry,M., Gambier,B., Bourezgui,Y. and Garnier-Sillam,E. (1999) Evaluation of purification procedures for DNA extracted from organic rich samples: Interference with humic substances. Analusis, 27 439-441.
29. Lebuhn,M., Effenberger,M., Garces,G., Gronauer,A. and Wilderer,P.A. (2004) Evaluating real-time PCR for the quantification of distinct pathogens and indicator organisms in environmental samples. Water Sci. Technol., 50, 263-270.
30. Moreira,D. (1998) Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Res., 26, 3309-3310.
31. Schneegurt,M.A., Dore,S.Y. and Kulpa,C.F. (2003) Direct extraction of DNA from soils for studies in microbial ecology. Curr. Issues Mol. Biol., 5, 1-8.
32. Burgmann,H., Pesaro,M., Widmer,F. and Zeyer,J. (2001) A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods, 45, 7-20.
33. Kramvis,A., Bukovzer,S. and Kew,M.C. (1996) Comparison of hepatitis B virus DNA extractions from serum by the QIAamp blood kit, Genereleaser, and the phenol-chloroform method. J. Clin. Microbiol., 34, 2731-2733.
34. Ong,J.L., Loakes,D., Jaroslawski,S., Too,K. and Holliger,P. (2006) Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J. Mol. Biol., 361, 537-550.
35. Vichier-Guerre,S., Ferris,S., Auberger,N., Mahiddine,K. and Jestin,J.L. (2006) A population of thermostable reverse transcriptases evolved from Thermus aquaticus DNA polymerase I by phage display. Angew. Chem. Int. Ed. Engl., 45, 6133-6137.
36. Schönbrunner,N.J., Fiss,E.H., Budker,O., Stoffel,S., Sigua,C.L., Gelfand,D.H. and Myers,T.W. (2006) Chimeric thermostable DNA polymerases with reverse transcriptase and attenuated 3′-5′ exonuclease activity. Biochemistry, 45, 12786-12795.
37. Gloeckne,R.C., Sauter,K.B. and Marx,A. (2007) Evolving a thermostable DNA polymerase that amplifies from highly damaged templates. Angew. Chem. Int. Ed. Engl., 46, 3115-3117.
38. Weiner,M.P., Costa,G.L., Schoettlin,W., Cline,J., Mathur,E. and Bauer,J.C. (1994) Site-directed mutagenesis of double-stranded DNA by the polymerase chain reaction. Gene, 151, 119-123.
39. Kermekchiev,M.B., Tzekov,A. and Barnes,W. (2003) Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic Acids Res. 31, 6139-6147.
40. Desai,U.J. and Pfaffle,P.K. (1995) Single-step purification of a thermostabile DNA polymerase expressed in Escherichia coli. BioTechniques, 19, 780-784.
41. Barnes,W.M. (1992) The fidelity of Taq polymerase catalyzing PCR is improved by an N-terminal deletion. Gene, 112, 29-35.
42. Nath,K., Sarosy,J.W., Hahn,J. and Di Como,C.J. (2000) Effects of ethidium bromide and SYBR green I on different polymerase chain reaction systems. J. Biochem. Biophys. Methods., 42, 15-29.
43. Monis,P.T., Giglio,S. and Saint,C.P. (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, 24-34.
44. Wittwer,C.T., Reed,G.H., Gundry,C.N., Vandersteen,J.G. and Pryor,R.J. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem., 49, 853-860.
45. Gudnason,H., Dufva,M., Bang,D.D. and Wolff,A. (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.
46. Rees,W.A., Yager,T.D., Korte,J. and von Hippel,P.H. (1993) Betaine can eliminate the base pair composition dependence of DNA melting. Biochemistry, 32, 137-144.
47. Zipper,H., Buta,C., Lämmle,K., Brunner,H., Bernhagen,J. and Frank Vitzthum,F. (2003) Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments. Nucleic Acids Res., 31, e39.
48. Sutlovic,D., Gamulin,S., Definis-Gojanovic,M., Gugic,D. and Andjelinovic,S. (2008) Interaction of humic acids with human DNA: proposed mechanisms and kinetics. Electrophoresis, 7, 1467-1472.
49. Byrnes,J., Downey,K., Esserman,L. and So,A. (1975) Mechanism of hemin inhibition of erythroid cytoplasmic DNA polymerase. Biochemistry, 14, 796-799.
50. Korolev,S., Nayal,M., Barnes,W.M., DiCera,E. and Waksman,G. (1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 25Å resolution: Structural basis for thermostability. Proc. Natl Acad. Sci. USA, 92, 9264-9268.
51. Li,Y., Korolev,S. and Waksman,G. (1998) Chrystal structure of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J., 17, 7514-7525.
52. Levene,M., Korlach,J., Turner,S., Foquet,M., Craighead,H. and Webb,W. (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science, 299, 682-686.
53. Sayle,R.A. and Milner-White,E.J. (1995). RASMOL: Biomolecular graphics for all. Trends Biochem Sci., 20, 374-382.