Bias and Artifacts in Multitemplate Polymerase Chain Reactions (PCR)

Journal of Bioscience and Bioengineering

Volumn 96, Issue 4, 2003, Pages 317-323

  Kanagawa, Takahiro ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

16S rRNA gene; Chimera; Heteroduplex; Microbial community analysis; PCR bias

Indexed keywords

AMPLIFICATION; ENZYMES; GENES;

ARTIFACT FORMATIONS;

BIOMEDICAL ENGINEERING;

HETERODUPLEX;

ARTIFACT; CHIMERA; DNA POLYMORPHISM; GENE SEQUENCE; GENETIC VARIABILITY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVIEW;

EID: 0344629203     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1263/jbb.96.317     Document Type: Review

References (36)

1. Suzuki, M. T. and Giovannoni, S. J.: Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol., 62, 625-630 (1996).
2. ot effect' and its consequences. Nucleic Acids Res., 24, 2080-2086 (1996).
3. Polz, M. F. and Cavanaugh, C. M.: Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol., 64, 3724-3730 (1998).
4. Brunk, C. F. and Eis, N.: Quantitative measure of small-subunit rRNA gene sequences of the kingdom Korarchaeota. Appl. Environ. Microbiol., 64, 5064-5066 (1998).
5. Meyerhans, A., Vartanian, J-P., and Wain-Hobson, S.: DNA recombination during PCR. Nucleic Acids Res., 18, 1687-1691 (1990).
6. Pääbo, S., Irwin, D. M., and Wilson, A. C.: DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem., 265, 4718-4721 (1990).
7. Liesack, W., Weyland, H., and Stackebrandt, E.: Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol., 21, 191-198 (1991).
8. Odelberg, S. J., Weiss, R. B., Hata, A., and White, R.: Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. Nucleic Acids Res., 23, 2049-2057 (1995).
9. Patel, R., Lin, C., Laney, M., Kurn, N., Rose, S., and Ullman, E. F.: Formation of chimeric DNA primer extension products by template switching onto an annealed downstream oligonucleotide. Proc. Natl. Acad. Sci. USA, 93, 2969-2974 (1996).
10. Wang, G. C-Y. and Wang, Y.: The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology, 142, 1107-1114 (1996).
11. Wang, G. C-Y. and Wang, Y.: Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol., 63, 4645-4650 (1997).
12. Judo, M. S. B., Wedel, A. B., and Wilson, C.: Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res., 26, 1819-1825 (1998).
13. Speksnijder, A. G. C. L., Kowalchuk, G. A., De Jong, S., Kline, E., Stephen, J. R., and Laanbroek, H. J.: Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl. Environ. Microbiol., 67, 469-472 (2001).
14. Qiu, X., Wu, L., Huang, H., McDonel, P. E., Palumbo, A. V., Tiedje, J. M., and Zhou, J.: Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol., 67, 880-887 (2001).
15. Shammas, F. V., Heikkilä, R., and Osland, A.: Fluorescence-based method for measuring and determining the mechanisms of recombination in quantitative PCR. Clin. Chim. Acta, 304, 19-28 (2001).
16. von Wintzingerode, F., Göbel, U. B., and Stackebrandt, E.: Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev., 21, 213-229 (1997).
17. Wu, J-H., Liu, W-T., Tseng, I-C., and Cheng, S-S.: Characterization of a 4-methylbenzoate-degrading methanogenic consortium as determined by small-subunit rDNA sequence analysis. J. Biosci. Bioeng., 91, 449-455 (2001).
18. Yoshie, S., Noda, N., Miyano, T., Tsuneda, S., Hirata, A., and Inamori, Y.: Microbial community analysis in the denitrification process of saline-wastewater by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA and the cultivation method. J. Biosci. Bioeng., 92, 346-353 (2001).
19. Liu, W-T., Huang, C-L., Hu, J. Y., Song, L., Ong, S. L., and Ng, W. J.: Denaturing gradient gel electrophoresis polymorphism for rapid 16S rDNA clone screening and microbial diversity study. J. Biosci. Bioeng., 93, 101-103 (2002).
20. Osborn, A. M., Moore, E. R. B., and Timmis, K. N.: An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol., 2, 39-50 (2000).
21. Lueders, T. and Friedrich, M. W.: Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol., 69, 320-326 (2003).
22. Chandler, D. P., Fredrickson, J. K., and Brockman, F. J.: Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol., 6, 475-482 (1997).
23. Ishii, K. and Fukui, M.: Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol., 67, 3753-3755 (2001).
24. Boer, P. H. and Ramamoorthy, J.: How to correct for errors in mRNA quantification by competitive PCR due to heteroduplex formation of amplification products. Cell. Mol. Biol., 43, 841-850 (1997).
25. Learn, B. A. and Grafstrom, R. H.: Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli. J. Bacteriol., 171, 6473-6481 (1989).
26. Carraway, M. and Marinus, M. G.: Repair of heteroduplex DNA molecules with multibase loops in Escherichia coli. J. Bacteriol., 175, 3972-3980 (1993).
27. Sancar, A. and Hearst, J. E.: Molecular matchmakers. Science, 259, 1415-1420 (1993).
28. Thompson, J. R., Marcelino, L. A., and Polz, M. F.: Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res., 30, 2083-2088 (2002).
29. Shuldiner, A. R., Nirula, A., and Roth, J.: Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res., 17, 4409 (1989).
30. Wagner, A., Blackstone, N., Cartwright, P., Dick, M., Misof, B., Snow, P., Wagner, G. P., Bartels, J., Murtha, M., and Pendleton, J.: Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol., 43, 250-261 (1994).
31. Mackay, I. M., Arden, K. E., and Nitsche, A.: Real-time PCR in virology. Nucleic Acids Res., 30, 1292-1305 (2002).
32. Higuchi, R., Fockler, C., Dollinger, G., and Watson, R.: Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Bio/Technology, 11, 1026-1030 (1993).
33. Holland, P. M., Abramson, R. D., Watson, R., and Gelfand, D. H.: Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA, 88, 7276-7280 (1991).
34. Cardullo, R. A., Agrawal, S., Flores, C., Zamecnik, P. C., and Wolf, D. E.: Detection of nucleic acid hybridization by nonradioactive fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA, 85, 8790-8794 (1988).
35. Kurata, S., Kanagawa, T., Yamada, K., Torimura, M., Yokomaku, T., Kamagata, Y., and Kurane, R.: Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer. Nucleic Acids Res., 29, e34 (2001).
36. Torimura, M., Kurata, S., Yamada, K., Yokomaku, T., Kamagata, Y., Kanagawa, T., and Kurane, R: Fluorescence-quenching phenomenon by photo-induced electron transfer between a fluorescent dye and a nucleotide base. Anal. Sci., 17, 155-160 (2001).