Optimization of Annealing Temperature to Reduce Bias Caused by a Primer Mismatch in Multitemplate PCR

Applied and Environmental Microbiology

Volumn 67, Issue 8, 2001, Pages 3753-3755

  Ishii, Kousuke ^a   Fukui, Manabu ^a  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RIBOSOME DNA; RNA 16S;

AGAR GEL ELECTROPHORESIS; ARTICLE; BASE MISPAIRING; DNA TEMPLATE; GENETICS; METHODOLOGY; MICROCOCCUS LUTEUS; PEDIOCOCCUS; POLYMERASE CHAIN REACTION; TEMPERATURE;

BASE PAIR MISMATCH; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, AGAR GEL; MICROCOCCUS LUTEUS; PEDIOCOCCUS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; TEMPERATURE; TEMPLATES, GENETIC;

EID: 0035432220     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.8.3753-3755.2001     Document Type: Article

References (14)

1. Dutton, C. M., C. Paynton, and S. S. Sommer. 1993. General method for amplifying regions of very high G + C content. Nucleic Acids Res. 21:2953-2954.
2. Farrelly, V., F. A. Rainey, and E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:2798-2801.
3. Felske, A., A. D. L. Akkermans, and W. M. De Vos. 1998. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl. Environ. Microbiol. 64:4581-4587.
4. Fogel, G. B., C. R. Collins, J. Li, and C. F. Brunk. 1999. Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microb. Ecol. 38:93-113.
5. Ishii, K., M. Fukui, and S. Takii. 2000. Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J. Appl. Microbiol. 89:768-777.
6. Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt. 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66:1328-1333.
7. Maidak, B. L., J. R. Cole, C. T. Parker, Jr., G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDF (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
8. Muyzer, G., T. Brinkhoff, U. Nübel, C. Santegoeds, H. Schäfer, and C. Wawer. 1997. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-27. In A. D. L. Akkermans, J. D. V. Elsas, and F. J. D. Bruijn (ed.), Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, The NetherlandsF. J..
9. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
10. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
11. Reysenbach, A.-L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
12. Strunk, O., W. Ludwig, O. Gross, B. Reichel, N. Stuckmann, M. May, B. Nonhoff, M. Lenke, T. Ginhart, A. Vilbig, and R. Westran. 1998. ARB - a software environment for sequence data. Technische Universität München, Munich, Germany.
13. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
14. Zheng, D., E. W. Alm, D. A. Stahl, and L. Raskin. 1996. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl. Environ. Microbiol. 62:4504-4513.