Bias in template-to-product ratios in multitemplate PCR

Applied and Environmental Microbiology

Volumn 64, Issue 10, 1998, Pages 3724-3730

  Polz, Martin F ^a,b   Cavanaugh, Colleen M ^a  

^a HARVARD UNIVERSITY   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; DNA TEMPLATE; ESCHERICHIA COLI; GENE NUMBER; NONHUMAN; POLYMERASE CHAIN REACTION; SITE DIRECTED MUTAGENESIS; VIBRIO;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; VIBRIO;

EID: 0031711754     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.10.3724-3730.1998     Document Type: Article

References (31)

1. Alm, W. E., D. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide database project. Appl. Environ. Microbiol. 62:3557-3559.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Arnheim, N., and H. Erlich. 1992. Polymerase chain reaction strategy. Annu. Rev. Biochem. 61:131-156.
4. Chandler, D. P., J. K. Fredrickson, and F. J. Brockman. 1997. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:475-483.
5. Erlich, H. A., D. Gelfand, and J. J. Sninsky. 1991. Recent advances in the polymerase chain reaction. Science 252:1643-1651.
6. 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.
7. Head, I. M., J. R. Saunders, and R. W. Pickup. 1998. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1-21.
8. Hektor, H. Personal communication.
9. Jarrell, K. F., D. Faguy, A. M. Herbert, and M. L. Kalmkoff. 1991. A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can J. Microbiol. 38:65-68.
10. Karrer, E. E., J. E. Lincoln, S. Hogenhout, A. B. Bennet, R. M. Bostock, B. Martineau, W. J. Lucas, D. G. Gilchrist, and D. Alexander. 1995. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc. Natl. Acad. Sci. USA 92:3814-3818.
11. Kerkhof, L., and M. Speck. 1997. Ribosomal RNA gene dosage in marine bacteria. Mol. Mar. Biol. Biotechnol. 6:260-267.
12. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. Wiley & Sons, Chichester, United Kingdom.
13. Lee, S.-Y., J. Bollinger, D. Bezdicek, and A. Ogram. 1996. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62:3787-3793.
14. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1996. The Ribosomal Database Project (RDP). Nucleic Acids Res. 24:82-85.
15. Mutter, G., and K. A. Boynton. 1995. PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies. Nucleic Acids Res. 23:1411-1418.
16. 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.
17. Norrman, B., U. L. Zweifel, C. S. Hopkinson, and B. Fry. 1995. Production and utilization of dissolved organic carbon during an experimental diatom bloom. Limnol. Oceanogr. 40:898-907.
18. Polz, M. F., E. V. Odintsova, and C. M. Cavanaugh. 1996. Phylogenetic relationships of the filamentous sulfur bacterium Thiothrix ramosa based on 16S rRNA sequence analysis. Int. J. Syst. Bacteriol. 46:94-97.
19. Polz, M. F., and C. M. Cavanaugh. 1997. A simple method for the quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl. Environ. Microbiol. 63:1028-1033.
20. Raskin, L., L. K. Poulsen, D. R. Noguera, B. E. Rittmann, and D. A. Stahl. 1994. Quantification of methanogenic groups in anaerobic biological reactors by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 60: 1241-1248.
21. Raskin, L., J. M. Stromley, B. E. Rittmann, and D. A. Stahl. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60:1232-1240.
22. 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.
23. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
24. Sardelli, A. D. 1993. Plateu effect - understanding PCR limitations. Amplifications 9:1-5.
25. Splinter, P. L., and M. A. Rott. 1997. Physical and genetic map of Vibrio fischeri MJ1, abstr. H-212, p. 636. In Abstracts of the 97th General Meeting of the American Society for Microbiology 1997. American Society for Microbiology, Washington, D.C.
26. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
27. Steffan, R. J., and R. M. Atlas. 1991. Polymerase chain reaction: applications in environmental microbiology. Annu. Rev. Microbiol. 45:137-161.
28. Suzuki, M., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
29. Torsvik, V., J. Goksøyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
30. Wagner, A., N. Blackstone, P. Cartwright, M. Dick, B. Misof, P. Snow, G. P. Wagner, J. Bartels, M. Murtha, and J. Pendleton. 1994. Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43:250-261.
31. 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.