Gradient decrement of annealing time can improve PCR with fluorescent-labeled primers

Journal of Bioscience and Bioengineering

Volumn 110, Issue 4, 2010, Pages 500-504

  Yu, Su Lin ^a   Tang, Yue Qin ^a   Li, Yan ^a   Zhang, Husen ^b   Wu, Xiao Lei ^a  

^a PEKING UNIVERSITY   (China)

^b University of Central Florida   (United States)

Author keywords

Fluorescence labeling; Gradient decreasing annealing time PCR program; Microbial community analysis; PCR amplification efficiency; Terminal restriction fragment length polymorphism (T RFLP)

Indexed keywords

FLUORESCENCE LABELING; GRADIENT-DECREASING ANNEALING TIME PCR PROGRAM; MICROBIAL COMMUNITY ANALYSIS; PCR AMPLIFICATION; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS;

ANNEALING; CLONING; MOLECULAR WEIGHT; POLYMORPHISM;

FLUORESCENCE;

FLUORESCENT DYE;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA TEMPLATE; FLUORESCENCE; MICROBIAL COMMUNITY; MOLECULAR WEIGHT; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SOIL MICROFLORA; THERMODYNAMICS;

DNA PRIMERS; FLUORESCENT DYES; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 77956648371     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2010.05.005     Document Type: Article

References (34)

1. Liu W., Marsh T., Cheng H., Forney L. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 1997, 63:4516-4522.
2. Wu X.L., Chin K.J., Conrad R. Effect of temperature stress on the structure and function of the methanogenic archaeal community in a rice field soil. FEMS Microbiol. Ecol. 2002, 39:211-218.
3. Singh B.K., Nazaries L., Munro S., Anderson I.C., Campbell C.D. Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community. Appl. Environ. Microbiol. 2006, 72:7278-7285.
4. Wu X.L., Friedrich M.W., Conrad R. Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils. Environ. Microbiol. 2006, 8:394-404.
5. Blackwood C.B., Paul E.A. Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biol. Biochem. 2003, 35:1245-1255.
6. Abdo Z., Schüette U.M.E., Bent S.J., Williams C.J., Forney L.J., Joyce P. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 2006, 8:929-938.
7. Paul D., Pandey G., Meier C., Roelof van der Meer J., Jain R.K. Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation. FEMS Microbiol. Ecol. 2006, 57:116-127.
8. Briones A.M., Daugherty B.J., Angenent L.T., Rausch K.D., Tumbleson M.E., Raskin L. Microbial diversity and dynamics in multi- and single-compartment anaerobic bioreactors processing sulfate-rich waste streams. Environ. Microbiol. 2007, 9:93-106.
9. Moeseneder M.M., Winter C., Arrieta J.M., Herndl G.J. Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J. Microbiol. Meth. 2001, 44:159-172.
10. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
11. Schwieger F., Tebbe C.C. A new approach to utilize PCR-single-strand- conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl. Environ. Microbiol. 1998, 64:4870-4876.
12. Lagace L., Pitre M., Jacques M., Roy D. Identification of the bacterial community of maple sap by using amplified ribosomal DNA (rDNA) restriction analysis and rDNA sequencing. Appl. Environ. Microbiol. 2004, 70:2052-2060.
13. Bruce K.D. Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 1997, 63:4914-4919.
14. Lueders T., 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. 2003, 69:320-326.
15. Farrelly V., Rainey F.A., Stackebrandt E. 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. 1995, 61:2798-2801.
16. Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 1996, 62:625-630.
17. Wang G.C., 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. 1997, 63:4645-4650.
18. Hansen M.C., Tolker-Nielsen T., Givskov M., Molin S. (1998) Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 1998, 26:141-149.
19. Danovaro R., Luna G.M., Dell'Anno A., Pietrangeli B. Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl. Environ. Microbiol. 2006, 72:5982-5989.
20. Pandey J., Ganesan K., Jain R.K. Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J. Microbiol. Meth. 2007, 68:633-638.
21. Moré M.I., Herrick J.B., Silva M.C., Ghiorse W.C., Madsen E.L. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 1994, 60:1572-1580.
22. Henckel T., Friedrich M., Conrad R. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 1999, 65:1980-1990.
23. Grosskopf R., Janssen P.H., Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 1998, 64:960-969.
24. Dojka M.A., Hugenholtz P., Haack S.K., Pace N.R. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 1998, 64:3869-3877.
25. Park S., Ku Y.K., Seo M.J., Kim D.Y., Yeon J.E., Jeong S.-C., Yoon W.K., Kim H.M. The characterization of bacterial community structure in the rhizosphere of watermelon (Citrullus vulgaris SCHARD.) using culture-based approaches and terminal fragment length polymorphism (T-RFLP). Appl. Soil Ecol. 2006, 33:79-86.
26. Gilmour L.M.R., Macleod K.G., McCaig A., Gullick W.J., Smyth J.F., Langdon S.P. Expression of erbB-4/HER-4 growth factor receptor isoforms in ovarian cancer. Cancer Res. 2001, 61:2169-2176.
27. 3CL1 production by human airway smooth muscle cells: induction by IFN- γ and TNF-α and regulation by TGF-β and corticosteroids. Am. J. Physiol. Lung Cell. Mol. Physiol. 2004, 287:L1230-L1240.
28. Liu Y., Zhang X. Expression of cellular oncogene Bcl-xL prevents coronavirus-induced cell death and converts acute infection to persistent infection in progenitor rat oligodendrocytes. J. Virol. 2005, 79:47-56.
29. Osborn A.M., Moore E.R.B., 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. 2000, 2:39-50.
30. Chandler D.P., Fredrickson J.K., Brockman F.J. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 1997, 6:475-482.
31. Acinas S.G., Sarma-Rupavtarm R., Klepac-Ceraj V., Polz M.F. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 2005, 71:8966-8969.
32. Sipos R., Szekely A.J., Palatinszky M., Revesz S., Marialigeti K., Nikolausz M. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targeting bacterial community analysis. FEMS Microbiol. Ecol. 2007, 60:341-350.
33. Zhang Q. Statistical Physics (the third part of theoretical physics) 2004, 386-388. Science Press, Beijing, China.
34. Wintzingerode F.V., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 1997, 21:213-229.