Inhibition of DNA Polymerases Used in Q-PCR by Structurally Different Soil-Derived Humic Substances

Geomicrobiology Journal

Volumn 30, Issue 8, 2013, Pages 675-681

  Albers, Christian Nyrop ^a   Jensen, Anders ^a   Bælum, Jacob ^a   Jacobsen, Carsten Suhr ^a,b  

^a GEOLOGICAL SURVEY OF DENMARK AND GREENLAND   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

BSA; DNA polymerase; fulvic acids; humic acids; inhibition; Q PCR

Indexed keywords

DNA; FULVIC ACID; HUMIC ACID; HUMIC SUBSTANCE; INHIBITION; POLYMERASE CHAIN REACTION;

EID: 84879952254     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490451.2012.758193     Document Type: Article

References (24)

1. Albers, C N, Banta, G T, Jacobsen, O S and Hansen, P E. 2008. Characterization and structural modelling of humic substances in field soil displaying significant differences from previously proposed structures. Eur J Soil Sci, 59: 693 - 705.
2. Albers, C N and Hansen, P E. 2010. 13C-NMR Chemical shift databases as a quick tool to evaluate structural models of humic substances. Open Magn Reson J, 3: 96 - 105.
3. Bælum, J, Henriksen, T, Hansen, H CB and Jacobsen, C S. 2006. Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene. Appl Environ Microbiol, 72: 1476 - 1486.
4. Bælum, J and Jacobsen, C S. 2009. TaqMan probe-based real-time PCR assay for detection and discrimination of class I, II, and III tfdA genes in soils treated with phenoxy acid herbicides. Appl Environ Microbiol, 75: 2969 - 2972.
5. Bælum, J, Nicolaisen, M H, Holben, W E, Strobel, B W, Sørensen, J and Jacobsen, C S. 2008. Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil. The ISME Journal, 2: 677 - 687.
6. Hata, A, Katayama, H, Kitajima, M, Visvanathan, C, Nol, C and Furumai, H. 2011. Validation of internal controls for nucleic acid extraction and amplification of enteric viruses in water samples. Appl Environ Microbiol, 77: 4336 - 4343.
7. Hayes, M and Malcolm, R L. 2001. " Considerations of compositions and aspects of the structures of humic acids ". In Humic Substances and Chemical Contaminants, Edited by: Clapp, C, Hayes, M, Senesi, N, Bloom, P R and Jardine, P. p3 - 40. Madison, WI: Soil Science Society of America.
8. Howeler, M, Ghiorse, W C and Walker, L. 2003. A quantitative analysis of DNA extraction and purification from compost. J Microbiol Meth, 54: 37 - 45.
9. Jacobsen, C. 1995. Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Appl Environ Microbiol, 61: 3347 - 3352.
10. Kennedy, S and Oswald, N. 2011. PCR Troubleshooting and Optimization: The Essential Guide, Norfolk, UK: Caister Academic Press.
11. Kermekchiev, M B, Kirilova, L I, Vail, E E and Barnes, W M. 2009. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res, 37: e40
12. Kreader, CA. 1996. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol, 62: 1102 - 1106.
13. Lakay, F M, Botha, A and Prior, B A. 2007. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. J Appl Microbiol, 102: 265 - 273.
14. Lindberg, E, Albrechtsen, H-J and Jacobsen, C S. 2007. Inhibition of real-time PCR in DNA extracts from aquifer sediment. Geomicrobiol J, 24 343 - 352.
15. Malcolm, R L and MacCarthy, P. 1986. Limitations in the use of commercial humic acids in water and soil research. Environ Sci Technol, 20: 904 - 911.
16. Miller, DN. 2001. Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soils and sediments. J Microbiol Meth, 44: 49 - 58.
17. Opel, K L, Chung, D and McCord, B R. 2010. A study of PCR inhibition mechanisms using real time PCR. J Forens Sci, 55: 25 - 33.
18. Schneider, S, Enkerli, J and Widmer, F. 2009. A generally applicable assay for the quantification of inhibitory effects on PCR. J Microbiol Meth, 78: 351 - 353.
19. Sierra, M MD, Giovanela, M, Parlanti, E and Soriano-Sierra, E J. 2005. Fluorescence fingerprint of fulvic and humic acids from varied origins as viewed by single-scan and excitation/emission matrix techniques. Chemosphere, 58: 715 - 733.
20. Stevenson, F. 1994. Humus Chemistry, 2nd ed, New York: Wiley-VCH.
21. 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, 29: 1467 - 1472.
22. Tebbe, C C and Vahjen, W. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol, 59: 2657 - 2665.
23. Tipping, E. 2005. Cation Binding by Humic Substances, Cambridge, U.K.: Cambridge University Press.
24. Tsai, Y L and Olson, B H. 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Appl Environ Microbiol, 58: 754 - 757.