Novel perspectives to purify genomic DNA from high humic acid content and contaminated soils

Separation and Purification Technology

Volumn 75, Issue 1, 2010, Pages 81-86

  Técher, Didier ^a   Martinez Chois, Claudia ^a   D'Innocenzo, Marielle ^a   Laval Gilly, Philippe ^a   Bennasroune, Amar ^a   Foucaud, Laurent ^a   Falla, Jairo ^a  

^a Faculté des Sciences et Technologies   (France)

Author keywords

DNA purification; Humic acid; Rapid method; Soils; Vitamins

Indexed keywords

BACTERIAL DIVERSITY; CETYLTRIMETHYLAMMONIUM BROMIDE; CO-PRECIPITATED; CONTAMINATED SOILS; DNA EXTRACTS; DNA ISOLATION; DNA PURIFICATION; GENOMIC DNA; HIGH ORGANIC; HIGH PURITY; HIGH QUALITY; HUMIC ACID; LYSIS BUFFER; MOLECULAR DIVERSITY; PCR AMPLIFICATION; POLLUTED SOILS; POTASSIUM CHLORIDE; PURIFICATION METHOD; RAPID METHOD; SALTING-OUT; SHORT PROCESSING TIME; SOIL SAMPLE; SOIL WASHING; THIAMINE HYDROCHLORIDE;

AMPLIFICATION; BACTERIOLOGY; BROMINE COMPOUNDS; CHLORINE COMPOUNDS; DNA; ENZYME IMMOBILIZATION; EXTRACTION; GENES; NUCLEIC ACIDS; NUTRITION; OPTIMIZATION; ORGANIC ACIDS; POTASSIUM; PURIFICATION; RECOVERY; SOILS; VITAMINS;

SOIL POLLUTION;

BACTERIA (MICROORGANISMS);

EID: 77956440758     PISSN: 13835866     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.seppur.2010.07.014     Document Type: Article

References (29)

1. C. Desai, and D. Madamwar Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments Bioresour. Technol. 98 2007 761 768
2. D Thakuria, O. Schmidt, M. Mac Siúrtáin, D. Egan, and F.M. Doohan Importance of DNA quality in comparative soil microbial community structure analyses Soil Biol. Biochem. 40 2008 1390 1403
3. J. Rajendhran, and P. Gunasekaran Strategies for accessing soil metagenome for desired applications Biotechnol. Adv. 26 2008 576 590
4. C.C. Tebbe, and W. Vahjen 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 1993 2657 2665
5. Y.L. Tsai, and B.H. Olson Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction Appl. Environ. Microbiol. 58 1992 2292 2295
6. C.C. Young, R.L. Burghoff, L.G. Keim, V. Minak-Bernero, J.R. Lute, and S.M. Hinton Polyvinylpyrrolidone-agarose gel electrophoresis purification of polymerase chain reaction-amplifiable DNA from soils Appl. Environ. Microbiol. 59 1993 1972 1974
7. F. von Wintzingerode, U.B. Gobel, and E. Stackebrandt Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol. Rev. 21 1997 213 229
8. M. Krsek, and E.M. Wellington Comparison of different methods for the isolation and purification of total community DNA from soil J. Microbiol. Methods 39 1999 1 16
9. M.A. Heitkamp, J.P. Freeman, D.W. Miller, and C.E. Cerniglia Pyrene degradation by a Mycobacterium sp.: identification of ring oxidation and ring fission products Appl. Environ. Microbiol. 54 1988 2556 2565
10. D. Persoh, S. Theuerl, F. Buscot, and G. Rambold Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil J. Microbiol. Methods 75 2008 19 24
11. M. Sagova-Mareckova, L. Cermak, J. Novotna, K. Plhackova, J. Forstova, and J. Kopecky Innovative methods for soil DNA purification tested in soils with widely differing characteristics Appl. Environ. Microbiol. 74 2008 2902 2907
12. J.M. Dunbar, P.C. Stark, T.W. Robison, R.A. Lazarin, Methods and compositions for the removal of nucleic acid amplification inhibitors, United States Patent Application US 2007/0,065,841 A1, United States, 2007.
13. H. Burgmann, M. Pesaro, F. Widmer, and J. Zeyer A strategy for optimizing quality and quantity of DNA extracted from soil J. Microbiol. Methods 45 2001 7 20
14. A. Frostegard, S. Courtois, V. Ramisse, S. Clerc, D. Bernillon, F. Le Gall, P. Jeannin, X. Nesme, and P. Simonet Quantification of bias related to the extraction of DNA directly from soils Appl. Environ. Microbiol. 65 1999 5409 5420
15. M. Harry, B. Gambier, Y. Bourezgui, and E. Garnier-Sillam Evaluation of purification procedures for DNA extracted from organic rich samples: interference with humic substances Analysis 27 1999 439 442
16. Y. Matsuo Formation of Schiff bases of pyridoxal phosphate. Reaction with metal ions1 J. Am. Chem. Soc. 79 2002 2011 2015
17. N. Fortin, D. Beaumier, K. Lee, and C.W. Greer Soil washing improves the recovery of total community DNA from polluted and high organic content sediments J. Microbiol. Methods 56 2004 181 191
18. D. Moreira Efficient removal of PCR inhibitors using agarose-embedded DNA preparations Nucleic Acids Res. 26 1998 3309 3310
19. F.M. Lakay, A. Botha, and B.A. Prior Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils J. Appl. Microbiol. 102 2007 265 273
20. G. Muyzer, E.C. de Waal, and A.G. Uitterlinden 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 1993 695 700
21. V.C. Sheffield, D.R. Cox, L.S. Lerman, and R.M. Myers Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes Proc. Natl. Acad. Sci. U.S.A. 86 1989 232 236
22. P.E. Olson, A. Castro, M. Joern, N.M. DuTeau, E. Pilon-Smits, and K.F. Reardon Effects of agronomic practices on phytoremediation of an Aged PAH-contaminated soil J. Environ. Qual. 37 2008 1439 1446
23. I. Janse, J. Bok, and G. Zwart A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis J. Microbiol. Methods 57 2004 279 281
24. Y.C. Han, C.Z. Teng, Z.L. Hu, and Y.C. Song An optimal method of DNA silver staining in polyacrylamide gels Electrophoresis 29 2008 1355 1358
25. A.A. Booth, R.G. Khalifah, and B.G. Hudson Thiamine pyrophosphate and pyridoxamine inhibit the formation of antigenic advanced glycation end-products: comparison with aminoguanidine Biochem. Biophys. Res. Commun. 220 1996 113 119
26. R.G. Khalifah, J.W. Baynes, and B.G. Hudson Amadorins: novel post-Amadori inhibitors of advanced glycation reactions Biochem. Biophys. Res. Commun. 257 1999 251 258
27. M.C. Brum, and J.F. Oliveira Removal of humic acid from water by precipitate flotation using cationic surfactants Miner. Eng. 20 2007 945 949
28. H.Y. Song, S.W. Oh, S.D. Moon, and Y.S. Kang Spectroscopic study on the precipitation of sodium alkyl sulfate with cetylpyridinium chloride J. Colloid Interface Sci. 314 2007 683 688
29. L. Monferrer-Pons, M.E. Capella-Peiró, M. Gil-Agustí, and J. Esteve-Romero Micellar liquid chromatography determination of B vitamins with direct injection and ultraviolet absorbance detection J. Chromatogr. A 984 2003 223 231