Evaluation of a new fluorimetric DNA-DNA hybridization method

Canadian Journal of Microbiology

Volumn 57, Issue 3, 2011, Pages 250-255

  Loveland Curtze, Jennifer ^a   Miteva, Vanya I ^a   Brenchley, Jean E ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

DNA DNA hybridization; Fluorescence; SYBR Green I

Indexed keywords

RNA 16S;

ANALYTIC METHOD; DNA DENATURATION; DNA DNA HYBRIDIZATION; FLUOROMETRY; GENE SEQUENCE; NOTE; PRIORITY JOURNAL; RENATURATION; SCREENING TEST;

BACTERIA; BASE COMPOSITION; BASE SEQUENCE; DNA, BACTERIAL; FLUOROMETRY; NUCLEIC ACID HYBRIDIZATION; ORGANIC CHEMICALS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS);

EID: 79952239284     PISSN: 00084166     EISSN: 14803275     Source Type: Journal    
DOI: 10.1139/W10-121     Document Type: Note

References (26)

1. AL. In Bergey's manual of systematic bacteriology. Vol. 2. Williams & Wilkins, Baltimore, Md., USA. pp. 1105-1139.
2. De Ley, J., Cattoir, H., and Reynaerts, A. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12(1): 133-142. doi:10.1111/j.1432-1033. 1970.tb00830.x. PMID:4984993.
3. Fox, G.E., Wisotzkey, J.D., and Jurtshuk, P., Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42(1): 166-170. doi:10.1099/00207713-42-1-166. PMID:1371061.
4. Gonzalez, J.M., and Saiz-Jimenez, C. 2002. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4(11): 770-773. doi:10.1046/j.1462-2920.2002.00362.x. PMID: 12460286.
5. Gonzalez, J.M., and Saiz-Jimenez, C. 2005. A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles, 9(1): 75-79. doi:10.1007/s00792-004-0417-0. PMID:15351875.
6. Heyrman, J., Verbeeren, J., Schumann, P., Swings, J., and De Vos, P.D. 2005. Six novel Arthrobacter species isolated from deteriorated mural paintings. Int. J. Syst. Evol. Microbiol. 55(4): 1457-1464. doi:10.1099/ijs.0.63358-0. PMID:16014466.
7. Huß, V.A.R., Festl, H., and Schleifer, K.H. 1983. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol. 4: 184-192.
8. Jakava-Viljanen, M., Murros, A., Palva, A., and Björkroth, K.J. 2008. Lactobacillus sobrius Konstantinov et al. 2006 is a later synonym of Lactobacillus amylovorus Nakamura 1981. Int. J. Syst. Evol. Microbiol. 58(4): 910-913. doi:10.1099/ijs.0.65432-0.
9. AL. In Bergey's manual of systematic bacteriology. Vol. 2. Williams & Wilkins, Baltimore, Md., USA. pp. 1288-1301.
10. Kim, K.K., Lee, K.C., Oh, H.-M., and Lee, J.-S. 2008. Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. Int. J. Syst. Evol. Microbiol. 58(3): 533-537. doi:10.1099/ijs.0. 65491-0. PMID:18319450.
11. Lang, E., Swiderski, J., Stackebrandt, E., Schumann, P., Spröer, C., and Sahin, N. 2007. Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock. Int. J. Syst. Evol. Microbiol. 57(11): 2618-2622. doi:10.1099/ijs.0.65163-0. PMID:17978229.
12. Loveland-Curtze, J., Miteva, V.I., and Brenchley, J.E. 2009. Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. Int. J. Syst. Evol. Microbiol. 59(6): 1272-1277. doi:10.1099/ijs.0.001685-0. PMID:19502300.
13. Loveland-Curtze, J., Miteva, V., and Brenchley, J. 2010. Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles, 14(1): 61-69. doi:10.1007/s00792-009-0287-6. PMID:19888547.
14. Mandel, M., and Marmur, J. 1968. Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol. 12(B): 195-206.
15. Mehlen, A., Goeldner, M., Ried, S., Stindl, S., Ludwig, W., and Schleifer, K.-H. 2004. Development of a fast DNA-DNA hybridization method based on melting profiles in microplates. Syst. Appl. Microbiol. 27(6): 689-695. doi:10.1078/0723202042369875. PMID:15612626.
16. Nakamura, L.K. 1984. Bacillus psychrophilus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 34(2): 121-123. doi:10.1099/00207713-34-2-121.
17. Padonou, S.W., Schillinger, U., Nielsen, D.S., Franz, C.M.A.P., Hansen, M., Hounhouigan, J.D., et al. 2010. Weissella beninensis sp. nov., a motile lactic acid bacterium from submerged cassava fermentations, and emended description of the genus Weissella. Int. J. Syst. Evol. Microbiol. 60(9): 2193-2198. doi:10.1099/ijs.0.014332-0. PMID:19897612.
18. Rosselló-Mora, R. 2006. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In Molecular identification, systematics, and population structure of prokaryotes. Edited by E. Stackebrandt. Springer-Verlag, Berlin Heidelberg, Germany. pp. 23-50.
19. Rosselló-Mora, R., and Amann, R. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25(1): 39-67. doi:10.1016/ S0168-6445(00)00040-1. PMID:11152940.
20. Stackebrandt, E., and Fiedler, F. 1979. DNA-DNA homology studies among strains of Arthrobacter and Brevibacterium. Arch. Microbiol. 120(3): 289-295. doi:10.1007/BF00423078. PMID: 443991.
21. Tindall, B.J., Rosselló-Móra, R., Busse, H.-J., Ludwig, W., and Kämpfer, P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60(1): 249-266. doi:10.1099/ijs.0.016949-0. PMID:19700448.
22. Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37(4): 463-464. doi:10.1099/00207713-37-4-463.
23. Weon, H.-Y., Kim, B.-Y., Yoo, S.-H., Kwon, S.-W., Stackebrandt, E., and Go, S.-J. 2008. Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov., isolated from soil samples from Jeju, Korea. Int. J. Syst. Evol. Microbiol. 58(2): 470-473. doi:10.1099/ijs.0.65295-0. PMID:18218951.
24. Westerberg, K., Elväng, A.M., Stackebrandt, E., and Jansson, J.K. 2000. Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol. Int. J. Syst. Evol. Microbiol. 50(Pt 6): 2083-2092. PMID:11155983.
25. Xu, H.-X., Kawamura, Y., Li, N., Zhao, L., Li, T.-M., Li, Z.-Y., et al. 2000. A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube. Int. J. Syst. Evol. Microbiol. 50(Pt 4): 1463-1469. PMID:10939651.
26. Zipper, H., Brunner, H., Bernhagen, J., and Vitzthum, F. 2004. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 32(12): e103. doi:10.1093/nar/gnh101. PMID:15249599.