Checkerboard DNA-DNA hybridization technology using digoxigenin detection

Methods in Molecular Biology

Volumn 353, Issue , 2007, Pages 39-67

  Gellen, Lisa S ^a   Wall Manning, Glenn M ^a   Sissons, Chris H ^a  

^a NONE

Author keywords

Checkerboard DNA hybridization; Dental caries; Dental plaque; Microbial ecosystem; Species fingerprinting

Indexed keywords

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

BACTERIAL DNA; DIGOXIGENIN;

ARTICLE; DENTAL CARIES; DNA PROBE; GENETIC PROCEDURES; GENETICS; GRAM NEGATIVE BACTERIUM; HUMAN; INSTRUMENTATION; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOLECULAR BIOLOGY; NUCLEIC ACID HYBRIDIZATION; PERIODONTITIS; STANDARD; TOOTH PLAQUE;

DENTAL CARIES; DENTAL PLAQUE; DIGOXIGENIN; DNA PROBES; DNA, BACTERIAL; GRAM-NEGATIVE BACTERIA; HUMANS; MOLECULAR BIOLOGY; MOLECULAR PROBE TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; PERIODONTITIS; REFERENCE STANDARDS;

EID: 34247217281     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-229-7:39     Document Type: Article

References (29)

1. Ward, B. B. (2002) How many species of procaryotes are there? Proc. Nat. Acad. Sci. USA 99, 10, 234-10, 236.
2. Paster, B. J., Boches, S. K., Galvin, J. L., et al. (2001) Bacterial diversity in human subgingival plaque. J. Bacteriol. 183, 3770-3783.
3. Becker, M. R., Paster, B. J., Leys, E. J., et al. (2002) Molecular analysis of bacterial species associated with childhood caries. J. Clin. Microbiol. 40, 1001-1009.
4. Brinig, M. M., Lepp, P. W., Ouverney, C. C., Armitage, G. C., and Relman, D. A. (2003) Prevalence of bacteria of division TM7 in human subgingival plaque and their asociation with disease. Appl. Environ. Microbiol. 69, 1687-1694.
5. Harper-Owen, R., Dymock, D., Booth, V., Weightman, A. J., and Wade, W. G. (1999) Detection of unculturable bacteria in periodontal health and disease by PCR. J. Clin. Microbiol. 37, 1469-1473.
6. Torsvik, V., Øveras, L., and Thingstad, T. (2002) Prokaryotic diversity-magnitude, dynamics and controlling factors. Science 296, 1064-1066.
7. Osborn, A. M., Moore, E. R. B., and Timmis, K. N. (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2, 39-50.
8. Muyzer, G., De Wall, E. C., and Unterlinden, A. G. (1993) Profiling of complex microbial population by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified genes coding for 16S RNA. Appl. Environ. Microbiol. 59, 695-700.
9. Munson, M. A., Bannerjee, A., Watson, T. F., and Wade, W G. (2004) Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol. 42, 3023-3029.
10. Anderson, S. A., Sissons, C. H., Coleman, M. J., and Wong, L. (2002) Application of carbon-source utilisation patterns to measue the metabolic similarity of complex dental plaque biofilm microcosms. Appl. Environ. Microbiol. 68, 5779-5783.
11. Roche Applied Science. (2000) The DIG Application Manual for Filter Hybridization. Available at: http://www.roche-applied-science.com/.
12. Socransky, S. S., Smith, C., Martin, L., Paster, B. J., Dewhirst, F. E., and Levin, A. E. (1994) "Checkerboard" DNA-DNA hybridization. Biotechniques 17, 788-792.
13. Socransky, S. S., Haffajee, A. D., Cugini, M. A., Smith, C., and Kent, R. L. (1998) Microbial complexes in subgingival plaque. J. Clin. Periodontol. 25, 134-144.
14. Socransky, S. S., Haffajee, A. D., Smith, C., et al. (2004) The use of checkerboard DNA:DNA hybridization to study complex microbial ecosystems. Oral Microbiol. Immunol. 19, 352-362.
15. Socransky, S. S. and Haffajee, A. D. (2002) Dental biofilms: difficult therapeutic targets. Periodontology 2000 28, 12-55.
16. Haffajee, A. D., Socransky, S. S., Feres, M., and Ximenez-Fyvie, L. A. (1999) Plaque microbiology in health and disease, in Dental Plaque Revisited (Newman, H. N. and Wilson, M., eds.), Bioline, Cardiff, UK, pp. 255-282.
17. Wall-Manning, G. and Sissons, C. H. (2002) The effect of regrowth after treatment with antimicrobial on the species composition of dental plaque microcosms, in New Zealand Microbiological Society Conference, Christchurch, New Zealand, p. 156.
18. Sissons, C. H., Wong, L., and An, Y. H. (2000) Culture and analysis of bacterial biofilms, in Handbook for Studying Bacterial Adhesion (An, Y. H. and Friedman, R. J., eds.), Humana, Totowa, NJ, pp. 133-169.
19. Sissons, C. H. (1997) Artificial dental plaque biofilm model systems. Adv. Dent. Res. 11, 110-126.
20. Sissons, C. H., Cutress, T. W., Hoffman, M. P., and Wakefield, J. S. J. (1991) A multi-station dental plaque microcosm (artificial mouth) for the study of plaque growth, metabolism, pH and mineralisation. J. Dent. Res. 70, 1409-1416.
21. Tanner, A., Maiden, M. F. J., Macuch, P. J., Murray, L. L., and Kent, R. L. (1998) Microbiota of health, gingivitis and initial periodontitis. J. Clin. Periodontal. 25, 134-144.
22. Smith, G. L. F., Sockransky, S. S., and Smith, C. M. (1989) Rapid method for the purification of DNA from subgingival organisms. Oral Microbiol. Immunol. 4, 47-51.
23. Wall-Manning, G. M., Sissons, C. H., Anderson, S. A., and Lee, M. (2002) Checkerboard DNA-DNA hybridisation technology focussed on the analysis of Gram-positive cariogenic bacteria. J. Microbiol. Meth. 51, 301-311.
24. Ludwig, J. A. and Reynolds, J. F. (eds.) (1988) Statistical Ecology, John Wiley and Sons, New York.
25. Ximenez-Fyvie, L. A., Haffajee, A. D., Martin, L., Tanner, A., Macuch, P., and Socransky, S. S. (1999) Identification of oral Actinomyces species using DNA probes. Oral Microbiol. Immunol. 14, 257-265.
26. Bjournson, A. J. and Cooper, J. E. (1996) Subtraction hybridization for the isolation of strain-specific Rhizobium DNA probes. Meth. Mol. Biol. 50, 145-154.
27. Janda, J. M. and Abbott, S. A. (2002) Bacterial identification for publication: when is enough enough? J. Clin. Microbiol. 46, 1887-1891.
28. Paster, B. J., Bartoszyk, I. M., and Dewhirst, F. E. (1998) Identification of oral streptococci using PCR-based reverse-capture, checkerboard hybridization. Meth. Cell Sci. 20, 223-231.
29. Socransky, S. S., Haffajee, A. D., Smith, C., Martin, L., Haffajee, J. A., Uzel, N. G., and Goodson, J. M. (2004) Use of Checkerboard DNA-DNA hybridization to study complex microbial ecosystems. Oral Microbiol. Immunol. 19, 352-362.