In silico Double Digestion Selective Label (DDSL) fingerprinting

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Double Digestion Selective Label (DDSL) fingerprinting is new typing technique described by Terletsky et al. (2008). DDSL is an implementation of Subtracted Restriction Fingerprinting technique (SRF; Terletsky et al., 2004). A simulation tool for SRF is also available.

Briefly, genomic DNA is extracted from fresh cultures of the microorganisms to be searched. DNA is digested with two endonucleases: a rare cutting enzyme (typically a PFGE one), and a frequent cutting one. After digestion, the overhang ends yielded by the rare cutting endonuclease as labeled with biotin. Overhang end (or blunt ends) yielded by frequent cutting enzyme will not be labeled. For detection of labeled bands, electrophoresis and blotting is performed, and finally, labeled bands are detected using standard methods. .

In silico DDSL fingerprinting allows simulating this technique, so that feasibility of the technique may be searched before trying to perform the wet experiments. A suggestion tool for DDSL has been developed that allows finding combinations of endonucleases that may be used to perform this technique against up-to-date sequenced genomes. The suggestion tool may be used as a reference, but the combinations of endonucleases yielded by the service must be considered as a "computer" suggestion, and may not be useful for wet experiments.

When the programs for simulation of Double Digest Selective Label (DDSL) or the associated databased are used, please cite this paper.

Terletskiy, V., Tyshchenko, V., Matinez-Ballesteros, I., Garaizar, J., and Bikandi, J. Validation of Double Double Digest Selective Label for sequenced prokaryotic genomes. Bioinformatics 2009; in press.doi.


Figure 1: example of bands patterns obtained by DDSL fingerprinting of Staphylococcus aureus strains.




References

Terletski V, Michael GB, Schwarz S. Subtracted restriction fingerprinting--a new typing technique using magnetic capture of tagged restriction fragments. FEMS Immunol Med Microbiol. 2004  ;41:1-8. PubMed

Terletskiy V, Kuhn G, Francioli P, Blanc DS. Application and evaluation of double digest selective label (DDSL) typing technique for Pseudomonas aeruginosa hospital isolates. J Microbiol Methods. 2008 ;72:283-7. PubMed

   
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