Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

Hdl Handle:
http://hdl.handle.net/10147/124467
Title:
Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes
Authors:
Scheler, Ott; Kaplinski, Lauris; Glynn, Barry; Palta, Priit; Parkel, Sven; Toome, Kadri; Maher, Majella; Barry, Thomas; Remm, Maido; Kurg, Ants
Issue Date:
28-Feb-2011
URI:
http://hdl.handle.net/10147/124467
Abstract:
Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.
ISSN:
http://dx.doi.org/10.1186/1472-6750-11-17

Full metadata record

DC FieldValue Language
dc.contributor.authorScheler, Otten
dc.contributor.authorKaplinski, Laurisen
dc.contributor.authorGlynn, Barryen
dc.contributor.authorPalta, Priiten
dc.contributor.authorParkel, Svenen
dc.contributor.authorToome, Kadrien
dc.contributor.authorMaher, Majellaen
dc.contributor.authorBarry, Thomasen
dc.contributor.authorRemm, Maidoen
dc.contributor.authorKurg, Antsen
dc.date.accessioned2011-03-14T10:06:01Z-
dc.date.available2011-03-14T10:06:01Z-
dc.date.issued2011-02-28-
dc.identifier.issnhttp://dx.doi.org/10.1186/1472-6750-11-17-
dc.identifier.urihttp://hdl.handle.net/10147/124467-
dc.description.abstractAbstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.-
dc.titleDetection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probesen
dc.language.rfc3066en-
dc.rights.holderScheler et al.; licensee BioMed Central Ltd.-
dc.description.statusPeer Reviewed-
dc.date.updated2011-03-10T18:48:58Z-
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