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

BMC Biotechnol 2011 Feb 28;11:17. Epub 2011 Feb 28.

Dept, of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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.

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Source
http://dx.doi.org/10.1186/1472-6750-11-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051898PMC
February 2011
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