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

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    Authors
    Scheler, Ott
    Kaplinski, Lauris
    Glynn, Barry
    Palta, Priit
    Parkel, Sven
    Toome, Kadri
    Maher, Majella
    Barry, Thomas
    Remm, Maido
    Kurg, Ants
    Issue Date
    2011-02-28
    
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    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
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