Open Access Methodology article

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

Ott Scheler12*, Lauris Kaplinski23, Barry Glynn4, Priit Palta23, Sven Parkel12, Kadri Toome1, Majella Maher4, Thomas Barry4, Maido Remm23 and Ants Kurg12

Author Affiliations

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

2 Estonian Biocentre, Tartu, Estonia

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

4 Molecular Diagnostics Research Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland

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BMC Biotechnology 2011, 11:17  doi:10.1186/1472-6750-11-17

Published: 28 February 2011



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.


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.


The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.