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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

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.