Detection of nasba amplified bacterial tmrna molecules on slicsel designed microarray probes

Scheler, Ott
Kaplinski, Lauris
Glynn, Barry
Palta, Priit
Parkel, Sven
Toome, Kadri
Maher, Majella
Barry, Thomas
Remm, Maido
Kurg, Ants
Scheler, Ott; Kaplinski, Lauris; Glynn, Barry; Palta, Priit; Parkel, Sven; Toome, Kadri; Maher, Majella; Barry, Thomas; Remm, Maido; Kurg, Ants (2011). Detection of nasba amplified bacterial tmrna molecules on slicsel designed microarray probes. BMC Biotechnology 11 ,
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.
Springer Nature
Publisher DOI
Attribution-NonCommercial-NoDerivs 3.0 Ireland