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

• Main Authors: Toome Kadri, Parkel Sven, Palta Priit, Glynn Barry, Kaplinski Lauris, Scheler Ott, Maher Majella, Barry Thomas, Remm Maido, Kurg Ants
• Format: Article
• Language: English
• Published: BMC 2011-02-01
• Series: BMC Biotechnology
• Online Access: http://www.biomedcentral.com/1472-6750/11/17

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Streptococcus pneumoniae </it>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 <it>S. pneumoniae </it>tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU.</p> <p>Conclusions</p> <p>The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.</p>