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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
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.
Keyword(s): sequence-based amplification; oligonucleotide microarrays; DNA microarrays; messenger-rna; thermodynamics; hybridization
Publication Date:
2018
Type: Journal article
Peer-Reviewed: Unknown
Institution: NUI Galway
Publisher(s): Springer Nature
First Indexed: 2019-03-23 06:28:44 Last Updated: 2019-03-23 06:28:44