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Scheler, O,Kaplinski, L,Glynn, B,Palta, P,Parkel, S,Toome, K,Maher, M,Barry, T,Remm, M,Kurg, A
2011
February
BMC Biotechnol
Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes
Published
()
Optional Fields
SEQUENCE-BASED AMPLIFICATION OLIGONUCLEOTIDE MICROARRAYS DNA MICROARRAYS MESSENGER-RNA THERMODYNAMICS HYBRIDIZATION
11
1
1
17
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.
doi:10.1186/1472-6750-11-17
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