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Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes
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...
Autores principales: | , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051898/ https://www.ncbi.nlm.nih.gov/pubmed/21356118 http://dx.doi.org/10.1186/1472-6750-11-17 |
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author | Scheler, Ott Kaplinski, Lauris Glynn, Barry Palta, Priit Parkel, Sven Toome, Kadri Maher, Majella Barry, Thomas Remm, Maido Kurg, Ants |
author_facet | Scheler, Ott Kaplinski, Lauris Glynn, Barry Palta, Priit Parkel, Sven Toome, Kadri Maher, Majella Barry, Thomas Remm, Maido Kurg, Ants |
author_sort | Scheler, Ott |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-3051898 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30518982011-03-10 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 BMC Biotechnol Methodology Article 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. BioMed Central 2011-02-28 /pmc/articles/PMC3051898/ /pubmed/21356118 http://dx.doi.org/10.1186/1472-6750-11-17 Text en Copyright ©2011 Scheler et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Scheler, Ott Kaplinski, Lauris Glynn, Barry Palta, Priit Parkel, Sven Toome, Kadri Maher, Majella Barry, Thomas Remm, Maido Kurg, Ants Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title | Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title_full | Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title_fullStr | Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title_full_unstemmed | Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title_short | Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes |
title_sort | detection of nasba amplified bacterial tmrna molecules on slicsel designed microarray probes |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051898/ https://www.ncbi.nlm.nih.gov/pubmed/21356118 http://dx.doi.org/10.1186/1472-6750-11-17 |
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