ArticleBMC biotechnology2011
Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.
Article in BMC biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 13 citations in OpenAlex.
- Molecular Mechanisms Underlying CRISPR/Cas-Based Assays for Nucleic Acid Detection.Current issues in molecular biology · 2023Review
- Tuberculosis diagnostics: Challenges and opportunities.Lung India : official organ of Indian Chest Society · 2012Article
- Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators.Biosensors & bioelectronicsArticle
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe 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.
resultsWe 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.
conclusionsThe described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.
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