title: Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.
abstract: 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.
authors.affiliation: Dept, of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. ott.scheler@gmail.com
authors.forename: Ott
authors.initials: O
authors.lastname: Scheler
authors.forename: Lauris
authors.initials: L
authors.lastname: Kaplinski
authors.forename: Barry
authors.initials: B
authors.lastname: Glynn
authors.forename: Priit
authors.initials: P
authors.lastname: Palta
authors.forename: Sven
authors.initials: S
authors.lastname: Parkel
authors.forename: Kadri
authors.initials: K
authors.lastname: Toome
authors.forename: Majella
authors.initials: M
authors.lastname: Maher
authors.forename: Thomas
authors.initials: T
authors.lastname: Barry
authors.forename: Maido
authors.initials: M
authors.lastname: Remm
authors.forename: Ants
authors.initials: A
authors.lastname: Kurg
mesh_terms: D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015347:RNA Probes / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D021161:Self-Sustained Sequence Replication / Q000379:methods*; D012984:Software; D013045:Species Specificity; D013296:Streptococcus pneumoniae / Q000235:genetics*
chemical_list: D015347:RNA Probes; D012329:RNA, Bacterial; C096222:tmRNA