title: Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.
abstract: BACKGROUND
  The hybridization of synthetic Streptococcus pneumoniae tmRNA on a detection microarray is slow at 34 degrees C resulting in low signal intensities.
  
  
  RESULTS
  We demonstrate that adding specific DNA helper oligonucleotides (chaperones) to the hybridization buffer increases the signal strength at a given temperature and thus makes the specific detection of Streptococcus pneumoniae tmRNA more sensitive. No loss of specificity was observed at low temperatures compared to hybridization at 46 degrees C. The effect of the chaperones can be explained by disruption of the strong secondary and tertiary structure of the target RNA by the selective hybridization of helper molecules. The amplification of the hybridization signal strength by chaperones is not necessarily local; we observed increased signal intensities in both local and distant regions of the target molecule.
  
  
  CONCLUSIONS
  The sensitivity of the detection of tmRNA at low temperature can be increased by chaperone oligonucleotides. Due to the complexity of RNA secondary and tertiary structures the effect of any individual chaperone is currently not predictable.
authors.affiliation: Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia. lauris@ebc.ee
authors.forename: Lauris
authors.initials: L
authors.lastname: Kaplinski
authors.forename: Ott
authors.initials: O
authors.lastname: Scheler
authors.forename: Sven
authors.initials: S
authors.lastname: Parkel
authors.forename: Priit
authors.initials: P
authors.lastname: Palta
authors.forename: Kadri
authors.initials: K
authors.lastname: Toome
authors.forename: Ants
authors.initials: A
authors.lastname: Kurg
authors.forename: Maido
authors.initials: M
authors.lastname: Remm
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry*; D012329:RNA, Bacterial / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D013296:Streptococcus pneumoniae / Q000235:genetics; D013696:Temperature
chemical_list: D009841:Oligonucleotides; D012329:RNA, Bacterial; C096222:tmRNA