Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.
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.
Kaplinski
Lauris
L
Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia. lauris@ebc.ee
Scheler
Ott
O
Parkel
Sven
S
Palta
Priit
P
Toome
Kadri
K
Kurg
Ants
A
Remm
Maido
M
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
D009841:Oligonucleotides; D012329:RNA, Bacterial; C096222:tmRNA