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Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides
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Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides
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Journal Article
Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides
2010
Overview
Background
The hybridization of synthetic
Streptococcus pneumoniae
tmRNA on a detection microarray is slow at 34°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°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.
Publisher
BioMed Central,BioMed Central Ltd,BMC
Subject
/ Biomedical Engineering/Biotechnology
/ Buffers
/ Cellular signal transduction
/ Chemistry and Materials Science
/ Identification and classification
/ Oligonucleotide Array Sequence Analysis - methods
/ Oligonucleotides - chemistry
/ Plant Breeding/Biotechnology
/ RNA, Bacterial - isolation & purification
