Last week, researchers from the Karolinska Institute and the University of London released data on an innovative approach for studying RNA-RNA interactions.
Data supporting the multitude of RNA functions in our cells continues to pour in, but challenges in analyzing the effecting complexes in cellular processes persist, so we tip our hats to this team for developing a method that facilitates the study of RNA-RNA interactions. The method involves ligating double stranded RNA adaptors to double stranded native RNA substrates like those involved in the RNAi pathway or chromatin remodeling.
The method requires just a few steps:
- Double stranded RNA is conjugated to FAM for quick, gel-based detection
- T4 RNA Ligase addition of an adenine hexamer oligo producing sticky end
- T4 Kinase phosphorylation of sticky ended RNA
- T4 DNA Ligase addition of double stranded RNA adaptors
According to the group, the two step ligation method is the only available protocol for double stranded specific labeling.
The method can be combined with powerful downstream methods like RT-PCR for sensitive studies of RNA-RNA interactions and could be tweaked for global, double stranded RNA amplification and library construction.
An additional bonus is that the approach does not require any prior sequence or termini knowledge, making it a useful tool for discovery studies or a nice complement to the many in silico predictions of RNA interactions. Check out all the details at Nucleic Acids Research, July 2008