A Technique for Targeted RNA Cutting
I would like to inform anyone who is interested in the SuPER methodology of a similar technique for RNA. This other methodology, Sequence-specific cleavage of SSU rRNA with oligonucleotides and RNase H, is similar conceptually. Extracted RNA is incubated with a specific DNA probe and RNase H is added to the mixture. RNase H will cut an RNA:DNA hybrid, but will not damage single-stranded RNA. Thus, a specific primer can be used to cut an RNA target, leaving non-target molecules intact. These intact molecules can be recovered and used as a template for downstream applications such as reverse transcription. Dr. Uyeno et al. took the further step of using the technique to quantify microbial populations. A very clever technique indeed.
Yutaka Uyeno, Yuji Sekiguchi, Akiko Sunaga, Hiroki Yoshida, and Yoichi Kamagata (2004). Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms. Appl. Environ. Microbiol. 70:3650-3663.