FRAG-Seq
FRAG-Seq
Fragmentation sequencing (FRAG-Seq) is a method for probing RNA structure. In this method, RNA is digested using nuclease P1, followed by reverse transcription. Deep sequencing of the cDNA provides high-resolution single-stranded reads, which can be used to determine the structure of RNA by mapping P1 endonuclease digestion sites.
Pros:
- Simple and fast protocol compared to PARS-Seq
- High throughput
- Alternative to mass spectrometry, NMR, and crystallography
Cons:
- Need endogenous controls
- Potential for contamination between samples and controls
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