PARS/dsRNA-Seq
PARS/dsRNA-Seq
PARS-Seq mapping provides information about the secondary and tertiary structure of RNA. In this method, RNA is digested with RNases that are specific for double-stranded and single-stranded RNA, respectively. The resulting fragments are reverse-transcribed to cDNA. Deep sequencing of the cDNA provides high-resolution sequences of the RNA. The RNA structure can be deduced by comparing the digestion patterns of the various RNases.
Pros:
- Provides RNA structural information
- Distinguishes between paired and unpaired bases
- Alternative to mass spectrometry, NMR, and crystallography
Cons:
- Enzyme digestion can be nonspecific
- Digestion conditions must be carefully controlled
- RNA can be overdigested
- Limited to in vitro applications