A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment

Baptiste Bogard (1) , Gilles Tellier (1) , Claire Francastel (1) , Florent Hubé (1)

1 EDC (UMR_7216) - Centre épigénétique et destin cellulaire

Abstract: Pseudouridylation is one of the most abundant modifications found in RNAs. To identify the Pseudouridylation sites (Psi) in RNAs, several techniques have been developed, but the most common and robust is the CMC (N-cyclohexyl-N0-(2-morpholinoethyl)carbodiimide) treatment, which consists in the addition of an adduct on Psi that inhibits the reverse transcription. Here, we describe a turnkey method and a tool to design the bridging oligo (DBO), which is somewhat difficult to design. Finally, we propose a trouble-shooting guide to help users.

Keywords: Oligonucleotide design; tool; Pseudouridylation; snoRNA; CMC treatment

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Molecular biology; Life Sciences [q-bio]

Baptiste Bogard, Gilles Tellier, Claire Francastel, Florent Hubé. A Tool to Design Bridging Oligos Used to Detect Pseudouridylation Sites on RNA after CMC Treatment. Non-Coding RNA, 2022, 8, ⟨10.3390/ncrna8050063⟩. ⟨hal-03799770⟩