Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.

Frank KaiserBurkhard EndewardAlberto CollautoUte SchefferThomas F Prisner Michael W Göbel

Published in: Chemistry (Weinheim an der Bergstrasse, Germany) (2022)

The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.

Keyphrases

single molecule
room temperature
density functional theory
pet imaging
transition metal
photodynamic therapy
molecular dynamics
molecular dynamics simulations
radiation therapy
nucleic acid