Issue 5, 2018

A semi-rigid isoindoline-derived nitroxide spin label for RNA

Abstract

A new isoindoline-derived benzimidazole nitroxide spin label, ImUm, was synthesized and incorporated into RNA oligoribonucleotides. ImUm is the first example of a conformationally unambiguous spin label for RNA, in which the nitroxide N–O bond lies on the same axis as the single bond used to attach the rigid isoindoline-based spin label to a uridine base. This results in minimal displacement of the nitroxide upon rotation of this single bond, which is a useful property for a label to be used for distance measurements. Continuous-wave (CW) EPR measurements of RNA duplexes containing ImUm indicate a restricted rotation around this single bond, presumably due to an intramolecular hydrogen bond between the benzimidazole N–H and O4 of the uracil. Orientation-selective pulsed electron–electron double resonance (PELDOR, also called double electron–electron resonance, or DEER) distance measurements between two spin labels in two RNA duplexes showed in one case a strong orientation dependence, further confirming the restricted motion of the spin labels in RNA duplexes.

Graphical abstract: A semi-rigid isoindoline-derived nitroxide spin label for RNA

Supplementary files

Article information

Article type
Paper
Submitted
21 Nov 2017
Accepted
05 Jän 2018
First published
12 Jän 2018

Org. Biomol. Chem., 2018,16, 816-824

A semi-rigid isoindoline-derived nitroxide spin label for RNA

D. B. Gophane, B. Endeward, T. F. Prisner and S. Th. Sigurdsson, Org. Biomol. Chem., 2018, 16, 816 DOI: 10.1039/C7OB02870A

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