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Issue 5, 2018
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A semi-rigid isoindoline-derived nitroxide spin label for RNA

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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

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Article information

21 Nov 2017
05 Jan 2018
First published
12 Jan 2018

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

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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