Háskóli ÍslandsUniversity of IcelandGophane, Dnyaneshwar B.Endeward, BurkhardPrisner, Thomas F.Sigurdsson, Snorri2020-08-102020-08-102018Gophane, D. B., Endeward, B., Prisner, T. F., & Sigurdsson, S. T. (2018). A semi-rigid isoindoline-derived nitroxide spin label for RNA. Organic and Biomolecular Chemistry, 16(5), 816-824 doi: 10.1039/c7ob02870a1477-05201477-0539 (eISSN)https://hdl.handle.net/20.500.11815/1962Post-print (lokagerð höfundar)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.816-824eninfo:eu-repo/semantics/openAccessDNA-rannsóknirKjarnsýrurRafeindirinfo:eu-repo/semantics/articleOrganic & Biomolecular Chemistry10.1039/C7OB02870A