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A Cytidine Phosphoramidite with Protected Nitroxide Spin Label: Synthesis of a Full‐Length TAR RNA and Investigation by In‐Line Probing and EPR Spectroscopy
Author(s) -
Weinrich Timo,
Jaumann Eva A.,
Scheffer Ute,
Prisner Thomas F.,
Göbel Michael W.
Publication year - 2018
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201800167
Subject(s) - nitroxide mediated radical polymerization , chemistry , site directed spin labeling , phosphoramidite , rna , oligonucleotide , electron paramagnetic resonance , tar (computing) , amide , steric effects , stereochemistry , photochemistry , combinatorial chemistry , organic chemistry , nuclear magnetic resonance , biochemistry , copolymer , dna , membrane , physics , radical polymerization , computer science , gene , programming language , polymer
Abstract EPR studies on RNA are complicated by three major obstacles related to the chemical nature of nitroxide spin labels: Decomposition while oligonucleotides are chemically synthesized, further decay during enzymatic strand ligation, and undetected changes in conformational equilibria due to the steric demand of the label. Herein possible solutions for all three problems are presented: A 2‐nitrobenzyloxymethyl protective group for nitroxides that is stable under all conditions of chemical RNA synthesis and can be removed photochemically. By careful selection of ligation sites and splint oligonucleotides, high yields were achieved in the assembly of a full‐length HIV‐1 TAR RNA labeled with two protected nitroxide groups. PELDOR measurements on spin‐labeled TAR in the absence and presence of arginine amide indicated arrest of interhelical motions on ligand binding. Finally, even minor changes in conformation due to the presence of spin labels are detected with high sensitivity by in‐line probing.