EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription

Abstract

We present herein a novel nitroxide spin label-containing RNA triphosphate TPT3^NO and its application for site-specific spin-labeling of RNA through in vitro transcription using an expanded genetic alphabet. Our strategy allows the facile preparation of spin-labeled RNAs with sizes ranging from short RNA oligonucleotides to large, complex RNA molecules with over 370 nucleotides by standard in vitro transcription. As a proof of concept, inter-spin distance distributions are measured by pulsed electron paramagnetic resonance (EPR) spectroscopy in short self-complementary RNA sequences and in a well-studied 185 nucleotide non-coding RNA, the B. subtilis glmS ribozyme. The approach is then applied to probe for the first time the folding of the 377 nucleotide A-region of the long non-coding RNA Xist, by PELDOR.

Keywords: EPR spectroscopy; PELDOR; RNA; spin labeling; unnatural base pairs.