Reduction Resistant and Rigid Nitroxide Spin-Labels for DNA and RNA

Electron paramagnetic resonance (EPR) spectroscopy, coupled with site-directed spin labeling (SDSL), is a useful method for studying conformational changes of biomolecules in cells. To employ in-cell EPR using nitroxide-based spin labels, the structure of the nitroxides must confer reduction resistance to withstand the reductive environment within cells. Here, we report the synthesis of two new spin labels, EC and ECm, both of which possess the rigidity and the reduction resistance needed for extracting detailed structural information by EPR spectroscopy. EC and ECm were incorporated into DNA and RNA, respectively, by oligonucleotide synthesis. Both labels were shown to be nonperturbing of the duplex structure. The partial reduction of ECm during RNA synthesis was circumvented by the protection of the nitroxide as a benzoylated hydroxylamine.