Site directed nitroxide spin labeling of oligonucleotides for NMR and EPR studies

Nitroxide labels are useful probes of biomolecule structure that can be detected by NMR and EPR spectroscopy. Although many methods exist for labeling oligonucleotides with nitroxides, most require reagents that are expensive or laborious to prepare. A simpler approach is described herein using commercially available phosphorothioate oligonucleotides and 2-(3-iodoacetamidomethyl)-PROXYL. We describe semi-optimized conditions for labeling DNA and RNA oligonucleotides and methodology for purifying and identifying these reagents by MALDI-MS. The nitroxide label showed some propensity to hydrolyze at high temperature and over prolonged periods at room temperature. Nitroxide-labeled DNA oligonucleotides gave characteristic EPR spectra and caused the disappearance of bound protein signals in 15N HSQC spectra consistent with the paramagnetic relaxation enhancement (PRE) effect.