Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry
Trenton M. Peters-Clarke, Qiuwen Quan, Dain R. Brademan, Alexander S. Hebert, Michael S. Westphall, Joshua J. Coon
Abstract
Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD can be successfully implemented on a widely available quadrupole-Orbitrap-linear ion trap mass spectrometer that uses a front-end glow discharge source to generate radical fluoranthene reagent cations. We characterize both unmodified and modified ribonucleic acids and present the first application of activated-ion negative electron transfer dissociation (AI-NETD) to nucleic acids. AI-NETD achieved 100% sequence coverage for both a 6-mer (5′-rGmUrArCmUrG-3′) with 2′-O-methyl modifications and a 21-mer (5′-rCrArUrCrCrUrCrUrArGrArGrGrArUrArGrArArUrG-3′), the luciferase antisense siRNA. Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a relatively low degree of undesired base-loss products and internal products relative to collision-based methods.