title: On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent.
abstract: Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in 'top-down' strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)(n+) and (M-nH)(n-) ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into C: and Y: ions from phosphodiester bond cleavage.
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Riml
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
authors.forename: Heidelinde
authors.initials: H
authors.lastname: Glasner
authors.affiliation: Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202-3489, United States.
authors.forename: M T
authors.initials: MT
authors.lastname: Rodgers
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
authors.forename: Ronald
authors.initials: R
authors.lastname: Micura
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria kathrin.breuker@uibk.ac.at.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Breuker
mesh_terms: D006860:Hydrogen Bonding; D007477:Ions / Q000737:chemistry; D011522:Protons; D012313:RNA / Q000737:chemistry*; D059367:RNA Cleavage; D021241:Spectrometry, Mass, Electrospray Ionization
chemical_list: D007477:Ions; D011522:Protons; D012313:RNA