title: DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation.
abstract: Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine](-) fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine](-) and complementary y-B type product ions.
authors.affiliation: Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA.
authors.forename: Brett
authors.initials: B
authors.lastname: Harper
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Neumann
authors.forename: Touradj
authors.initials: T
authors.lastname: Solouki
mesh_terms: D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
chemical_list: D007477:Ions; D009838:Oligodeoxyribonucleotides; D004247:DNA