title: Hybrid activation methods for elucidating nucleic acid modifications.
abstract: Hybrid tandem mass spectrometry (MS/MS) techniques combining electron transfer (ET) and collision activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), or ultraviolet photodissociation (UVPD) were implemented and evaluated for the characterization of a series of oligonucleotides and oligoribonucleotides, including both native single strands and single strands containing platinated, phosphorothioated, and 2'-O-methylated modification sites. ET-IRMPD and ET-UVPD of oligodeoxynucleotides and oligoribonucleotides resulted in rich fragmentation with respect to production of w, a, z, and d ions for DNA, and c, y, w, a-B, d, and z ions for RNA, with many product ions retaining the modification and thus allowing site specific identification. ET-IRMPD caused more extensive secondary dissociation of the ions, in addition to a broader distribution of detectable sequence ions attributed to using a lower mass cutoff. ET-UVPD promoted higher energy fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques resulted in specific and extensive backbone cleavages which allowed the modification sites of multiply modified oligonucleotides to be elucidated.
authors.affiliation: Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States.
authors.forename: Suncerae I
authors.initials: SI
authors.lastname: Smith
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Brodbelt
mesh_terms: D001483:Base Sequence; D002945:Cisplatin / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics; D004579:Electron Transport; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D016376:Oligonucleotides, Antisense / Q000737:chemistry / Q000235:genetics; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics; D010710:Phosphates / Q000737:chemistry; D055668:Photochemical Processes; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D004277:DNA, Single-Stranded; D009696:Nucleic Acids; D016376:Oligonucleotides, Antisense; D009843:Oligoribonucleotides; D010710:Phosphates; C083120:phosphorodithioic acid; D002945:Cisplatin