title: Electron transfer followed by collision-induced dissociation (NET-CID) for generating sequence information from backbone-modified oligonucleotide anions.
abstract: BACKGROUND
  Oligonucleotides with 2'-modifications and/or phosphorothioate (PS) backbones are prone to undergo limited backbone fragmentation upon ion trap collision-induced dissociation (CID). For better identification and characterization of chemically modified oligonucleotides, a more universal fragmentation method is desirable.
  
  
  METHODS
  Gas-phase dissociation of various 2'-position-modified oligonucleotides and mixed-backbone oligonucleotides (MBOs) has been studied by ion trap CID of the radical anion species formed via electron transfer ion/ion reactions.
  
  
  RESULTS
  For 2'-modified mix-mer radical anions, complete sequence information was generated with non-complementary d/w-ion series, while a/z-ions were observed randomly with relatively low intensity. The 2'-position modification, which has been observed to affect CID patterns of oligonucleotide anions, did not exhibit any observable influence on the dissociation patterns of oligonucleotide radical anions. For MBOs comprised of DNA nucleotides, ion trap CID of even-electron species generated complementary a-B/w-type ions and multiple fragment types at the phosphorothioate (PS) linkages. For MBOs comprised of 2'-OMe-modified nucleotides, only PS bond cleavage was observed for ion trap CID of doubly deprotonated precursor ions. Negative electron transfer reaction with or without supplemental activation of MBOs gave rise to a/d/w-type fragments similar to those of the 2'-modified mix-mers. PS bonds were observed to be more fragile under the electron detachment process, and phosphodiester (PO) bond cleavages were noted upon further collisional activation.
  
  
  CONCLUSIONS
  NET-CID proved to be an efficient method of generating full sequence information for 2'-modifications and/or mixed-backbone oligonucleotides.
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.forename: Scott A
authors.initials: SA
authors.lastname: McLuckey
mesh_terms: D000838:Anions / Q000737:chemistry; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D000838:Anions; D009841:Oligonucleotides