Electron transfer followed by collisioninduced dissociation (NET-CID) for generating sequence information from backbonemodified oligonucleotide anions

Abstract

RATIONALE: Oligonucleotides with 2'modifications and/or phosphorothioate (PS) backbones are prone to undergo limited backbone fragmentation upon ion trap collisioninduced dissociation (CID). For better identification and characterization of chemically modified oligonucleotides, a more universal fragmentation method is desirable. METHODS: Gasphase dissociation of various 2'positionmodified oligonucleotides and mixedbackbone 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 noncomplementary d/wion series, while a/zions 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 evenelectron species generated complementary aB/wtype 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: NETCID proved to be an efficient method of generating full sequence information for 2'modifications and/or mixedbackbone oligonucleotides. Copyright © 2012 John Wiley & Sons, Ltd.