Electron detachment dissociation (EDD) pathways in oligonucleotides

Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are two novel fragmentation methods yielding radicals from negatively charged ions. With the goal of comparing EDD, EPD and the more traditional Collision-Induced Dissociation (CID) and Infrared Multiphoton Disscociation (IRMPD) fragmentation processes in oligonucleotides, we studied here the EDD fragmentation pathways of oligonucleotides of varying length. We chose polythymine oligonucleotides because these are the least prone to secondary structure formation, and found complete sequence coverage by EDD for up to dT20. We also found that the fragmentation pathways change with oligonucleotide length: electron detachment is a mandatory step in the fragmentation of larger sequences, while shorter oligonucleotides can also fragment via direct electronic or vibrational excitation by the electrons. This is supported by (1) the fact that continuous ejection of the charge reduced species does not totally prevent fragmentation of short oligonucleotides dT5 and dT6, (2) the fact that CID and EDD fragments are more similar for small oligonucleotides (although double resonance experiments show that they are not all issued from the same mechanisms), and (3) the fact that electron-induced dissociation (EID) of singly charged dT3 and dT4 gives similar fragments as EDD of doubly charged dT5 and dT6. Finally, the detachment efficiency as a function of the nature of the nucleobase was studied. The effect of base on electron detachment in EDD (G > T > A > C) is different than in EPD (G > A > C > T), indicating different electron loss mechanisms.