A mechanistic study of the electron capture dissociation of oligonucleotides

Abstract

Electron capture dissociation (ECD) of a series of custom-synthesized oligonucleotide pentamers was performed in a Fourier-transform mass spectrometer with a conventional filamenttype electron gun. Dissociation of oligonucleotide ions by electron capture generates primarily w/d-type and z/a-type ions with and without the loss of a nucleobase fragment ions. Minor yields of radical [z/a ϩ H]· fragment ions were also observed in many cases. It is interesting to note that some nucleoside-like fragment ions and protonated nucleobase ions (except thymine-related nucleobases and nucleoside-like fragments) were observed in most ECD spectra. The formation of these low-mass fragment ions was tentatively attributed to the secondary fragmentation of the radical S tructural characterization of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) is important, as DNA and RNA play important roles in many biochemical processes. Even with the completion of the human genome project, the importance of studying nucleic acid remains. For instance, a large region of DNA requires re-sequencing [1] to allow the detection and characterization of nucleotide mutation. There is a constant demand for powerful and rapid analytical methods to determine the structure of nucleic acids and their constituents. With the development of "soft" desorption/ionization techniques, matrix-assisted laser desorption/ionization (MALDI) [2,3] and electrospray ionization (ESI) [4,5] methods, mass spectrometry has become an indispensable, quick, and reliable tool for the analysis of oligonucleotides [6]. However, simple mass measurement provides little structural information for confirmation of the sequence for unknown natural and synthetic oligonucleotides. Much research effort has recently been devoted to the development of various tandem mass spectrometry (MS/MS) methods for structural elucidation of biomolecules. The critical event in tandem mass spectrometry of biomolecules is the activation of the selected precursor ions to induce unimolecular dissociation. Common ion activation methods used for analysis of biomolecules include lowand high-energy collision-induced dissociation (CID) [7, 8], surface-induced dissociation (SID) [9], infrared multiphoton dissociation (IRMPD) [10], and blackbody infrared radiative dissociation (BIRD) [11]. However, fragment ions observed in the tandem mass spectra using these ion activation methods mostly originate from cleavages of weak bonds [12].A relatively new ion activation method, electron capture dissociation (ECD) [13] has demonstrated several interesting features. For example, for protein-type biomolecules, ECD leads predominantly to the dissociation of the N-C ␣ linkage even in the presence of labile post-translational modifications [14,15]. A combination of ECD and other dissociation methods, such as IRMPD and CID, has been shown to provide complementary information for unambiguous identification of the type and the position of several important protein posttranslational modifications [16 -18] and for de novo s...

Transition Metal-based Anticancer Drugs Targeting Nucleic Acids: A Tandem Mass Spectrometric Investigation

“…The transfer of an electron to nucleic acids is highly nucleobase-specific with a high preference for abstraction by a cytosine nucleobase. [17,18] Our recent ETD experiments on metallocene-DNA adducts of different charge states provided deeper insight into the radical-driven dissociation. Electron transfer to the doubly charged hexamer adduct resulted in charge reduction only.…”

Hybrid Activation Methods for Elucidating Nucleic Acid Modifications

“…[34][35][36][37][38] More recently, the development and investigation of photon-and electron-based activation methods that create radical sites and lead to new dissociation pathways has generated considerable interest. [39][40][41][42][43][44][45][46] Electron capture dissociation (ECD) [43][44][45] and electron-transfer dissociation (ETD) 46 of positively charged oligonucleotide precursors lead to radical cation products, primarily w/d type and z/a type ions. We have recently implemented ultraviolet photodissociation (UVPD) and electron photodetachment dissociation (EPD, using 193 nm photons) to determine the sites of modifications of oligodeoxynucleotides.…”

“…42 Elucidation of modified nucleic acids by tandem mass spectrometry (MS/MS) strategies is generally more challenging than structural characterization of unmodified nucleic acids because the ability to map the location(s) of modification depends on generating a comprehensive array of site-specific fragment ions. Because of the success of electron-based activation methods for elucidation of modifications of peptides (e.g., post-translational modifications of proteins) and the variety of diagnostic product ions that arise upon dissociation of radical ions during ECD [43][44][45] and ETD, 46 we anticipated that hybrid activation methods that combined the efficient charge-reduction, radical ion formation capabilities of electron transfer activation with the high efficiency and high energy deposition of photodissociation would afford a compelling strategy for elucidation of sites of modifications of nucleic acids. In the present study, we explore the fragmentation patterns of positively charged oligonucleotides, including both single strands and modified single strands, using electron transfer reactions to create radical cations and subsequently using CAD, IRMPD (10.6 µm), or UVPD (193 nm) for characterization of the charge-reduced species.…”

Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010–2020)

“…In an effort to overcome some of the limitations of using collisional activation methods, hybrid activation techniques incorporating radical‐based activation methods such as electron capture dissociation (ECD) [58–60], electron transfer dissociation (ETD) [61], negative electron transfer dissociation (NETD) [62], electron detachment dissociation (EDD) [63, 64], and electron photodetachment dissociation (EPD) [65–67] have also been explored for the top‐down characterization of nucleic acids. These approaches capitalize on the dissociation of odd‐electron precursor ions generated by ion‐ion reactions or interaction with electrons or photons, ultimately affording new dissociation pathways and more informative fragment ions.…”