Electron Photodetachment Dissociation of DNA Polyanions in a Quadrupole Ion Trap Mass Spectrometer

Abstract

We hereby explore the effects of irradiating DNA polyanions stored in a quadrupole ion trap mass spectrometer with an optical parametric oscillator laser between 250 and 285 nm. We studied DNA 6-20-mer single strands and 12-base pair double strands. In all cases, laser irradiation causes electron detachment from the multiply charged DNA anions. Electron photodetachment efficiency directly depends on the number of guanines in the strand, and maximum efficiency is observed between 260 and 275 nm. Subsequent collision-induced dissociation (CID) of the radical anions produced by electron photodetachment results in extensive fragmentation. In addition to neutral losses, a large number of fragments from the w, d, a*, and z* ion series are obtained, contrasting with the w and (a-base) ion series observed in regular CID. The major advantage of this technique, coined electron photodetachment dissociation (EPD) is the absence of internal fragments, combined with good sequence coverage. EPD is therefore a highly promising approach for de novo sequencing of oligonucleotides. EPD of nucleic acids is also expected to give specific radical-induced strand cleavages, with conservation of other fragile bonds, including noncovalent bonds. In effect, preliminary results on a DNA hairpin and on double strands suggest that EPD could also be used to probe intra- and intermolecular interactions in nucleic acids.

Excited states of multiply-charged anions probed by photoelectron imaging: riding the repulsive Coulomb barrier

“…To make a full quantitative comparison would require knowledge of the differential photodetachment cross section from the excited state, which can be measured using different relative polarisations of the pump and probe fields. An interesting consequence of this classical picture is that it 70 allows crude structural information to be gleaned from the PE angular distribution. Specifically, the structure and charge localisation determines the RCB, which in turn determines the PE angular distribution.…”

“…However, excited states can be used as sensitive probes of the tunnelling process and dynamics, as discussed below. The observation of electron tunnelling in a well-defined molecular 70 system provides a very elegant route to studying this fundamentally and technologically important process. A key aspect of the RCB is that it is anisotropic.…”

“…In addition to spectral and angular resolved PE spectra, temporal resolution can be introduced using standard pump-probe methods in which a femtosecond laser pulse excites an excited state of the MCA, [A n-] * , and a time-delayed femtosecond probe 70 detaches the electron from this transient excited state so that the PE spectrum corresponds to that of [A n-] * at a given point along its relaxation coordinate. Time-resolved (TR) PE spectroscopy has been instrumental in understanding excited state processes in gas-phase molecules and clusters and is particularly powerful in 75 anions as the detachment energies are often sufficiently low to enable the monitoring of the entire reaction coordinate including the ground state of the anion or MCA.…”

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

“…Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Since then, some major advances must be mentioned in electron activation methods [3][4][5] and in infrared photodissociation [6].We recently started exploring the gas-phase reaction pathways of multiply charged DNA single strands and double strands upon UV irradiation around 260 nm [7,8]. To our surprise, we found out that, instead of fragmentation, electron detachment was the major reaction pathway with strands containing guanines.…”

“…To our surprise, we found out that, instead of fragmentation, electron detachment was the major reaction pathway with strands containing guanines. Electron photodetachment itself is not useful for DNA structure analysis, but subsequent collisional activation of the oligonucleotide radicals produced by electron photodetachment gives fragmentation into w, d, a· and z· ions with good sequence coverage [7]. This technique combining electron photodetachment and collision-induced dissociation was coined electron photodetachment dissociation (EPD).…”