References of "Dugourd, Philippe"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailUV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase
Rosu, Frédéric ULg; Gabelica, Valérie ULg; De Pauw, Edwin ULg et al

in Journal of Physical Chemistry A (2012), 116

UV absorption spectroscopy is one of the most widely used methods to monitor nucleic acid folding in solution, but the absorption readout is the weighted average contribution of all species present in ... [more ▼]

UV absorption spectroscopy is one of the most widely used methods to monitor nucleic acid folding in solution, but the absorption readout is the weighted average contribution of all species present in solution. Mass spectrometry, on the other hand, is able to separate constituents of the solution based on their mass, but methods to probe the structure of each constituent are needed. Here, we explored whether gas-phase UV spectroscopy can give an indication of DNA folding in ions isolated by electrospray mass spectrometry. Model DNA single strands, duplexes, and G-quadruplexes were extracted from solution by electrospray; the anions were stored in a quadrupole ion trap and irradiated by a tunable laser to obtain the UV action spectra of each complex. We found that the duplex and quadruplex spectra are significantly different from the spectra of single strands, thereby suggesting that electronic spectroscopy can be used to probe the DNA gas-phase structure and obtain information about the intrinsic properties of high-order DNA structure. [less ▲]

Detailed reference viewed: 28 (8 ULg)
See detailElectronic spectroscopy of nucleic acids in the gas phase
Gabelica, Valérie ULg; Rosu, Frédéric ULg; Joly, Laure ULg et al

Conference (2010)

DNA polyanions trapped in a mass spectrometer undergo electron detachment following UV irradiation. Photodetachment is a single-photon process. Its efficiency depends on the nature of the DNA bases, the ... [more ▼]

DNA polyanions trapped in a mass spectrometer undergo electron detachment following UV irradiation. Photodetachment is a single-photon process. Its efficiency depends on the nature of the DNA bases, the ion's charge, and the excitation wavelength. Photodetachment can therefore be used to perform ion spectroscopy experiments, which probe electronic excitation within the initial charge state of the nucleic acids. Ion spectroscopy experiments on trapped nucleic acid cations and anions were performed from 4 to 20 eV using an OPO laser or using synchrotron radiation. Photoelectron spectroscopy experiments were also performed on multiply charged anions to probe direct detachment cross sections and electronic excitations within the final charge. The electronic spectra obtained from photodetachment integral cross sections show several resonances, provided that the photon energy is larger than the electron binding energy. We will also discuss whether the electronic spectra obtained via photodetachment can be used to probe gas phase ion structure. [less ▲]

Detailed reference viewed: 70 (5 ULg)
Peer Reviewed
See detailIR and UV spectroscopic signatures of DNA higher-order structures in the gas phase
Gabelica, Valérie ULg; Rosu, Frédéric ULg; Gregoire, Gilles et al

Conference (2008, June 03)

Introduction Electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase. However, a longstanding question is whether the gas-phase ... [more ▼]

Introduction Electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase. However, a longstanding question is whether the gas-phase multiply-charged ions produced by ESI-MS keep a folded conformation in the absence of solvent. Nucleic acid secondary structures are determined by hydrogen bonding interactions between nucleic bases and by stacking interactions between neighboring base pairs. Here we will show that infrared (IR) and ultraviolet (UV) action spectroscopies provide useful and complementary information on the structure of nucleic acid ions in the gas phase. Methods IR spectroscopy experiments on DNA negative ions were carried out at the CLIO free electron laser (FEL) center (Orsay, France) using an Esquire 3000 (Bruker) mass spectrometer modified to inject the IR beam through the ring electrode. IRMPD spectra are recorded by monitoring the fragmentation of mass-selected parent ions as a function of the excitation wavenumber, in the range 1000-2000 cm-1. UV spectroscopy experiments were carried out using a tunable OPO laser (Continuum Lasers) with frequency doubling. The laser is interfaced with either a Finnigan LCQ ESI-QIT mass spectrometer or a Bruker Apex-Qe 9.4 T ESI-FTICR mass spectrometer. The UV action spectra were recorded by monitoring electron detachment as a function of the wavelength between 220 and 300 nm. Preliminary results First, DNA oligonucleotide ions forming G-quadruplex structures were studied in the gas phase using IR multiple-photon dissociation spectroscopy. Data interpretation on these large biomolecule ions is made using carefully chosen control experiments. The IR spectrum of the (dTG4T)4 quadruplex has been recorded, and compared to that of the single strand. Given the strand stoichiometry and the selective incorporation of three ammonium cations, there is little doubt about the quadruplex structure of [(dTG4T)4•(NH4+)3]5-. The major finding is a fingerprint of hydrogen bonding in the gas phase in the guanine C6=O6 stretching mode, that allows probing the conservation of G-quartets in the gas phase. Further experiments also demonstrate the conservation of G-quadruplex hydrogen bonds in the human telomeric sequence d(TTAGGG)4 [Gabelica et al., JACS, accepted]. Second, we also studied DNA duplexes and G-quadruplex ions in the gas phase by UV spectroscopy. We recorded the UV spectra of the (dTG4T)4 quadruplex, with and without ammonium ions. Molecular modeling [Rueda et al., JACS, 2006, p3608] and ion mobility spectrometry data [Gabelica et al., JACS, 2007, 895] showed that G-quadruplexes keep their hydrogen-bonded structure but become more floppy if inner cations are removed. We found that the UV spectra differ dramatically with and without inner cations, suggesting that UV spectroscopy is very sensitive to stacking interactions between neighboring G-quartets. We also used UV spectroscopy to probe the structure of 12-mer DNA duplexes, by comparing the duplex spectra to those obtained on single strands. Preliminary results show that stacking interactions may be preserved in duplexes containing GC base pairs, but not in duplexes containing AT base pairs. Altogether, these results show the complementarities between IR and UV spectroscopy to characterize DNA structures in the gas phase: IR data mainly give access to information on hydrogen bonding of bases, and UV spectroscopy provides information on stacking interactions. [less ▲]

Detailed reference viewed: 32 (2 ULg)
See detailElectron Photodetachment of DNA Polyanions: Photoelectron Spectroscopy and UV Action Spectroscopy
Gabelica, Valérie ULg; Rosu, Frédéric ULg; De Pauw, Edwin ULg et al

Conference (2008, April 15)

DNA polyanions trapped in a mass spectrometer undergo electron detachment following irradiation with UV light [1-3]. Electron photodetachment is a 1-photon process, and its efficiency depends on: - The ... [more ▼]

DNA polyanions trapped in a mass spectrometer undergo electron detachment following irradiation with UV light [1-3]. Electron photodetachment is a 1-photon process, and its efficiency depends on: - The nature of the DNA bases: guanine-containing strands are the most prone to electron photodetachment, followed by adenine, cytosine, and finally thymine. - The excitation wavelength: electron detachment is maximum around 260 nm, corresponding to base excitation. - The charge of the polyanion: higher charge state ions undergo more efficient electron detachment because of the Coulombic repulsion. Here we will discuss the electron photodetachment mechanism in the light of the most recent experimental results. Because the base-dependence of electron photodetachment efficiency is correlated with the base ionization potential and is maximum at wavelengths corresponding to the base absorption, we initially proposed that electron photodetachment might occur directly from the base, and that the photodetachment yield was correlated with the electron binding energy to the base [2]. Photoelectron spectroscopy experiments were performed on DNA multiply charged anions with varying base composition to probe how the electron binding energies changes with the base composition. Finally, the electron detachment channel was used to perform UV spectroscopy experiments on large DNA polyanions trapped in the gas phase. Gas-phase UV spectra of DNA duplexes and G-quadruplexes containing up to 24 bases (> 7000 Da) will be presented. [1] V. Gabelica, T. Tabarin, R. Antoine, F. Rosu, I. Compagnon, M. Broyer, E. De Pauw, and P. Dugourd, Anal. Chem. 78, 6564 (2006). [2] V. Gabelica, F. Rosu, T. Tabarin, C. Kinet, R. Antoine, M. Broyer, E. De Pauw, and P. Dugourd, J. Am. Chem. Soc. 129, 4706 (2007). [3] V. Gabelica, F. Rosu, E. De Pauw, R. Antoine, T. Tabarin, M. Broyer, and P. Dugourd, J. Am. Soc. Mass Spectrom. 18, 1990 (2007). [less ▲]

Detailed reference viewed: 41 (2 ULg)
See detailIR and UV spectroscopy of DNA ions stored in a quadrupole ion trap mass spectrometer
Gabelica, Valérie ULg; Rosu, Frédéric ULg; Gregoire, Gilles et al

Conference (2008, February 15)

Electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase. However, a longstanding question is whether the gas-phase multiply-charged ... [more ▼]

Electrospray mass spectrometry (ESI-MS) can be used to transfer large biomolecular complexes from the solution to the gas phase. However, a longstanding question is whether the gas-phase multiply-charged ions produced by ESI-MS keep a folded conformation in the absence of solvent. Nucleic acid secondary structures are determined by hydrogen bonding interactions between nucleic bases and by stacking interactions between neighboring base pairs. In solution, infrared (IR) and ultraviolet (UV) spectroscopies provide information on hydrogen bonding and stacking interactions in nucleic acids, respectively. Here we will show how IR and UV spectra of gas-phase ions can be recorded, and what can be learned on the structure of nucleic acids (double helices and quadruple helices) in the gas phase. The IR spectroscopy experiments on DNA negative ions were carried out at the CLIO free electron laser (FEL) center using an electrospray quadrupole ion trap mass spectrometer (Esquire 3000, Bruker Daltonics, Germany) modified to inject the IR beam in the trap through the ring electrode. IRMPD spectra are recorded by monitoring the relative fragmentation efficiency of mass-selected parent ions as a function of the excitation wavenumber, in the range 1000-2000 cm-1. Data interpretation on these large biomolecule ions is made using carefully chosen control experiments. The major finding is a fingerprint of hydrogen bonding in the gas phase in the guanine C6=O6 stretching mode, that allows probing the conservation of G-quartets in the gas phase. The experiments demonstrate the conservation of G-quadruplex hydrogen bonds in the human telomeric sequence d(TTAGGG)4. The UV spectroscopy experiments were carried out using a tunable OPO laser (Continuum Lasers, Santa Clara, CA, USA) with frequency doubling. The laser is interfaced with a Finnigan LCQ ESI-QIT mass spectrometer. The UV action spectra were recorded by monitoring electron detachment from DNA multiply charged anions as a function of the wavelength between 220 and 300 nm. Preliminary results suggest that stacking interactions are preserved in duplexes containing GC base pairs, and in G-quadruplexes containing inner cations. [less ▲]

Detailed reference viewed: 35 (1 ULg)
Full Text
See detailPhotodetachment and photodissociation mass spectrometry of DNA multiply charged ions
Gabelica, Valérie ULg; Rosu, Frédéric ULg; De Pauw, Edwin ULg et al

in Beck, Rainer D.; Drabbels, Marcel; Rizzo, Thomas R. (Eds.) Contributions 16th Symposium on Atomic and Surface Physics and Related Topics (2008)

Detailed reference viewed: 42 (2 ULg)
See detailPhotodissociation spectroscopy of cationic porphyrins in the gas phase. Influence of the complexation with DNA. Comparison with solution phase
Rosu, Frédéric ULg; De Pauw, Edwin ULg; Gabelica, Valérie ULg et al

in Beck, Rainer D.; Drabbels, Marcel; Rizzo, Thomas R. (Eds.) Contributions 16th Symposium on Atomic and Surface Physics and Related Topics (2008)

Detailed reference viewed: 21 (0 ULg)
Full Text
Peer Reviewed
See detailBase-dependent electron photodetachment from negatively charged DNA strands upon 260-nm laser irradiation
Gabelica, Valérie ULg; Rosu, Frédéric ULg; Tabarin, Thibault et al

in Journal of the American Chemical Society (2007), 129(15), 4706-4713

DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a ... [more ▼]

DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a fast process, given that photodetachment is able to compete with internal conversion or radiative relaxation to the ground state. The DNA [6-mer](3-) ions studied here show a marked sequence dependence of electron photodetachment yield. Remarkably, the photodetachment yield (dG(6) > dA(6) > dC(6) > dT(6)) is inversely correlated with the base ionization potentials (G < A < C < T). Sequences with guanine runs show increased photodetachment yield as the number of guanine increases, in line with the fact that positive holes are the most stable in guanine runs. This correlation between photodetachment yield and the stability of the base radical may be explained by tunneling of the electron through the repulsive Coulomb barrier. Theoretical calculations on dinucleotide monophosphates show that the HOMO and HOMO-1 orbitals are localized on the bases. The wavelength dependence of electron detachment yield was studied for dG(6)(3-). Maximum electron photodetachment is observed in the wavelength range corresponding to base absorption (260-270 nm). This demonstrates the feasibility of gas-phase UV spectroscopy on large DNA anions. The calculations and the wavelength dependence suggest that the electron photodetachment is initiated at the bases and not at the phosphates. This also indicates that, although direct photodetachment could also occur, autodetachment from excited states, presumably corresponding to base excitation, is the dominant process at 260 nm. Excited-state dynamics of large DNA strands still remains largely unexplored, and photo-oxidation studies on trapped DNA multiply charged anions can help in bridging the gap between gas-phase studies on isolated bases or base pairs and solution-phase studies on full DNA strands. [less ▲]

Detailed reference viewed: 61 (7 ULg)
Full Text
Peer Reviewed
See detailElectron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores
Gabelica, Valérie ULg; Rosu, Frédéric ULg; De Pauw, Edwin ULg et al

in Journal of the American Society for Mass Spectrometry (2007), 18(11), 1990-2000

Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation. in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound ... [more ▼]

Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation. in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS3 fragmentation of radicals produced by photodetachment at lambda = 260 nm (DNA excitation) and by photodetachment at lambda > 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. 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 Forster resonance energy transfer (FRET). [less ▲]

Detailed reference viewed: 60 (5 ULg)
See detailFormation de radicaux anions d'ADN par irradiation laser UV et visible et nouveaux canaux de dissociation
Gabelica, Valérie ULg; Tabarin, Thibault; Kinet, Catherine ULg et al

Conference (2006, September 13)

Nous avons exploré récemment les effets de l'irradiation laser dans l'UV ou le visible de polyanions d'ADN dans un piège à ions quadripolaire. Lors de l'irradiation de simple brins ou de double hélices d ... [more ▼]

Nous avons exploré récemment les effets de l'irradiation laser dans l'UV ou le visible de polyanions d'ADN dans un piège à ions quadripolaire. Lors de l'irradiation de simple brins ou de double hélices d'ADN en UV autour de 260 nm, nous avons observé un détachement d'électrons, donnant lieu à des radicaux anions. L'étude de la dépendence de l'efficacité de ce photodétachement d'électrons en fonction de la séquence des brins a révélé que ce phénomène était corrélé au potentiel d'ionisation des bases nucléiques. La guanine est la base la plus facilement oxydée, suivie de l'adénine, de la cytosine et de la thymine. En pratique, plus un brin contient de guanines, plus la formation de radicaux par photodétachement d'électrons est efficace. L'efficacité du photodétachement montre également une dépendence envers l'état de charge du brin (les plus chargés ont une efficacité de détachement plus élevée) et en fonction de la longueur d'onde (avec un maximum d'efficacité autour de 265 nm), montrant que la transition vers un état électronique excité des bases facilite le détachement d'électrons. Plus surprenant encore, des complexes avec des chromophores (ligands du sillon de l'ADN et intercalants) montrent également un photodétachement d'électrons, et ce avec des énergies de photons encore plus basses, correspondant à une absorption dans le visible (i.e. 550 nm pour l'éthidium). Ceci montre que les énergies de liaisons des électrons sont relativement faibles, puisqu'ils peuvent être détachés par des photons de 2.25 eV. Nous avons également étudié la fragmentation des radiaux ainsi produits, par CID dans le piège. Dans le cas des complexes avec les chromophores, les canaux de fragmentation principaux sont des pertes de neutres, y compris des morceaux de ligands. Il est intéressant de constater que les radicaux se fragmentent de la même manière, quel que soit le chromophore irradié qui a donné lieu à sa formation. Cecis suggère que les radicaux se réorganisent rapidement par rapport au temps de l'expérience. Dans le cas de simples brins (12-mères à 20-mères), nous avons constaté une fragmentation plus efficace des radicaux comparés aux ions à couches complètes de même charge. Plus intéressant, les canaux de dissociation sont très particuliers : alors que la CID sur ions à couches complètes donne majoritairement des ions 'w' et 'a-Base', la CID sur les radicaux donne des ions 'w', 'd', 'a radicalaires', et 'z radicalaires'. Il est aisé d'obtenir une bonne couverture de séquence à des énergies de collision faibles. A nouveau, bien que le détachement d'électrons soit initié par les bases guanines, la couverture de séquence est indépendante de la composition, suggérant une redistribution dans les radicaux. L'avantage principal de la fragmentation des radicaux est l'absence de fragments internes (ou 'double fragments'), ce qui facilite le séquencage de novo. De plus, selon notre expérience, la formation des radicaux est plus aisée par irradiation laser que par EDD. [less ▲]

Detailed reference viewed: 26 (0 ULg)
Full Text
Peer Reviewed
See detailElectron photodetachment dissociation of DNA polyanions in a quadrupole ion trap mass spectrometer
Gabelica, Valérie ULg; Tabarin, Thibault; Antoine, Rodolphe et al

in Analytical Chemistry (2006), 78(18), 6564-6572

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 ... [more ▼]

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. [less ▲]

Detailed reference viewed: 63 (1 ULg)