References of "Gabelica, Valérie"
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See detailMass spectrometry of G-quadruplexes
Gabelica, Valérie ULg

Conference (2010, May 31)

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See detailTetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry
Rosu, Frédéric ULg; Gabelica, Valérie ULg; Poncelet, Harmonie et al

in Nucleic Acids Research (2010)

Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG5T, in ammonium acetate. The intermediates and products were ... [more ▼]

Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG5T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal evolution of each species allows us to propose the following formation mechanism. (i) Monomers, dimers and trimers are present at equilibrium already in the absence of ammonium acetate. (ii) The addition of cations promotes the formation of tetramers and pentamers that incorporate ammonium ions and therefore presumably have stacked guanine quartets in their structure. (iii) The pentamers eventually disappear and tetramers become predominant. However, these tetramers do not have their four strands perfectly aligned to give five G-quartets: the structures contain one ammonium ion too few, and ion mobility spectrometry shows that their conformation is more extended. (iv) At 4°C, the rearrangement of the kinetically trapped tetramers with presumably slipped strand(s) into the perfect G-quadruplex structure is extremely slow (not complete after 4 months). We also show that the addition of methanol to the monomer solution significantly accelerates the cation-induced G-quadruplex assembly. [less ▲]

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See detailNew Advances in the Understanding of the In-Source Decay Fragmentation of Peptides in MALDI-TOF-MS.
Demeure, Kevin ULg; Gabelica, Valérie ULg; De Pauw, Edwin ULg

in Journal of the American Society for Mass Spectrometry (2010), 21(11), 1906-17

In-source decay (ISD) is a rapid fragmentation occurring in the matrix-assisted laser desorption/ionization (MALDI) source before the ion extraction. Despite the increasing interest for peptides de novo ... [more ▼]

In-source decay (ISD) is a rapid fragmentation occurring in the matrix-assisted laser desorption/ionization (MALDI) source before the ion extraction. Despite the increasing interest for peptides de novo sequencing by ISD, the influence of the matrix and of the peptide itself is not yet fully understood. Here we compare matrices with high ISD efficiencies to gain deeper insight in the ISD fragmentation process(es). The major ISD fragments are the c- and z-ions, but other types of fragments are also observed, and their origin is studied here. Two main pathways lead to fragmentation in the source: a radical-induced pathway that leads to c-, z-, w-, and d-ions, and a thermally activated pathway that leads to y-, b-, and a-ions. A detailed analysis of the ISD spectra of selected peptides revealed that (1) the extents of the two in-source pathways are differently favored depending on the matrix used, that (2) the presence of a positive/negative charge on the radical-induced fragments is necessary for their observation in positive/negative mode, respectively, and that (3), for a same peptide, the patterns of the different types of fragments differ according to the matrix used. [less ▲]

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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 ▲]

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See detailInternal energy content of ions in a travelling wave ion guide
Morsa, Denis ULg; Gabelica, Valérie ULg; Rosu, Frédéric ULg et al

Conference (2010)

Travelling wave ion guides (TWIGs) separate of ions according to their mobility and, at constant charge, according to their shape. The ion mobility separation itself should not modify the shape of the ... [more ▼]

Travelling wave ion guides (TWIGs) separate of ions according to their mobility and, at constant charge, according to their shape. The ion mobility separation itself should not modify the shape of the systems investigated. It was recently suggested by Shvartsburg et al. that the higher fields used in TWIGs than in traditional drift tubes would cause significant heating of the ions. We present a quantitative analysis of the amount of internal energy imparted to ions as they are separated in TWIGs. Benzylpyridinium ions were chosen as “thermometer” ions. Based on arrival time distributions, the fragment ion population is separated as a function of the place of formation: before, in, or after the TWIG. Fragmentation all along the TWIG was observed. The roles of the travelling wave’s voltage, speed, and of the gas nature and pressure will be discussed in detail as well of the consequences on instruments performances. [less ▲]

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See detailStructure-based design of selective high-affinity telomeric quadruplex-binding ligands
Lombardo, Caterina M.; Martínez, Iria S.; Haider, Shozeb et al

in Chemical Communications (2010), 46

A library of triazole-based telomeric quadruplex-selective ligands has been developed that mimic an established family of tri-substituted acridine-based ligands, using crystal structure data as a starting ... [more ▼]

A library of triazole-based telomeric quadruplex-selective ligands has been developed that mimic an established family of tri-substituted acridine-based ligands, using crystal structure data as a starting-point for computer-based design. Binding affinities, estimated by electrospray mass spectrometry, are in accord with the design concept [less ▲]

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See detailCation Involvement in Telomestatin Binding to G-Quadruplex DNA
Rosu, Frédéric ULg; Gabelica, Valérie ULg; Smargiasso, Nicolas ULg et al

in Journal of Nucleic Acids (2010)

The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show ... [more ▼]

The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show the incorporation of one extra ammonium ion in the telomestatin complexes. Experiments on telomestatin alone also show that the telomestatin alone is able to coordinate cations in a similar way as a crown ether. Finally, density functional theory calculations suggest that in the G-quadruplex-telomestatin complex, potassium or ammonium cations are located between the telomestatin and a G-quartet. This study underlines that monovalent cation coordination capabilities should be integrated in the rational design of G-quadruplex binding ligands. [less ▲]

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See detailElectrospray Mass Spectrometry of Telomeric RNA (TERRA) Reveals the Formation of Stable Multimeric G-Quadruplex Structures
Collie, Gavin W.; Parkinson, Gary N.; Neidle, Stephen et al

in Journal of the American Chemical Society (2010), 132(27), 93289334

We report on the self-assembled structures formed by 12-mer, 22-mer, and 45-mer telomeric RNA (telRNA/TERRA) sequences compared to their DNA analogues, as studied by electrospray mass spectrometry ... [more ▼]

We report on the self-assembled structures formed by 12-mer, 22-mer, and 45-mer telomeric RNA (telRNA/TERRA) sequences compared to their DNA analogues, as studied by electrospray mass spectrometry, circular dichroism, and thermal denaturation. The major difference between telomeric RNA and DNA sequences is the ability of telomeric RNA to form higher-order dimeric assemblies, initiated by cation-mediated stacking of two parallel G-quadruplex subunits. The 5′-5′ stacking had been observed recently by NMR for the r(GGGUUAGGGU) 10-mer (Martadinata, H.; Phan, A. T. J. Am. Chem. Soc. 2009, 131, 2570); the present work shows that stacking also occurs for the 22-mer containing four G-tracts and for the 45-mer containing eight G-tracts, suggesting a general structural feature of telomeric RNA. The importance of kinetic effects in multimer formation, unfolding, and structural rearrangements is also highlighted. [less ▲]

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See detailElectrospray mass spectrometry of noncovalent complexes between small molecule ligands and nucleic acids
Gabelica, Valérie ULg

in Joseph H., Banoub; Patrick A., Limbach (Eds.) Mass spectrometry of nucleosides and nucleic acids (2010)

CONTENTS 8.1 Introduction 8.1.1 ESI-MS of Noncovalent Complexes 8.1.2 Nucleic Acid Targeting by Small Molecules 8.2 Electrospray Mass Spectrometry of Nucleic Acid Noncovalent Complexes 8.2.1 ... [more ▼]

CONTENTS 8.1 Introduction 8.1.1 ESI-MS of Noncovalent Complexes 8.1.2 Nucleic Acid Targeting by Small Molecules 8.2 Electrospray Mass Spectrometry of Nucleic Acid Noncovalent Complexes 8.2.1 Stoichiometries: Number of Strands and Detection of Nucleic Acid Higher-Order Structures 8.2.2 Stoichiometries: Number of Bound Ligands 8.2.3 Role of Cations in Nucleic Acid Structure and Ligand Binding 8.2.4 Determination of Equilibrium Binding Constants 8.2.5 Are the Relative Intensities Proportional to the Abundances in Solution? 8.3 Characterizing Noncovalent Ligand Binding by MS/MS of the Complexes 8.3.1 Overview of Dissociation Pathways 8.3.2 How Observed Pathways Depend on Instrumental Parameters 8.3.3 How Observed Pathways Depend on Ligand Binding 8.3.4 Probing the Energetics of Ligand-DNA Interactions 8.3.5 Determining the Ligand Binding Mode 8.3.6 Determining the Ligand Binding Site by MS/MS 8.4 Conclusion and Outlook References [less ▲]

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See detailDetermination of equilibrium association constants of ligand-DNA complexes by electrospray mass spectrometry
Gabelica, Valérie ULg

in Keith R., Fox (Ed.) Drug-DNA Interaction Protocols (2010)

Electrospray mass spectrometry can be used to detect ligand-DNA noncovalent complexes formed in solution. This chapter describes how to determine equilibrium association constants of the complexes ... [more ▼]

Electrospray mass spectrometry can be used to detect ligand-DNA noncovalent complexes formed in solution. This chapter describes how to determine equilibrium association constants of the complexes. Particular attention is devoted to describing how to tune an electrospray mass spectrometer using a 12-mer oligodeoxynucleotides duplex in order to perform these experiments. This protocol can then be applied to any nucleic acid structure that can be ionized with electrospray mass spectrometry. [less ▲]

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See detailZwitterionic i-motif structures are preserved in DNA negatively charged ions produced by electrospray mass spectrometry
Rosu, Frédéric ULg; Gabelica, Valérie ULg; Joly, Laure ULg et al

in Physical Chemistry Chemical Physics [=PCCP] (2010), 12

DNA cytosine-rich strands can fold into an intercalated motif (i-motif) structure. The i-motif is formed by mutually intercalated duplexes containing proton-mediated C-H(+)-C (cytosine-proton-cytosine ... [more ▼]

DNA cytosine-rich strands can fold into an intercalated motif (i-motif) structure. The i-motif is formed by mutually intercalated duplexes containing proton-mediated C-H(+)-C (cytosine-proton-cytosine) base pairs. Negatively charged ions of DNA i-motifs produced by electrospray mass spectrometry are therefore zwitterionic if the base pairing motif is preserved in the gas phase. Here we used IRMPD spectroscopy and ion mobility spectrometry to assess whether i-motif structures were preserved in the gas phase. We first investigated the IRMPD spectral signature of the tetramer [dC(6)](4), which can only be formed via C-H(+)-C base pairing, compared to the single strand dC(6). The IR signature of i-motif formation is an apparent broadening of the band at 1650 cm(-1). DFT calculations show this apparent broadening is actually due to blue-shifts of the NH(2) scissoring modes and red shifts of C[double bond, length as m-dash]O stretching modes. We then investigated the gas-phase conformations of the telomeric sequence d(CCCAAT)(3)CCC, that can form an intramolecular i-motif, by performing IRMPD spectroscopy and ion mobility spectrometry as a function of the charge state. We show that the negative ions of the lowest charge states correspond to a preserved i-motif structure. This is the first demonstration of the native extraction of solution-phase zwitterionic nucleic acids using negative electrospray ionization. [less ▲]

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See detailSelectivity in small molecule binding to human telomeric RNA and DNA quadruplexes
Collie, Gavin; Reszka, Anthony P.; Haider, Shozeb M. et al

in Chemical Communications (2009), (48), 7482-7484

Quadruplex RNAs are less well understood than their DNA counterparts, yet of potentially high biological relevance. The interactions of several quadruplex-binding ligands with telomeric RNA quadruplexes ... [more ▼]

Quadruplex RNAs are less well understood than their DNA counterparts, yet of potentially high biological relevance. The interactions of several quadruplex-binding ligands with telomeric RNA quadruplexes are reported and compared with their binding to the analogous DNA quadruplexes. [less ▲]

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See detailIR and UV spectroscopic signatures of DNA structures in the gas phase
Gabelica, Valérie ULg

Conference (2009, July 08)

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See detailIR spectroscopy of DNA structures
Gabelica, Valérie ULg

Conference (2009, June 11)

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See detailA simple method for determination of electrospray response factors of noncovalent complexes: application to DNA G-quadruplex binding and self-assembly
Gabelica, Valérie ULg; Amato, Jussara; Oliviero, Giorgia et al

Conference (2009, June 04)

Introduction Electrospray mass spectrometry (ESI-MS) is now widely used to investigate non-covalent assemblies, and the power of the method resides in the individual detection of the various ... [more ▼]

Introduction Electrospray mass spectrometry (ESI-MS) is now widely used to investigate non-covalent assemblies, and the power of the method resides in the individual detection of the various stoichiometries present in the mixture. However, to characterize the mixture quantitatively (i.e. to determine the concentration of each constituent), the biggest challenge comes from the fact that electrospray response factors of all constituents can be different, especially for constituents of significantly different masses and charges. Here we present a novel and simple method to determine the response factors of all constituents, using an internal standard. The method can be transposed to a wide variety of biological problems and to different ionization methods. Experimental All oligodeoxynucleotides were purchased from Eurogentec (Seraing, Belgium). G-quadruplexes formation is induced by addition of ammonium acetate (150 mM) to the guanine-rich strand. Polythymines (e.g. dT6) with m/z not overlapping with those of the complexes were used as internal standards. The ESI mass spectra were acquired using a Q-TOF Ultima Global (Waters, Manchester, UK) in the negative ion mode, with source parameters optimized for detecting the intact complexes. Quadruplex-ligand binding constants were quantified by titration of the quadruplex with the ligand (BOQ1, Dr. Teulade-Fichou). The kinetics of G-quadruplex self-assembly was monitored on-line, with the starting time defined by the addition of ammonium to the single strand. Peak areas were calculated using MassLynx and data were processed using Mathcad. Preliminary results Let us illustrate the method for the characterization of the self-assembly of dCGGTGGT. In NH4OAc, this G-rich strand forms a tetramer within a few hours, but the most stable species is an octamer, which is formed after a few days. The relative intensities of monomer, tetramer and octamer vary with the experimental settings: harsher conditions favor the transmission of the larger complexes. It is therefore foolish to assume that the response factors of the monomer, tetramer and octamer are equal. Using dT6 as an internal reference, we monitored the self-assembly kinetics by recording at several time points the following intensities: I(ref2-), I(G12-), I(G45-) and I(G89-), where Gn indicates a complex containing n G-rich strands. For each species Gn, we define Rn as its response factor relative to that of the reference: [Gn]/[ref] = Rn * I(Gn)/I(ref). At each time point the mass balance equation for the strand concentration must be satisfied: [G]tot = [G1] + 4[G4] + 8[G8]. Substituting with the definition of Rn’s one obtains a set of equations: [G]tot = [ref] * {R1*(I(G1)/I(ref) + 4R4*I(G4)/I(ref) + 8R8*I(G8)/I(ref)}. If the number of equations (time points) is greater than the number of unknown response factors, the least-squares fit to this system of equations is calculated using the Moore-Penrose pseudoinverse of the matrix constituted by the intensity ratios. Once all response factors are known, concentrations are recalculated at each time point, providing detailed characterization of the reaction kinetics, including reaction intermediates. We will also show that the same method can be used to quantify ligand binding using titration of the substrate by the ligand. This will be illustrated with titration of the quadruplex (TGGGGT)4 by ligand BOQ1. This ligand binds to the quadruplex and also produces ligand-bridged quadruplex multimers, which the present method allows quantifying for the first time. [less ▲]

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See detailElectron detachment dissociation (EDD) pathways in oligonucleotides
Kinet, Catherine ULg; Gabelica, Valérie ULg; Balbeur, Dorothée ULg et al

in International Journal of Mass Spectrometry (2009), 283

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 ... [more ▼]

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. [less ▲]

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See detailHybridization of short complementary PNAs to G-quadruplex forming oligonucleotides: An electrospray mass spectrometry study.
Amato, Jussara; Oliviero, Giorgia; De Pauw, Edwin ULg et al

in Biopolymers (2009), 91(4), 244-255

We investigated the interaction of the short PNA strand [acccca]-PNA with oligodeoxynucleotides containing one, two, or four tracts of TGGGGT units. Electrospray ionization mass spectrometry allowed ... [more ▼]

We investigated the interaction of the short PNA strand [acccca]-PNA with oligodeoxynucleotides containing one, two, or four tracts of TGGGGT units. Electrospray ionization mass spectrometry allowed exploring the wide variety of complex stoichiometries that were found to coexist in solution. In water, the PNA strand forms short heteroduplexes with the complementary DNA sequences, but higher-order structures are also found, with PNA(2n)*DNA(n) triplex units, culminating in precipitation at very low ionic strength. In the presence of ammonium acetate, there is a competition between PNA*DNA heteroduplex formation and DNA G-quadruplex formation. Heteroduplex formation is favored when the PNA + DNA mixture in ammonium acetate is heated and cooled at room temperature, but not if the PNA is added at room temperature to the pre-formed G-quadruplex. We also found that the short [acccca]-PNA strand binds to G-quadruplexes. (c) 2008 Wiley Periodicals, Inc. Biopolymers, 2008. [less ▲]

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See detailPutative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes
Smargiasso, Nicolas ULg; Gabelica, Valérie ULg; Damblon, Christian ULg et al

in BMC Genomics (2009), 10

Background. Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can ... [more ▼]

Background. Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS) in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro. Results. We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes). The var gene family encodes PfEMP1, the parasite’s major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q) to form stable Gquadruplex structures in vitro was confirmed using 1H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q. Conclusions. This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family. [less ▲]

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