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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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See detailA Simple Method to Determine Electrospray Response Factors of Noncovalent Complexes
Gabelica, Valérie ULg; Rosu, Frédéric ULg; De Pauw, Edwin ULg

in Analytical Chemistry (2009), 81(16), 6708-6715

The quantitative study of noncovalent complexes by electrospray mass spectrometry requires the determination of the relative response of each species. The method proposed here to determine the ... [more ▼]

The quantitative study of noncovalent complexes by electrospray mass spectrometry requires the determination of the relative response of each species. The method proposed here to determine the electrospray response factors is based on the use of (1) an internal standard and (2) the mass balance equation applied to one binding partner M, for which different complexes MxLy are detected in the electrospray mass spectra. A set of experiments providing various ratios between the complexes (e.g. different ligand concentrations in a titration experiment or different time points in a kinetics experiment) is used to generate a set of independent linear equations that can be solved using simple matrix algebra to find the response factors of each MxLy complex relative to that of the internal standard. The response factors can then be used to determine equilibrium dissociation constants or for the quantitative monitoring of reaction kinetics. The first is illustrated with a study of DNA-ligand complexes, where we show that neither minor groove binding nor intercalation dramatically affects the DNA response factor. The second is illustrated with a study of the association kinetics of the telomeric G-quadruplex dGGG(TTAGGG)3 with its complementary strand, where the response factors allow correcting for the relative response of the quadruplex and the long duplex and obtaining reproducible association rate constants independently of the source tuning potentials. [less ▲]

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See detailIR and UV Spectroscopy of DNA Ions Stored in Trap Instruments
Gabelica, Valérie ULg

Conference (2008, October 11)

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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 ▲]

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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 ▲]

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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 ▲]

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See detailProteome alteration induced by hTERT transfection of human fibroblast cells
Mazzucchelli, Gabriel ULg; Gabelica, Valérie ULg; Smargiasso, Nicolas ULg et al

in Proteome Science (2008), 6(1), 12

Background: Telomerase confers cellular immortality by elongating telomeres, thereby circumventing the Hayflick limit. Extended-life-span cells have been generated by transfection with the human ... [more ▼]

Background: Telomerase confers cellular immortality by elongating telomeres, thereby circumventing the Hayflick limit. Extended-life-span cells have been generated by transfection with the human telomerase reverse transcriptase (hTERT) gene. hTERT transfected cell lines may be of outstanding interest to monitor the effect of drugs targeting the telomerase activity. The incidence of hTERT gene transfection at the proteome level is a prerequisite to that purpose. The effect of the transfection has been studied on the proteome of human fibroblast (W138). Cytosolic and nuclear fractions of W138 cells, empty vector transfected W138 (W138-HPV) and hTERT W138 cells were submitted to a 2D-DIGE (Two-Dimensional Differential In-Gel Electrophoresis) analysis. Only spots that had a similar abundance in W138 and W138-HPV, but were differentially expressed in W138 hTERT were selected for MS identification. This method directly points to the proteins linked with the hTERT expression. Number of false positive differentially expressed proteins has been excluded by using control W138-HPV cells. The proteome alteration induced by hTERT W138 transfection should be taken into account in subsequent use of the cell line for anti-telomerase drugs evaluation. Results: 2D-DIGE experiment shows that 57 spots out of 2246 are significantly differentially expressed in the cytosolic fraction due to hTERT transfection, and 38 were confidently identified. In the nuclear fraction, 44 spots out of 2172 were selected in the differential proteome analysis, and 14 were identified. The results show that, in addition to elongating telomeres, hTERT gene transfection has other physiological roles, among which an enhanced ER capacity and a potent cell protection against apoptosis. Conclusion: We show that the methodology reduces the complexity of the proteome analysis and highlights proteins implicated in other processes than telomere elongation. hTERT induced proteome changes suggest that telomerase expression enhances natural cell repair mechanisms and stress resistance probably required for long term resistance of immortalized cells. Thus, hTERT transfected cells can not be only consider as an immortal equivalent to parental cells but also as cells which are over-resistant to stresses. These findings are the prerequisite for any larger proteomics aiming to evaluate anti-telomerase drugs proteome alteration and thus therapeutics induced cell reactions. [less ▲]

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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)

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See detailProteomic analysis of telomerase inhibition by telomere specific ligands
Mazzucchelli, Gabriel ULg; Gabelica, Valérie ULg; Smargiasso, Nicolas ULg et al

in Anticancer Research (2008), 28(5c), 3257-3258

Telomeres consist of protein complexes and repeated ‘TTAGGG’ double strand DNA sequences ended by a 3’ single strand DNA of the same sequence. Progressive telomere shortening is observed in vitro upon ... [more ▼]

Telomeres consist of protein complexes and repeated ‘TTAGGG’ double strand DNA sequences ended by a 3’ single strand DNA of the same sequence. Progressive telomere shortening is observed in vitro upon cell divisions and with ageing in vivo. At a critical telomere length, shortened telomeres trigger a permanent growth arrest known as replicative senescence. Telomerase is an RNA-dependent DNA polymerase that extends telomeres by adding ‘TTAGGG’ repeats. It consists of a functional RNA component (hTR) which serves as template and a catalytic protein (hTERT) with reverse transcriptase activity. The expression of hTERT alone is sufficient for the immortalisation of cells. Telomerase is highly expressed in tumor cells but at very low level in most somatic cells. These observations make the telomerase an attractive target for anticancer strategies. One of these strategies relies on the use of drug candidates able to stabilize the particular telomere G-quadruplex DNA structures. The stabilization of these structures makes the telomere inaccessible for telomerase and thus inhibits telomerase activity. The effect of the hTERT transfection was first studied on the proteome of human WI38 fibroblast cells (1). Then, the proteome alteration response of hTERT transfected WI38 cells induced by the treatment of two G-quadruplexes ligands, telomestatin and TMPyP4, was analyzed. Both compounds can inhibit telomerase but have different selectivity for the different G-quadruplexes structures. Proteome analysis of the treated cells reveals that TMPyP4 induces much more protein expression alterations than telomestatin probably due to its poor selectivity. TMPyP4 induces especially a drastic down expression of the hnRNPs, a modulation of the proteasome pathway, an apparent decrease of the translation and an over expression of several molecular chaperones. Telomestatin induces in particular an over expression of the protein BCL2A1 which is involved in drug resistance of cancer cells and a probable increase of the translation. Both treatments have a common effect particularly on the molecular chaperone CCT (down expression), HSP90 alpha (over expression) and hnRNP D (down expression). The protein HSP90 alpha is also over expressed in hTERT transfected cells compared to parental cells. This protein is already a promising anticancer target protein due to its central role in oncogenesis and in telomerase activity regulation. 1 Mazzucchelli et al: Proteome Science 6: 12, 2008. [less ▲]

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See detailSelective recognition of pyrimidine–pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
Bahr, Matthias; Gabelica, Valérie ULg; Granzhan, Anton et al

in Nucleic Acids Research (2008), 36

Binding of three macrocyclic bis-intercalators, derivatives of acridine and naphthalene, and two acyclic model compounds to mismatch-containing and matched duplex oligodeoxynucleotides was analyzed by ... [more ▼]

Binding of three macrocyclic bis-intercalators, derivatives of acridine and naphthalene, and two acyclic model compounds to mismatch-containing and matched duplex oligodeoxynucleotides was analyzed by thermal denaturation experiments, electrospray ionization mass spectrometry studies (ESI-MS) and fluorescent intercalator displacement (FID) titrations. The macrocyclic bis-intercalators bind to duplexes containing mismatched thymine bases with high selectivity over the fully matched ones, whereas the acyclic model compounds are much less selective and strongly bind to the matched DNA. Moreover, the results from thermal denaturation experiments are in very good agreement with the binding affinities obtained by ESI-MS and FID measurements. The FID results also demonstrate that the macrocyclic naphthalene derivative BisNP preferentially binds to pyrimidine– pyrimidine mismatches compared to all other possible base mismatches. This ligand also efficiently competes with a DNA enzyme (M.TaqI) for binding to a duplex with a TT-mismatch, as shown by competitive fluorescence titrations. Altogether, our results demonstrate that macrocyclic distance- constrained bis-intercalators are efficient and selective mismatch-binding ligands that can interfere with mismatch-binding enzymes. [less ▲]

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See detailA short C-rich PNA fragment capable to form novel G-quadruplex-PNA complexes
Amato, Jussara; Gabelica, Valérie ULg; Borbone, Nicola et al

in Nucleic Acids Symposium Series (2008), 52

In this work we investigated the interaction between the short ac(4)a C-rich peptide nucleic acid (PNA) probe and two intramolecular G-quadruplex targets having the same G-tetrad core, but different ... [more ▼]

In this work we investigated the interaction between the short ac(4)a C-rich peptide nucleic acid (PNA) probe and two intramolecular G-quadruplex targets having the same G-tetrad core, but different folding topologies. The T(G(4)T)(3)G(4)T and the recently reported tetra-end-linked-(TG(4)T)(4) G-rich oligonucleotides (GROs) were chosen and synthesized for this study. UV, CD, and MS experiments revealed the formation of novel 1:1 G-quadruplex-PNA complexes besides the expected DNA-PNA heteroduplexes [less ▲]

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See detailLigand binding to tetra-end-linked (TGGGGT)4 G-quadruplexes: an electrospray mass spectroscopy study
Amato, Jussara; Oliviero, Giorgia; Borbone, Nicola et al

in Nucleic Acids Symposium Series (2008), 52

The binding properties of a series of known G-quadruplex ligands have been studied by ESI-MS experiments. The tetramolecular (TG(4)T)(4) quadruplex and its analogues I and II blocked, respectively, at the ... [more ▼]

The binding properties of a series of known G-quadruplex ligands have been studied by ESI-MS experiments. The tetramolecular (TG(4)T)(4) quadruplex and its analogues I and II blocked, respectively, at the 3' or 5'-end by a tetra-end-linker (TEL) unit were chosen as the ligands targets. The stoichiometries of the obtained complexes as well as the ligand affinity and selectivity to the different quadruplexes were determined to deduce the ligand binding site. The TEL derivatives I and II allowed the probing of the grooves contribution to the binding of ligands to G-quadruplexes, demonstrating that the 3' and 5' quartets are not equivalent binding sites for ligand end-stacking. [less ▲]

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See detailElectrospray Mass Spectrometry to Study Drug-Nucleic Acids Interactions
Rosu, Frédéric ULg; De Pauw, Edwin ULg; Gabelica, Valérie ULg

in Biochimie (2008), 90(7), 1074-1087

We present here a tutorial review on the electrospray mass spectrometry technique and its applications to the study of drug-nucleic acid non-covalent complexes. Particular emphasis has been made on the ... [more ▼]

We present here a tutorial review on the electrospray mass spectrometry technique and its applications to the study of drug-nucleic acid non-covalent complexes. Particular emphasis has been made on the basic principles of the technique, to allow even the non-specialist to design fit-for-purpose mass spectrometry experiments and interpret the results. Standard applications will be described in detail, including the determination of stoichiometries and equilibrium binding constants of non-covalent complexes, the study of binding kinetics, and the development of ligand screening assays. We also outline the potentials of more advanced and/or more recent MS-based techniques (tandem mass spectrometry, ion mobility spectrometry and gas-phase spectroscopy) for the study of the nucleic acid-ligand complexes. [less ▲]

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See detailLigands playing musical chairs with G-quadruplex DNA: A rapid and simple displacement assay for identifying selective G-quadruplex binders
Monchaud, David; Allain, C.; Bertrand, Hélène et al

in Biochimie (2008), 90(8), 1207-1223

We report here the details of G4-FID (G-quadruplex fluorescent intercalator displacement), a simple method aiming at evaluating quadruplex DNA binding affinity and quadruplex- over duplex-DNA selectivity ... [more ▼]

We report here the details of G4-FID (G-quadruplex fluorescent intercalator displacement), a simple method aiming at evaluating quadruplex DNA binding affinity and quadruplex- over duplex-DNA selectivity of putative ligands. This assay is based on the loss of fluorescence upon displacement of thiazole orange from quadruplex and duplex-DNA matrices. The original protocol was tested using various quadruplex and duplex-DNA targets, and with a wide panel of G-quadruplex ligands belonging to different families (i.e. from quinacridines to metalloorganic ligands) likely to display various binding modes. The reliability of the assay is further supported by comparisons with FRET-melting and ESI-MS assays. [less ▲]

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See detailInfrared Signature of DNA G-Quadruplexes in the Gas Phase
Gabelica, Valérie ULg; Rosu, Frédéric ULg; De Pauw, Edwin ULg et al

in Journal of the American Chemical Society (2008), 130(6), 1810-1

DNA oligonucleotide ions forming G-quadruplex structures were studied in the gas phase using IRMPD spectroscopy. Data interpretation on these large biomolecule ions was made using carefully chosen control ... [more ▼]

DNA oligonucleotide ions forming G-quadruplex structures were studied in the gas phase using IRMPD spectroscopy. Data interpretation on these large biomolecule ions was 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. [less ▲]

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See detailCooperative 2:1 Binding of a Bisphenothiazine to Duplex DNA
Rosu, Frédéric ULg; Gabelica, Valérie ULg; De Pauw, Edwin ULg et al

in Chembiochem : A European Journal of Chemical Biology (2008), 9

Highly cooperative formation of a 2:1 complex was revealed by electrospray mass spectrometry experiments, and a structural model is proposed.

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See detailG-Quadruplex DNA Assemblies: Loop Length, Cation Identity, and Multimer Formation
Smargiasso, Nicolas ULg; Rosu, Frédéric ULg; Hsia, Wei et al

in Journal of the American Chemical Society (2008), 130(31), 10208-10216

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied ... [more ▼]

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGWiGGGWjGGGWkGGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K+ inducing more parallel multimers than NH4+ and Na+. Structural possibilities are discussed for the new quadruplex higher-order assemblies. [less ▲]

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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)

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