0000000000627000

AUTHOR

David Monchaud

showing 49 related works from this author

“ One Ring to Bind Them All ”—Part I: The Efficiency of the Macrocyclic Scaffold for G-Quadruplex DNA Recognition

2010

International audience; Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the "standard" B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding …

ScaffoldArticle Subjectlcsh:QH426-470Review ArticleBiology010402 general chemistryBioinformaticsRing (chemistry)G-quadruplex01 natural sciencesBiochemistryTelomestatinlcsh:Biochemistrychemistry.chemical_compound[CHIM] Chemical Sciences[CHIM]Chemical Scienceslcsh:QD415-436Molecular BiologyDna recognitionComputingMilieux_MISCELLANEOUSNatural product010405 organic chemistryBinding propertiesPorphyrinCombinatorial chemistry3. Good health0104 chemical scienceslcsh:Geneticschemistry
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An oxidatively damaged G-quadruplex/hemin DNAzyme.

2020

International audience; Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex stability, lower hemin affinity and a modification of the nature of hemin binding sites.

GuanineGuanineDeoxyribozyme010402 general chemistryG-quadruplex01 natural sciencesCatalysisOxidative damage03 medical and health scienceschemistry.chemical_compoundMaterials Chemistrypolycyclic compoundsheterocyclic compoundsBinding site[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biochemistry [q-bio.BM]030304 developmental biology0303 health sciencesMolecular StructureMetals and AlloysGeneral ChemistryDNA Catalyticequipment and supplies0104 chemical sciencesSurfaces Coatings and FilmsElectronic Optical and Magnetic MaterialsG-QuadruplexeschemistryCeramics and CompositesBiophysicsOxidation-ReductionHeminChemical communications (Cambridge, England)
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Template-Assembled Synthetic G-Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies

2010

A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular…

Models MolecularDna duplexPorphyrinsStereochemistryOligonucleotides010402 general chemistryG-quadruplexLigands01 natural sciencesCatalysischemistry.chemical_compoundStructure-Activity Relationship[CHIM.ANAL]Chemical Sciences/Analytical chemistry[CHIM]Chemical SciencesComputer SimulationBinding siteSurface plasmon resonancePromoter Regions GeneticNuclear Magnetic Resonance BiomolecularComputingMilieux_MISCELLANEOUSBinding SitesMolecular Structure010405 organic chemistryChemistryOrganic ChemistryGeneral ChemistryDNASurface Plasmon ResonanceAffinities0104 chemical sciencesQuadruplex DNAG-QuadruplexesIntramolecular forceNucleic Acid Conformation[ CHIM.ANAL ] Chemical Sciences/Analytical chemistryDNA
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Quadruplex detection in human cells

2020

Abstract The precise detection of both DNA and RNA quadruplexes in human cells remains challenging. Efforts are being invested to design, synthesize and operate molecular tools to track and detect quadruplexes in cells. Such probes now have sufficient molecular specificity and suitable spectroscopic properties to shed light on quadruplexes in their cellular context, thus providing reliable details about their existence in cells. Herein, the most important steps in this line of development are summarized, from the very first attempts with organometallic complexes to the development of immunodetection technologies; and from in vitro to live-cell investigations performed with cell-permeable qu…

0301 basic medicine[SDV.GEN]Life Sciences [q-bio]/Genetics[SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/ImagingRNAContext (language use)Computational biology[CHIM.THER]Chemical Sciences/Medicinal Chemistry[SDV.BC]Life Sciences [q-bio]/Cellular BiologyMolecular systems010402 general chemistry01 natural sciencesSmall molecule0104 chemical sciences03 medical and health scienceschemistry.chemical_compound030104 developmental biologychemistryheterocyclic compounds[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular BiologyDNAComputingMilieux_MISCELLANEOUS
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The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties.

2020

While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ–DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biot…

[SDV.BIO]Life Sciences [q-bio]/BiotechnologyDeoxyribozyme010402 general chemistryG-quadruplex01 natural sciencesCofactor03 medical and health scienceschemistry.chemical_compoundheterocyclic compounds030304 developmental biologychemistry.chemical_classification0303 health sciencesbiologyChemistryActive siteGeneral Chemistry[CHIM.CATA]Chemical Sciences/CatalysisCombinatorial chemistry[SDE.ES]Environmental Sciences/Environmental and Society0104 chemical sciencesChemistryEnzymebiology.proteinSelectivityPeroxidaseHeminChemical science
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The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation

2019

Recent advances in the use of radiometals for both imaging and therapy has spurred on the development of an original chemistry that endows radionuclide-chelating molecular cages with ever sharper physicochemical properties. Macrocyclic polyamines (MPAs) such as cyclen and DOTA are among the most frequently encountered cages for the design of new radiotracers, owing to their versatile chemistry that makes them customizable molecular tools. The idea of using MPAs for alternative purposes has recently emerged, with an eye towards benefiting from their unique topology, versatility, symmetry and water-solubility. This review summarizes strategies that have been recently implemented in which MPAs…

Scope (project management)010405 organic chemistryOrganic ChemistryChemical biologyNanotechnology010402 general chemistry01 natural sciences0104 chemical sciencesMetal chelationchemistry.chemical_compoundCyclenchemistryPhysical and Theoretical ChemistryTopology (chemistry)Material chemistryEuropean Journal of Organic Chemistry
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Applications of guanine quartets in nanotechnology and chemical biology

2019

Guanine and related nucleobases such as guanosine, deoxyguanosine and isoguanosine are notable molecular tools for designing functional supramolecular assemblies. This popularity originates in their ability to self-assemble via a unique topological pluralism — as isolated nucleobases, discrete macrocyclic quartets and virtually infinite linear ribbons — that endows them with a considerable functional versatility. Many programmes have been launched to fine-tune the chemical properties of guanine derivatives, to make them usable under different experimental conditions, such as in organic or aqueous environments, and responsive to external stimuli, such as ionic strength, pH, light or temperat…

[SDV.BIO]Life Sciences [q-bio]/Biotechnology[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM]010405 organic chemistryGuanineGeneral Chemical EngineeringChemical biologySupramolecular chemistryGuanosineNanotechnologyGeneral Chemistry010402 general chemistry01 natural sciences0104 chemical sciencesNucleobasechemistry.chemical_compound[CHIM.GENI]Chemical Sciences/Chemical engineeringchemistryGuanine-QuartetsDeoxyguanosineSoft matter[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]ComputingMilieux_MISCELLANEOUS
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Prefolded Synthetic G-Quartets Display Enhanced Bioinspired Properties

2016

International audience; A water-soluble template-assembled synthetic G-quartet (TASQ) based on the use of a macrocyclodecapeptide scaffold was designed to display stable intramolecular folds alone in solution. The preformation of the guanine quartet, demonstrated by NMR and CD investigations, results in enhanced peroxidase-type biocatalytic activities and improved quadruplex-interacting properties. Comparison of its DNAzyme-boosting properties with the ones of previously published TASQ revealed that, nowadays, it is the best DNAzyme-boosting agent.

0301 basic medicineModels MolecularGuanineStereochemistryDNAzymewaterSupramolecular chemistryDeoxyribozymednainsights010402 general chemistryG-QuartetsG-quadruplexchemistry[ CHIM ] Chemical Sciences01 natural sciencesCatalysissupramolecular chemistryg-quadruplex structures03 medical and health scienceschemistry.chemical_compoundG-quartets[CHIM]Chemical SciencesrnaComputingMilieux_MISCELLANEOUSligandsbiologyOrganic Chemistry[CHIM.CATA]Chemical Sciences/CatalysisGeneral ChemistryDNA CatalyticSmall moleculeG-quadruplexes0104 chemical sciencesSolutionssmall molecules030104 developmental biologychemistryBiocatalysisIntramolecular forceBiocatalysisNucleic Acid Conformationcyclodecapeptideacid
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Dual targeting of higher-order DNA structures by azacryptands induces DNA junction-mediated DNA damage in cancer cells

2021

Abstract DNA is intrinsically dynamic and folds transiently into alternative higher-order structures such as G-quadruplexes (G4s) and three-way DNA junctions (TWJs). G4s and TWJs can be stabilised by small molecules (ligands) that have high chemotherapeutic potential, either as standalone DNA damaging agents or combined in synthetic lethality strategies. While previous approaches have claimed to use ligands that specifically target either G4s or TWJs, we report here on a new approach in which ligands targeting both TWJs and G4s in vitro demonstrate cellular effects distinct from that of G4 ligands, and attributable to TWJ targeting. The DNA binding modes of these new, dual TWJ-/G4-ligands w…

AcademicSubjects/SCI00010DNA damage[SDV]Life Sciences [q-bio][CHIM.THER] Chemical Sciences/Medicinal ChemistryCellAntineoplastic Agents[SDV.CAN]Life Sciences [q-bio]/CancerSynthetic lethality[CHIM.THER]Chemical Sciences/Medicinal ChemistryStructure-Activity Relationship03 medical and health scienceschemistry.chemical_compound0302 clinical medicineChemical Biology and Nucleic Acid Chemistry[SDV.CAN] Life Sciences [q-bio]/CancerNeoplasmsGeneticsmedicineHumans[CHIM]Chemical Sciences030304 developmental biology0303 health sciencesbiologyTopoisomeraseDNASmall moleculeIn vitroCell biologyG-Quadruplexesmedicine.anatomical_structurechemistry030220 oncology & carcinogenesisCancer cellMCF-7 Cellsbiology.proteinAzabicyclo CompoundsDNADNA Damage
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Deciphering the DNAzyme activity of multimeric quadruplexes: insights into their actual role in the telomerase activity evaluation assay.

2011

The end of human telomeres is comprised of a long G-rich single-stranded DNA (known as 3'-overhang) able to adopt an unusual three-dimensional "beads-on-the-string" organization made of consecutively stacked G-quadruplex units (so-called quadruplex multimers). It has been widely demonstrated that, upon interaction with hemin, discrete quadruplexes acquire peroxidase-mimicking properties, oxidizing several organic probes in H(2)O(2)-rich conditions; this property, known as DNAzyme, has found tens of applications in the last two decades. However, little is known about the DNAzyme activity of multimeric quadruplexes; this is an important question to address, especially in light of recent repor…

TelomeraseDeoxyribozyme010402 general chemistryG-quadruplex01 natural sciencesBiochemistryCatalysischemistry.chemical_compoundColloid and Surface Chemistry[CHIM]Chemical Sciencesheterocyclic compoundsBinding siteTelomeraseComputingMilieux_MISCELLANEOUSBinding Sites010405 organic chemistryChemistryGeneral Chemistry[CHIM.CATA]Chemical Sciences/CatalysisDNA Catalytic0104 chemical sciencesTelomereG-QuadruplexesBiochemistryHeminDNAHeminJournal of the American Chemical Society
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How Proximal Nucleobases Regulate the Catalytic Activity of G-Quadruplex/Hemin DNAzymes

2018

International audience; G-quadruplexes (G4s) are versatile catalytic DNAs when combined with hemin. Despite the repertoire of catalytically competent G4/hemin complexes studied so far, little is known about the detailed catalytic mechanism of these biocatalysts. Herein, we have carried out an in-depth analysis of the hemin binding site within the G4/hemin catalysts, providing the porphyrinic cofactor with a controlled nucleotidic environment. We intensively assessed the position-dependent catalytic enhancement in model reactions and found that proximal nucleobases enhance the catalytic ability of the G4/hemin complexes. Our results allow for revisiting the mechanism of the G4/hemin-based ca…

G4-based catalystDNAzymeproximal nucleobasesDeoxyribozyme010402 general chemistryG-quadruplex01 natural sciencesCatalysisCofactorCatalysisNucleobasechemistry.chemical_compoundG4/hemin complexpolycyclic compoundsNucleotideheterocyclic compoundsBinding sitechemistry.chemical_classificationbiology010405 organic chemistryG-quartetGeneral Chemistry[CHIM.CATA]Chemical Sciences/Catalysisequipment and suppliesCombinatorial chemistry0104 chemical scienceschemistrybiology.proteinHemin
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Identification of Three-Way DNA Junction Ligands through Screening of Chemical Libraries and Validation by Complementary in Vitro Assays

2019

International audience; The human genome is replete with repetitive DNA sequences that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes. Cellular enzymes exist to cope with these structures whose stable accumulation would result in DNA damage through interference with DNA transactions such as transcription and replication. Therefore, the chemical stabilization of secondary DNA structures offers an attractive way to foster DNA transaction-associated damages to trigger cell death in proliferating cancer cells. While much emphasis has been recently given to DNA quadruplexes, we focused here on three-way DNA junctions (TWJ) and report on a strategy t…

Spectrometry Mass Electrospray IonizationDNA damageElectrospray ionization[CHIM.THER] Chemical Sciences/Medicinal ChemistrySulforhodamine BAntineoplastic Agents[SDV.CAN]Life Sciences [q-bio]/Cancer[CHIM.THER]Chemical Sciences/Medicinal ChemistryLigands01 natural sciencesSmall Molecule Libraries03 medical and health scienceschemistry.chemical_compoundTranscription (biology)Cell Line Tumor[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN]Drug DiscoveryFluorescence Resonance Energy Transfer[SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular BiologyHumans[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular BiologyRepeated sequenceCell Proliferation030304 developmental biology0303 health sciencesDNA0104 chemical sciences010404 medicinal & biomolecular chemistryFörster resonance energy transferBiochemistrychemistryNucleic Acid ConformationMolecular MedicineElectrophoresis Polyacrylamide GelHuman genomeDNA
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Visualization of RNA-Quadruplexes in Live Cells

2015

Visualization of DNA and RNA quadruplex formation in human cells was demonstrated recently with different quadruplex-specific antibodies. Despite the significant interest in these immunodetection approaches, dynamic detection of quadruplex in live cells remains elusive. Here, we report on NaphthoTASQ (N-TASQ), a next-generation quadruplex ligand that acts as a multiphoton turn-on fluorescent probe. Single-step incubation of human and mouse cells with N-TASQ enables the direct detection of RNA-quadruplexes in untreated cells (no fixation, permeabilization or mounting steps), thus offering a unique, unbiased visualization of quadruplexes in live cells.

Static ElectricityMelanoma ExperimentalLigands010402 general chemistryG-quadruplex01 natural sciencesBiochemistryCatalysisMice03 medical and health scienceschemistry.chemical_compoundColloid and Surface ChemistryBiomimeticsCationsCell Line TumorFluorescence Resonance Energy TransferAnimalsHumans[CHIM]Chemical Sciences[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biologyheterocyclic compoundsComputingMilieux_MISCELLANEOUSChelating AgentsFluorescent Dyes030304 developmental biologyPhotons[SDV.GEN]Life Sciences [q-bio]/Genetics0303 health sciencesbiologyChemistryRNADNAGeneral ChemistryFluorescenceMolecular biology3. Good health0104 chemical sciencesCell biologyVisualizationG-QuadruplexesFörster resonance energy transferMicroscopy FluorescenceCell cultureMCF-7 Cellsbiology.proteinRNAAntibodyDNAJournal of the American Chemical Society
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Identifying three-way DNA junction-specific small-molecules

2012

Three-way junction DNA (TWJ-DNA, also known as 3WJ-DNA) is an alternative secondary DNA structure comprised of three duplex-DNAs that converge towards a single point, termed the branch point. This point is characterized by unique geometrical properties that make its specific targeting by synthetic small-molecules possible. Such a targeting has already been demonstrated in the solid state but not thoroughly biophysically investigated in solution. Herein, a set of simple biophysical assays has been developed to identify TWJ-specific small-molecule ligands; these assays, inspired by the considerable body of work that has been reported to characterize the interactions between small-molecules an…

Models MolecularPorphyrinsSolid-stateNanotechnologyComputational biology010402 general chemistryLigands01 natural sciencesBiochemistrySmall Molecule Libraries03 medical and health scienceschemistry.chemical_compoundPiperidinesFluorescence Resonance Energy TransferTransition TemperatureComputingMilieux_MISCELLANEOUS030304 developmental biology0303 health sciencesAza CompoundsSpectrum AnalysisGeneral MedicineDNASmall moleculePorphyrin0104 chemical sciencesG-QuadruplexesSolutions[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry Molecular Biology/BiophysicsKineticschemistryMetalsThree wayQuinolinesThermodynamicsSingle pointDNA
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Biomimetic G-quartet compounds

2021

[CHIM] Chemical Sciences[CHIM]Chemical Sciences
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A Thermophilic Tetramolecular G-Quadruplex/Hemin DNAzyme.

2017

International audience; The quadruplex-based DNAzyme system is one of the most useful artificial enzymes or catalysts; their unique properties make them reliable alternatives to proteins for performing catalytic transformation. The first prototype of a thermally stable DNAzyme system is presented. This thermophilic DNAzyme is capable of oxidizing substrates at high temperatures (up to 95 degrees C) and long reaction times (up to 18 h at 75 degrees C). The catalytic activity of the DNAzymes were investigated with the standard peroxidase-mimicking oxidation of 2,2'-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid) (ABTS) by H2O2. The step-by-step design of this unique heat-activated G-quadrup…

Catalytic transformationDNAzymeoxidationDeoxyribozymeaptamersspecificityNanotechnologyBiocompatible MaterialsdnainsightsG-quadruplex010402 general chemistry[ CHIM ] Chemical Sciences01 natural sciencesperoxidase-mimicking dnazymesCatalysisCatalysischemistry.chemical_compoundOxidizing agent[CHIM]Chemical SciencesBenzothiazolesthermophilicityComputingMilieux_MISCELLANEOUSPeroxidaseChemistry010405 organic chemistryThermophileperoxidase activityGeneral Chemistry[CHIM.CATA]Chemical Sciences/CatalysisGeneral MedicineDNA CatalyticHydrogen PeroxideCombinatorial chemistry0104 chemical sciencesG-QuadruplexesMethylene BluekineticsHeminactivity enhancementSulfonic AcidsporphyrinOxidation-ReductioncomplexHeminAngewandte Chemie (International ed. in English)
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Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol

2019

International audience; Guanine-rich DNA and RNA sequences can fold into higher-order structures known as G-quadruplexes (or G4-DNA and G4-RNA, respectively). The prevalence of the G4 landscapes in the human genome, transcriptome and ncRNAome (non-coding RNA), collectively known as G4ome, is strongly suggestive of biological relevance at multiple levels (gene expression , replication). Small-molecules can be used to track G4s in living cells for the functional characterization of G4s in both normal and disease-associated changes in cell biology. Here, we describe biotinylated biomimetic ligands referred to as Bio-TASQ and their use as molecular tools that allow for isolating G4s through aff…

Computational biologyBiologyG-quadruplexLigandsTranscriptome03 medical and health scienceschemistry.chemical_compound0302 clinical medicineChemical Biology and Nucleic Acid ChemistryGene expressionGeneticsHumansBiotinylation[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology030304 developmental biology0303 health sciencesGenome HumanReverse Transcriptase Polymerase Chain ReactionRNA[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biologyDNAG-QuadruplexeschemistryBiotinylationNucleic acidMCF-7 CellsRNAHuman genomeTranscriptome030217 neurology & neurosurgeryDNA
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The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation

2019

International audience; Recent advances in the use of radiometals for both imaging and therapy has spurred on the development of an original chemistry that endows radionuclide-chelating molecular cages with ever sharper physicochemical properties. Macrocyclic polyamines (MPAs) such as cyclen and DOTA are among the most frequently encountered cages for the design of new radiotracers, owing to their versatile chemistry that makes them customizable molecular tools. The idea of using MPAs for alternative purposes has recently emerged, with an eye towards benefiting from their unique topology, versatility, symmetry and water-solubility. This review summarizes strategies that have been recently i…

theranosticsbioactive compounds[CHIM.ORGA]Chemical Sciences/Organic chemistrymolecular platform[CHIM.THER]Chemical Sciences/Medicinal ChemistrymultivalencypolyazamacrocyclesEuropean Journal of Organic Chemistry
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Recognition of G-quadruplex DNA by triangular star-shaped compounds: with or without side chains?

2011

International audience; We report the synthesis of two new series of triangular aromatic platforms, either with three aminoalkyl side chains (triazatrinaphthylene series, TrisK: six compounds), or without side chains (triazoniatrinaphthylene, TrisQ). The quadruplex-DNA binding behavior of the two series, which differ essentially by the localization of the cationic charges, was evaluated by means of FRET-melting and G4-FID assays. For the trisubstituted triazatrinaphthylenes (TrisK), the length of the substituents and the presence of terminal hydrogen-bond-donor groups (NH(2)) were shown to be crucial for ensuring a high quadruplex affinity (ΔT(1/2) values of up to 20 °C at 1 μM for the best…

Models MolecularStereochemistryIonic bonding010402 general chemistryG-quadruplexLigands01 natural sciencesCatalysischemistry.chemical_compoundStructure-Activity RelationshipHeterocyclic Compounds[CHIM] Chemical SciencesSide chainMoleculeStructure–activity relationship[CHIM]Chemical SciencesComputingMilieux_MISCELLANEOUSMolecular Structure010405 organic chemistryHydrogen bond[CHIM.ORGA]Chemical Sciences/Organic chemistryOrganic ChemistryGeneral Chemistry0104 chemical sciencesG-QuadruplexeschemistryAcridinesSelectivityAzo CompoundsDNAChemistry (Weinheim an der Bergstrasse, Germany)
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Front Cover: The Scope of Application of Macrocyclic Polyamines Beyond Metal Chelation (Eur. J. Org. Chem. 36/2019)

2019

International audience

Metal chelationFront coverScope (project management)Chemistry[CHIM.ORGA]Chemical Sciences/Organic chemistryOrganic Chemistry[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular BiologyPhysical and Theoretical ChemistryCombinatorial chemistryComputingMilieux_MISCELLANEOUS
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DNA folds threaten genetic stability and can be leveraged for chemotherapy

2020

International audience; Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an…

0303 health sciencesDna targetingDNA damageGenetic stabilityCancer cell proliferationChemical biologySynthetic lethalityComputational biology[CHIM.THER]Chemical Sciences/Medicinal ChemistryBiochemistry Genetics and Molecular Biology (miscellaneous)Biochemistry03 medical and health scienceschemistry.chemical_compound0302 clinical medicinechemistryChemistry (miscellaneous)030220 oncology & carcinogenesis[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN]Cancer cellMolecular BiologyDNA030304 developmental biology
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Disclosing the actual efficiency of G-quadruplex-DNA–disrupting small molecules

2020

AbstractThe quest for small molecules that avidly bind to G-quadruplex-DNA (G4-DNA, or G4), so called G4-ligands, has invigorated the G4 research field from its very inception. Massive efforts have been invested to i- screen or design G4-ligands, ii- evaluate their G4-interacting properties in vitro through a series of now widely accepted and routinely implemented assays, and iii- use them as unique chemical biology tools to interrogate cellular networks that might involve G4s. In sharp contrast, only uncoordinated efforts at developing small molecules aimed at destabilizing G4s have been invested to date, even though it is now recognized that such molecular tools would have tremendous appl…

0303 health sciencesComputer scienceChemical biology[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry Molecular Biology/Molecular biology[CHIM.THER]Chemical Sciences/Medicinal ChemistryComputational biology010402 general chemistryG-quadruplex01 natural sciencesSmall moleculeIn vitro0104 chemical sciences03 medical and health scienceschemistry.chemical_compoundchemistryDNA030304 developmental biology
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DNA structure-specific sensitization of a metalloporphyrin leads to an efficient in vitro quadruplex detection molecular tool

2016

International audience; The search for convenient molecular probes for detecting DNA and RNA quadruplexes in vitro is marked by a rapid pace of progress, spurred on by the multiple roles these higher-order nucleic acid structures play in many genetic dysregulations. Here, we contribute to this search, reporting on a palladated porphyrin named Pd.TEGPy: its efficiency as quadruplex-selective fluorescent dye relies on a structural design that endows it with attractive supramolecular and electronic properties and makes it an efficient turn-on, quadruplex-selective fluorescent stain thanks to a DNA-mediated sensitization mechanism that ensures a high level of specificity.

0301 basic medicineSupramolecular chemistryNanotechnology[ CHIM ] Chemical SciencesCatalysis03 medical and health scienceschemistry.chemical_compoundenergy-transferMaterials Chemistrymedicine[CHIM]Chemical Sciencesheterocyclic compoundsrnaSensitizationComputingMilieux_MISCELLANEOUSvisualizationligandsaggregationselectivityRNAGeneral ChemistryFluorescencePorphyrindye-complexes030104 developmental biologymedicine.anatomical_structurechemistryBiophysicsNucleic acidcellsrecognitionMolecular probeporphyrinDNA
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Harnessing nature's insights: synthetic small molecules with peroxidase-mimicking DNAzyme properties.

2011

International audience

biology010405 organic chemistryOrganic ChemistryDeoxyribozymeNanotechnologyGeneral Chemistry[CHIM.CATA]Chemical Sciences/CatalysisDNA Catalytic010402 general chemistry01 natural sciencesSmall moleculeCatalysis0104 chemical scienceschemistry.chemical_compoundHeterocyclic Compounds 1-RingchemistryPeroxidasesBiomimetic MaterialsBiomimeticsbiology.proteinBioorganic chemistryHeminComputingMilieux_MISCELLANEOUSHeminPeroxidaseChemistry (Weinheim an der Bergstrasse, Germany)
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A Model of Smart G-Quadruplex Ligand

2012

An unprecedented strategy to control the quadruplex- vs duplex-DNA selectivity of a ligand is reported. We designed a compound whose structure can rearrange when it interacts with a G-quadruplex, thereby controlling its affinity. Thus, the first "smart G-quadruplex ligand" is reported, since this ligand experiences a structural change in the presence of quadruplexes but not in the presence of duplexes, ensuring a high level of quadruplex selectivity.

Models Molecular0303 health sciencesMagnetic Resonance SpectroscopyDose-Response Relationship DrugStereochemistryLigandChemistryGeneral ChemistryNuclear magnetic resonance spectroscopy010402 general chemistryG-quadruplexLigands01 natural sciencesBiochemistryCatalysis0104 chemical sciencesG-QuadruplexesSmall Molecule Libraries03 medical and health sciencesColloid and Surface Chemistry[CHIM]Chemical Sciencesheterocyclic compoundsSelectivityComputingMilieux_MISCELLANEOUS030304 developmental biology
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Multitasking Water-Soluble Synthetic G-Quartets: From Preferential RNA-Quadruplex Interaction to Biocatalytic Activity

2013

Natural G-quartets, a cyclic and coplanar array of four guanine res- idues held together through a Watson- Crick/Hoogsteen hydrogen-bond net- work, have received recently much at- tention due to their involvement in G- quadruplex DNA, an alternative higher-order DNA structure strongly suspected to play important roles in key cellular events. Besides this, syn- thetic G-quartets (SQ), which artificial- ly mimic native G-quartets, have also been widely studied for their involve- ment in nanotechnological applications (i.e., nanowires, artificial ion channels, etc.). In contrast, intramolecular syn- thetic G-quartets (iSQ), also named template-assembled synthetic G-quar- tets (TASQ), have been…

StereochemistryGuanineSupramolecular chemistryDeoxyribozyme010402 general chemistryG-QuartetsG-quadruplex01 natural sciencesCatalysischemistry.chemical_compound[CHIM]Chemical SciencesComputingMilieux_MISCELLANEOUS010405 organic chemistryOrganic ChemistryWaterRNADNAGeneral Chemistry0104 chemical sciencesG-QuadruplexeschemistryIntramolecular forceBiocatalysisHeminRNAOxidation-ReductionDNA
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Porphyrin-Based Design of Bioinspired Multitarget Quadruplex Ligands

2014

Secondary nucleic acid structures, such as DNA and RNA quadruplexes, are potential targets for cancer therapies. Ligands that interact with these targets could thus find application as anticancer agents. Synthetic G-quartets have recently found numerous applications, including use as bioinspired G-quadruplex ligands. Herein, the design, synthesis and preliminary biophysical evaluation of a new prototype multitarget G-quadruplex ligand, (PNA)PorphySQ, are reported, where peptidic nucleic acid guanine ((PNA)G) was incorporated in the porphyrin-templated synthetic G-quartet (PorphySQ). Using fluorescence resonance energy transfer (FRET)-melting experiments, PorphySQ was shown to possess enhanc…

Models MolecularPeptide Nucleic AcidsGuaninePorphyrinsStereochemistryGuanineLigands010402 general chemistryG-quadruplex01 natural sciencesBiochemistryStructure-Activity Relationship03 medical and health scienceschemistry.chemical_compoundDrug Discovery[CHIM]Chemical SciencesStructure–activity relationshipheterocyclic compoundsGeneral Pharmacology Toxicology and PharmaceuticsBinding siteComputingMilieux_MISCELLANEOUS030304 developmental biologyPharmacology0303 health sciencesBinding SitesChemistryLigandOrganic ChemistryDNA0104 chemical sciencesG-QuadruplexesFörster resonance energy transferNucleic acidNucleic Acid ConformationRNAMolecular MedicineDNAChemMedChem
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Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures

2012

The targeting of higher-order DNA structures has been thoroughly developed with G-quadruplex DNA but not with other structures like branched DNA (also known as DNA junctions). Because these alternative higher-order DNA architectures might be of high biological relevance, we implemented a high-throughput version of the FRET melting assay that enabled us to map the interactions of a candidate with four different DNA structures (duplex- and quadruplex DNA, three- and four-way junctions) in a rapid and reliable manner. We also introduce a novel index, the BONDS (branched and other noncanonical DNA selectivity) index, to conveniently quantify this differential affinity.

Models MolecularBase pairBiologyG-quadruplex01 natural sciencesBiochemistrySmall Molecule Libraries03 medical and health scienceschemistry.chemical_compoundCaffeineFluorescence Resonance Energy TransferAnticarcinogenic AgentsMolecular BiologyComputingMilieux_MISCELLANEOUS030304 developmental biology0303 health sciencesBase Sequence010405 organic chemistryOrganic ChemistrySmall Molecule LibrariesDNAMolecular biologySmall molecule0104 chemical sciencesG-Quadruplexes[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry Molecular Biology/BiophysicsQuadruplex DNAFörster resonance energy transferchemistryDuplex (building)BiophysicsNucleic Acid ConformationThermodynamicsMolecular MedicineOrganogold CompoundsDNAChemBioChem
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Closer to nature: an ATP-driven bioinspired catalytic oxidation process

2013

The capability of DNA to acquire enzyme-like properties has led to the emergence of the so-called DNAzyme field; herein, we take a further leap along this nature-inspired road, demonstrating that a template assembled synthetic G-quartet (TASQ) can act as a pre-catalyst for catalytic peroxidase-mimicking oxidation reactions, whatever its nature (guanine or guanosine-based G-quartets), in an ATP-dependent manner, thereby bringing this bioinspired TASQzyme process even closer to nature.

GuanineDeoxyribozymeGuanosineNanotechnology010402 general chemistry01 natural sciencesRedox[ CHIM ] Chemical SciencesCatalysisCatalysischemistry.chemical_compoundAdenosine TriphosphateMaterials Chemistry[CHIM]Chemical SciencesComputingMilieux_MISCELLANEOUS010405 organic chemistryMetals and AlloysDNA CatalyticGeneral Chemistry[CHIM.CATA]Chemical Sciences/Catalysis0104 chemical sciencesSurfaces Coatings and FilmsElectronic Optical and Magnetic MaterialsG-QuadruplexeschemistryCatalytic oxidationScientific methodCeramics and CompositesOxidation-Reduction
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DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells.

2019

International audience; Translocation of DNA and RNA polymerases along their duplex substrates results in DNA supercoiling. This torsional stress promotes the formation of plectonemic structures, including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA damage. While cells have evolved multiple mechanisms to prevent the accumulation of such structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA damage in cells with high level of transcription and replication, such as cancer cells. Here, we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-interacting properties in vitro and demonstrate their…

DNA RepairDNA repairDNA damage[SDV]Life Sciences [q-bio][SDV.CAN]Life Sciences [q-bio]/CancerSynthetic lethality[CHIM.THER]Chemical Sciences/Medicinal Chemistry010402 general chemistryLigands01 natural sciencesBiochemistryCatalysischemistry.chemical_compoundColloid and Surface ChemistryTranscription (biology)Cell Line TumorHumansPolymeraseCell Proliferationbiology[CHIM.ORGA]Chemical Sciences/Organic chemistryGeneral ChemistryDNA3. Good health0104 chemical sciencesCell biologychemistryCancer cellbiology.proteinMCF-7 CellsDNA supercoilNucleic Acid ConformationDNADNA DamageJournal of the American Chemical Society
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Porphyrin-templated synthetic G-quartet (PorphySQ): a second prototype of G-quartet-based G-quadruplex ligand.

2012

Template-assembled synthetic G-quartet (TASQ) has been reported recently as a G-quadruplex ligand interacting with DNA according to an unprecedented, nature-inspired ‘like likes like’ approach, based on the association between two G-quartets, one being native (quadruplex) and the other one artificial (ligand). Herein, a novel TASQ-based ligand is designed, synthesized and its quadruplex-recognition properties are evaluated in vitro: PorphySQ (for porphyrin-templated synthetic G-quartet) displays enhanced quadruplex recognition properties as compared to the very first reported prototype (DOTASQ, for DOTA-templated synthetic G-quartet), since the porphyrin template insures a more stable intra…

Models Molecular0303 health sciencesPorphyrinsStereochemistryOrganic ChemistryHydrogen Bonding010402 general chemistryG-quadruplexLigands01 natural sciencesBiochemistryPorphyrin0104 chemical sciencesG-Quadruplexes03 medical and health scienceschemistry.chemical_compoundchemistryIntramolecular force[CHIM]Chemical SciencesPhysical and Theoretical ChemistryDNAComputingMilieux_MISCELLANEOUS030304 developmental biologyOrganicbiomolecular chemistry
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Les structures de l'ADN

2017

International audience

[SDV.GEN]Life Sciences [q-bio]/Genetics[SDV.GEN] Life Sciences [q-bio]/GeneticsComputingMilieux_MISCELLANEOUS
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Surface-immobilized DNAzyme-type biocatalysis

2014

The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable i…

StreptavidinSurface PropertiesImmobilized Nucleic AcidsDeoxyribozymeContext (language use)Nanotechnology010402 general chemistryG-quadruplex01 natural sciences[ CHIM ] Chemical Scienceschemistry.chemical_compoundNanobiotechnology[CHIM]Chemical Sciencesheterocyclic compoundsGeneral Materials ScienceComputingMilieux_MISCELLANEOUS010405 organic chemistryDNA Catalytic[CHIM.CATA]Chemical Sciences/Catalysis0104 chemical sciencesG-QuadruplexesPeroxidaseschemistryBiotinylationHelixBiocatalysisOxidation-ReductionDNA
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DOTASQ as a prototype of nature-inspired G-quadruplex ligand

2011

DOTASQ (for DOTA-templated Synthetic G-quartet) is the first prototype of nature-inspired G-quadruplex ligand: its design, founded on a possible intramolecular G-quartet formation, enables it to interact with G-quadruplex DNA via an unprecedented nature-mimicking binding mode, based on the association between two G-quartets, one being native (quadruplex) and the other one artificial (ligand).

Models MolecularGuanineMacrocyclic CompoundsStereochemistryAntineoplastic AgentsLigands010402 general chemistryG-quadruplex01 natural sciencesCatalysischemistry.chemical_compoundMaterials ChemistryHumans[CHIM]Chemical SciencesNature inspiredTerbiumComputingMilieux_MISCELLANEOUSBinding SitesFourier Analysis010405 organic chemistryMetals and AlloysGeneral ChemistryLigand (biochemistry)0104 chemical sciencesSurfaces Coatings and FilmsElectronic Optical and Magnetic MaterialsG-QuadruplexeschemistryMolecular ProbesIntramolecular forceCeramics and CompositesNucleic Acid ConformationHydrophobic and Hydrophilic InteractionsDNA
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DNA quadruplexes: structures, functions and detection

2017

International audience

0301 basic medicineChemistry[ SDV.BC ] Life Sciences [q-bio]/Cellular BiologyGeneral Medicine[CHIM.THER]Chemical Sciences/Medicinal Chemistry[SDV.BC]Life Sciences [q-bio]/Cellular BiologyGeneral Biochemistry Genetics and Molecular Biology03 medical and health sciences030104 developmental biology[ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathologyhuman-cells[SDV.MHEP]Life Sciences [q-bio]/Human health and pathologyComputingMilieux_MISCELLANEOUSvisualization
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The catalytic properties of DNA G-quadruplexes rely on their structural integrity

2021

International audience; The influence of the G-quartet structural integrity on the catalytic activity of the G-quadruplex (G4) was investigated by comparing the G4-DNAzyme performances of a series of G4s with a G-vacancy site and a G-triplex (G-tri). The results presented herein not only confirm that the structural integrity of the 3’-end G-quartet is necessary for G4s to be catalytically competent but also show how to remediate G-vacancy-mediated catalytic activity losses via the addition of guanine surrogates in an approach referred to as G-vacancy complementation strategy that is applicable to parallel G4s only. Furthermore, this study demonstrates that the terminal G-quartet could act a…

GuanineG-vacancy02 engineering and technology010402 general chemistryG-quadruplex01 natural sciencesCofactorCatalysischemistry.chemical_compoundNucleotideG-quartet integrity[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry Molecular Biology/Biochemistry [q-bio.BM][SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry Molecular Biology/Biochemistry [q-bio.BM]chemistry.chemical_classificationbiologyG-quadruplex[CHIM.CATA] Chemical Sciences/CatalysisGeneral Medicine[CHIM.CATA]Chemical Sciences/Catalysis021001 nanoscience & nanotechnology0104 chemical sciencesComplementationGuanine surrogatechemistrybiology.proteinBiophysicsG-quadruplex DNAzyme0210 nano-technologyDNAHemin
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Insights into how nucleotide supplements enhance the peroxidase-mimicking DNAzyme activity of the G-quadruplex/hemin system

2012

Since the initial discovery of the catalytic capability of short DNA fragments, this peculiar enzyme-like property (termed DNAzyme) has continued to garner much interest in the scientific community because of the virtually unlimited applications in developing new molecular devices. Alongside the exponential rise in the number of DNAzyme applications in the last past years, the search for convenient ways to improve its overall efficiency has only started to emerge. Credence has been lent to this strategy by the recent demonstration that the quadruplex-based DNAzyme proficiency can be enhanced by ATP supplements. Herein, we have made a further leap along this path, trying first of all to deci…

DeoxyribozymeNanotechnologyBiology010402 general chemistryG-quadruplex01 natural sciencesCatalysischemistry.chemical_compoundAdenosine TriphosphateGeneticsNucleotideCatalytic efficiencyComputingMilieux_MISCELLANEOUSchemistry.chemical_classificationSupplementary data010405 organic chemistryNucleotides[CHIM.CATA]Chemical Sciences/CatalysisDNADNA Catalytic0104 chemical sciences[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry Molecular Biology/BiophysicsG-QuadruplexesCatalytic cyclechemistryBiochemistryPeroxidasesSynthetic Biology and ChemistryHeminOverall efficiencyHeminNucleic Acids Research
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Carbon nanotube – Protamine hybrid: Evaluation of DNA cell penetration

2016

International audience; Carbon nanotubes (CNTs) represent a class of nanomaterials with important potential for biomedical and biotechnological applications. CNT based vectorization is an emerging approach to the transport of nucleic acid through cell membrane but limited by detachment of DNA and degradation process. To increase DNA internalization, it was proved that cationic functionalized CNT was essential. In such a way, protamine efficiently used in several transfection processes is a cationic protein which was never associated to CNT.We propose here a novel nanovector based on single-walled carbon nanotubes (SWCNT) functionalized by protamine. Our results based on qPCR methods clearly…

Materials sciencemedia_common.quotation_subjectmammalian-cellsCarbon nanotubesnoncovalent sidewall-functionalizationProtamineNanotechnology02 engineering and technologyCarbon nanotubetransportersphysicochemical propertiesin-vitro010402 general chemistryEndocytosis01 natural sciences[ CHIM ] Chemical Scienceslaw.inventionnonviral gene deliveryCell membranechemistry.chemical_compoundlawCellular internalizationmedicineendocytosis[CHIM]Chemical SciencesGeneral Materials ScienceInternalizationFunctionalizationComputingMilieux_MISCELLANEOUSmedia_commonbiologyMolecular dynamic simulationGeneral ChemistryTransfection[CHIM.MATE]Chemical Sciences/Material chemistry021001 nanoscience & nanotechnologyProtamineproteins0104 chemical sciencesdrug-deliverymedicine.anatomical_structureplasmid dnachemistryBiophysicsNucleic acidbiology.protein0210 nano-technologyNanovectorizationDNA
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“One Ring to Bind Them All”—Part II: Identification of Promising G-Quadruplex Ligands by Screening of Cyclophane-Type Macrocycles

2010

A collection of 26 polyammonium cyclophane-type macrocycles with a large structural diversity has been screened for G-quadruplex recognition. A two-step selection procedure based on the FRET-melting assay was carried out enabling identification of macrocycles of high affinity (ΔT1/2up to30°C) and high selectivity for the human telomeric G-quadruplex. The four selected hits possess sophisticated architectures, more particularly the presence of a pendant side-arm as well as the existence of a particular topological arrangement appear to be strong determinants of quadruplex binding. These compounds are thus likely to create multiple contacts with the target that may be at the origin of their h…

lcsh:QH426-470Article SubjectHigh selectivityStructural diversityBiology010402 general chemistryRing (chemistry)G-quadruplexBioinformatics01 natural sciencesBiochemistrylcsh:Biochemistry03 medical and health scienceschemistry.chemical_compound[SDV.BBM] Life Sciences [q-bio]/Biochemistry Molecular Biology[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biologylcsh:QD415-436Molecular Biology030304 developmental biology0303 health sciencesCombinatorial chemistry0104 chemical scienceslcsh:GeneticschemistryIdentification (biology)CyclophaneResearch ArticleJournal of Nucleic Acids
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The Biotechnological Applications of G-Quartets

2015

International audience

[SDV.GEN]Life Sciences [q-bio]/Genetics010405 organic chemistryChemistry[CHIM.THER]Chemical Sciences/Medicinal Chemistry010402 general chemistryG-Quartets01 natural sciencesComputingMilieux_MISCELLANEOUS0104 chemical sciences
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Oligonucleotides in Sensing and Diagnostic Applications

2015

AnalyteChemistryOligonucleotideNucleic Acid ConformationsNucleic acidOrganic chemistryG-quadruplexG-QuartetsChemical reactionNucleobase
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How to untie G-quadruplex knots and why?

2021

International audience; For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, …

Clinical BiochemistryChemical biologyComputational biology[CHIM.THER]Chemical Sciences/Medicinal ChemistryBiology010402 general chemistryG-quadruplex01 natural sciencesBiochemistry03 medical and health sciencesgenetic diseasesDrug DiscoveryHumansMolecular Biologyunfolding030304 developmental biologyPharmacology0303 health sciencesG-quadruplex[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM]Genome Humanhelicasesgenetic instability0104 chemical sciencesG-Quadruplexessmall moleculesMolecular Medicine
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A Push-Pull Mechanism Helps Design Highly Competent G-Quadruplex-DNA Catalysts

2021

International audience; Massive efforts are currently being invested to improve the performance, versatility, and scope of applications of nucleic acid catalysts. G-quadruplex (G4)/hemin DNAzymes are of particular interest owing to their structural programmability and chemical robustness. However, optimized catalytic efficiency is still bottleneck and the activation mechanism is unclear. Herein, we have designed a series of parallel G4s with different proximal cytosine (dC) derivatives to fine-tune the hemin-binding pocket for G4-DNAzymes. Combining theoretical and experimental methods, we have assessed the dependence of catalytic enhancement on the electronic properties of proximal dCs and…

[SDV.BIO]Life Sciences [q-bio]/BiotechnologyDNAzymeDeoxyribozyme010402 general chemistryG-quadruplex01 natural sciencesCatalysischemistry.chemical_compoundPush–pull mechanismG-quadruplex010405 organic chemistryChemistryMechanism (biology)Robustness (evolution)[CHIM.CATA] Chemical Sciences/CatalysisGeneral Chemistry[CHIM.CATA]Chemical Sciences/CatalysisCombinatorial chemistry0104 chemical sciences[SDV.BIO] Life Sciences [q-bio]/Biotechnology[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry[CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistryNucleic acidHeminDNAHeminElectron density
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Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

2018

Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in…

Cell ExtractsNoncoding RnasScienceGene-Expression[SDV.CAN]Life Sciences [q-bio]/CancerWeb ServerLigandsModels BiologicalArticleExpression AnalysisTranslation Regulation Expression Analysis Gene-Expression Noncoding Rnas Dna Structures Small-Molecule Human Genome Web Server Real-Time ChromatinHumansImmunoprecipitation[CHIM]Chemical Sciences[SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular BiologyDna Structureslcsh:Science[SDV.GEN]Life Sciences [q-bio]/GeneticsTranslation RegulationQHuman GenomeReal-TimeChromatinG-QuadruplexesMCF-7 CellsRNARNA Long Noncodinglcsh:QTranscriptomeSmall-Molecule
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CCDC 829826: Experimental Crystal Structure Determination

2016

Related Article: Sophie Vuong, Loïc Stefan, Pauline Lejault, Yoann Rousselin, Franck Denat, David Monchaud|2012|Biochimie|94|442|doi:10.1016/j.biochi.2011.08.012

Space GroupCrystallographyCrystal SystemCrystal Structure(22'2''-((147-triazonane-147-triyl)tris(methylene))trisquinoline)-iron(ii) bis(tetrafluoroborate)Cell ParametersExperimental 3D Coordinates
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CCDC 977462: Experimental Crystal Structure Determination

2015

Related Article: Aurélien Laguerre, Nicolas Desbois, Loic Stefan, Philippe Richard, Claude P. Gros and David Monchaud|2014|ChemMedChem|9|2035|doi:10.1002/cmdc.201300526

Space GroupCrystallographyCrystal SystemCrystal StructureCell Parameters5101520-tetrakis(3-(2-Azidoethoxy)propyl)porphyrinExperimental 3D Coordinates
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CCDC 1952718: Experimental Crystal Structure Determination

2020

Related Article: Katerina Duskova, Pauline Lejault, Élie Benchimol, Régis Guillot, Sébastien Britton, Anton Granzhan, David Monchaud|2019|J.Am.Chem.Soc.|142|424|doi:10.1021/jacs.9b11150

Space GroupCrystallographyCrystal SystemCrystal StructureCell ParametersExperimental 3D Coordinates102845-trioxa-14161922343951-octa-azaoctacyclo[17.17.17.269.21114.22427.22932.24144.24649]pentahexaconta-6811132426293141434648545658606264-octadecaene-41622343951-hexaium hexachloride methanol solvate hydrate
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CCDC 977461: Experimental Crystal Structure Determination

2015

Related Article: Aurélien Laguerre, Nicolas Desbois, Loic Stefan, Philippe Richard, Claude P. Gros and David Monchaud|2014|ChemMedChem|9|2035|doi:10.1002/cmdc.201300526

Space GroupCrystallographyCrystal SystemCrystal StructureCell Parameters5101520-tetrakis(3-Azidopropyl)porphyrinExperimental 3D Coordinates
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CCDC 782553: Experimental Crystal Structure Determination

2016

Related Article: Hélène Bertrand, Anton Granzhan, David Monchaud, Nicolas Saettel, Régis Guillot, Sarah Clifford, Aurore Guédin, Jean-Louis Mergny, Marie-Paule Teulade-Fichou|2011|Chem.-Eur.J.|17|4529|doi:10.1002/chem.201002810

dipyrido[12-b:1'2'-j]quinolizino[32-f][28]phenanthrolinetriium tris(tetrafluoroborate) monohydrateSpace GroupCrystallographyCrystal SystemCrystal StructureCell ParametersExperimental 3D Coordinates
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