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Ledvinka J, Rota Sperti F, Paragi G, Pirrotta M, Chéron N, Valverde IE, Menova P, Monchaud D. Fluorescence Detection of DNA/RNA G-Quadruplexes (G4s) by Twice-as-Smart Ligands. ChemMedChem 2025; 20:e202400829. [PMID: 39714851 PMCID: PMC11961149 DOI: 10.1002/cmdc.202400829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 12/18/2024] [Accepted: 12/20/2024] [Indexed: 12/24/2024]
Abstract
Fluorescence detection of DNA and RNA G-quadruplexes (G4s) is a very efficient strategy to assess not only the existence and prevalence of cellular G4s but also their relevance as targets for therapeutic interventions. Among the fluorophores used to this end, turn-on probes are the most interesting since their fluorescence is triggered only upon interaction with their G4 targets, which ensures a high sensitivity and selectivity of detection. We reported on a series of twice-as-smart G4 probes, which are both smart G4 ligands (whose structure is reorganized upon interaction with G4s) and smart fluorescent probes (whose fluorescence is turned on upon interaction with G4s). The fine mechanistic details behind the excellent properties of the best prototype N-TASQ remain to be deciphered: to investigate this, we report here on the synthesis and studies of two analogues, TzN-TASQ and AlkN-TASQ, and on a careful analysis of their G4-interacting properties, investigated both in vitro and in silico. Our results show that fine-tuning their constitutive structural elements allows for increasing the efficiency of both their 'off' (i. e., a conformation with a low fluorescence) and 'on' states (i. e., a conformation with a high fluorescence), which opens interesting ways for the design of more efficient fluorogenic G4 probes.
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Affiliation(s)
- Jiri Ledvinka
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR6302, Université Bourgogne Europe (UBE)9, Av. Alain Savary21078DijonFR
- University of Chemistry and Technology, PragueTechnická 516628Prague 6CZ
- Current address: Max Planck Institute of Colloids and Interfaces, 14476 Postdam, DE; and Institute of Chemistry and BiochemistryFreie Universität Berlin14195BerlinDE
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR6302, Université Bourgogne Europe (UBE)9, Av. Alain Savary21078DijonFR
| | - Gabor Paragi
- Institute of PhysicsUniversity of PécsH-7624PécsIfjúság str 6HU
- Department of Theoretical PhysicsUniversity of SzegedTisza Lajos krt. 84–866720SzegedHU
- Department of Medical ChemistryUniversity of SzegedDóm tér 8SzegedHungary
| | - Marc Pirrotta
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR6302, Université Bourgogne Europe (UBE)9, Av. Alain Savary21078DijonFR
| | - Nicolas Chéron
- Chimie Physique et Chimie du Vivant (CPCV), Département de chimie, École Normale Supérieure (ENS), PSL UniversitySorbonne Université, CNRS UMR822875005ParisFrance
| | - Ibai E. Valverde
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR6302, Université Bourgogne Europe (UBE)9, Av. Alain Savary21078DijonFR
| | - Petra Menova
- University of Chemistry and Technology, PragueTechnická 516628Prague 6CZ
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR6302, Université Bourgogne Europe (UBE)9, Av. Alain Savary21078DijonFR
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Monchaud D. Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology. Acc Chem Res 2023; 56:350-362. [PMID: 36662540 DOI: 10.1021/acs.accounts.2c00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biomimetics is defined as a "practice of making technological design that copies natural processes", with the idea that "nature has already solved the challenges we are trying to solve" (Cambridge Dictionary). The challenge we decided to address several years ago was the selective targeting of G quadruplexes (G4s) by small molecules (G4 ligands). Why? Because G4s, which are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences, are suspected to play key biological roles in human cells and diseases. Selective G4 ligands can thus be used as small-molecule modulators to gain a deep understanding of cell circuitry where G4s are involved, thus complying with the very definition of chemical biology (Stuart Schreiber) applied here to G4 biology. How? Following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G quartets, and then of G quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G quartet as a G4 ligand represents a unique example of biomimetic recognition of G4s.We formulated this hypothesis more than a decade ago, stepping on years of research on Gs, G4s, and G4 ligands. Our approach led to the design, synthesis, and use of a broad family of synthetic G quartets, also referred to as TASQs for template-assembled synthetic G quartets (John Sherman). This quest led us across various chemical lands (organic and supramolecular chemistry, chemical biology, and genetics), along a route on which every new generation of TASQ was a milestone in the growing portfolio of ever smarter molecular tools to decipher G4 biology. As discussed in this Account, we detail how and why we successively develop the very first prototypes of (i) biomimetic ligands, which interact with G4s according to a bioinspired, like-likes-like interaction between two G quartets, one from the ligand, the other from the G4; (ii) smart ligands, which adopt their active conformation only in the presence of their G4 targets; (iii) twice-as-smart ligands, which act as both smart ligands and smart fluorescent probes, whose fluorescence is triggered (turned on) upon interaction with their G4 targets; and (iv) multivalent ligands, which display additional functionalities enabling the detection, isolation, and identification of G4s both in vitro and in vivo. This quest led us to gather a panel of 14 molecular tools which were used to investigate the biology of G4s at a cellular level, from basic optical imaging to multiomics studies.
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Affiliation(s)
- David Monchaud
- ICMUB, CNRS UMR6302, Université de Bourgogne, 21078 Dijon, France
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Asha H, Stadlbauer P, Martínez-Fernández L, Banáš P, Šponer J, Improta R, Esposito L. Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine. Int J Biol Macromol 2022; 194:882-894. [PMID: 34838862 DOI: 10.1016/j.ijbiomac.2021.11.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022]
Abstract
Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.
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Affiliation(s)
- Haritha Asha
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lara Martínez-Fernández
- Departamento de Quimica, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autonoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
| | - Luciana Esposito
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
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Sperti Rota F, Charbonnier T, Lejault P, Zell J, Bernhard C, Valverde IE, Monchaud D. Biomimetic, Smart, and Multivalent Ligands for G-Quadruplex Isolation and Bioorthogonal Imaging. ACS Chem Biol 2021; 16:905-914. [PMID: 33914525 DOI: 10.1021/acschembio.1c00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
G-quadruplexes (G4s) continue to gather wide attention in the field of chemical biology as their prevalence in the human genome and transcriptome strongly suggests that they play key regulatory roles in cell biology. G4-specific, cell-permeable small molecules (G4-ligands) innovatively permit the interrogation of cellular circuitries in order to assess to what extent G4s influence cell fate and functions. Here, we report on multivalent, biomimetic G4-ligands referred to as TASQs that enable both the isolation and visualization of G4s in human cells. Two biotinylated TASQs, BioTASQ and BioCyTASQ, are indeed efficient molecular tools to isolate G4s from mixtures of nucleic acids through simple affinity capture protocols and to image G4s in cells via a biotin/avidin pretargeted imaging system first applied here to G4s, found to be a reliable alternative to in situ click chemistry.
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Affiliation(s)
| | - Thibaut Charbonnier
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Pauline Lejault
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Joanna Zell
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Claire Bernhard
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - Ibai E Valverde
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
| | - David Monchaud
- ICMUB, CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, 21078 Dijon, France
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Xie X, Reznichenko O, Chaput L, Martin P, Teulade-Fichou MP, Granzhan A. Topology-Selective, Fluorescent “Light-Up” Probes for G-Quadruplex DNA Based on Photoinduced Electron Transfer. Chemistry 2018; 24:12638-12651. [DOI: 10.1002/chem.201801701] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Ludovic Chaput
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
- CNRS UPR2301; Institut de Chimie des Substances Naturelles (ICSN); 91198 Gif-sur-Yvette France
| | - Pascal Martin
- ITODYS, CNRS UMR7086; Université Paris Diderot; 75205 Paris France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
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Amor S, Yang SY, Wong JMY, Monchaud D. Cellular Detection of G-Quadruplexes by Optical Imaging Methods. ACTA ACUST UNITED AC 2017; 76:4.33.1-4.33.19. [PMID: 28862343 DOI: 10.1002/cpcb.29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G-quadruplexes (G4s) are higher-order nucleic acid structures that fold from guanine (G)-rich DNA and RNA strands. This field of research gains traction as a major chemical biology area since it aims at uncovering many key cellular mechanisms in which quadruplexes are involved. The wealth of knowledge acquired over the past three decades strongly supports pivotal roles of G4 in the regulation of gene expression at both transcriptional (DNA quadruplexes) and translational levels (RNA quadruplexes). Recent biochemical discoveries uncovered myriad of additional G4 actions: from chromosomal stability to the firing of replication origins, from telomere homeostasis to functional dysregulations underlying genetic diseases (including cancers and neurodegeneration). Here, we listed a repertoire of protocols that we have developed over the past years to visualize quadruplexes in cells. These achievements were made possible thanks to the discovery of a novel family of versatile quadruplex-selective fluorophores, the twice-as-smart quadruplex ligands named TASQ (for template-assembled synthetic G-quartet). The versatility of this probe allows for multiple imaging techniques in both fixed and live cells, including the use of the multiphoton microscopy, confocal microscopy, and real-time fluorescent image collection. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Souheila Amor
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
| | - Sunny Y Yang
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada
| | - Judy M Y Wong
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
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Saadallah D, Bellakhal M, Amor S, Lefebvre JF, Chavarot-Kerlidou M, Baussanne I, Moucheron C, Demeunynck M, Monchaud D. Selective Luminescent Labeling of DNA and RNA Quadruplexes by π-Extended Ruthenium Light-Up Probes. Chemistry 2017; 23:4967-4972. [DOI: 10.1002/chem.201605948] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Dounia Saadallah
- Laboratoire de Chimie Organique et Photochimie; Université Libre de Bruxelles; 1050 Bruxelles Belgium
- Departement de Pharmacochimie Moléculaire; Université Grenoble Alpes, CNRS UMR5063; 38041 Grenoble France
| | - Mehdi Bellakhal
- Institut de Chimie Moléculaire; ICMUB CNRS UMR6302, UBFC; 21078 Dijon France
| | - Souheila Amor
- Institut de Chimie Moléculaire; ICMUB CNRS UMR6302, UBFC; 21078 Dijon France
| | - Jean-François Lefebvre
- Departement de Pharmacochimie Moléculaire; Université Grenoble Alpes, CNRS UMR5063; 38041 Grenoble France
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CNRS UMR5249, CEA; 38054 Grenoble France
| | - Murielle Chavarot-Kerlidou
- Laboratoire de Chimie et Biologie des Métaux; Université Grenoble Alpes, CNRS UMR5249, CEA; 38054 Grenoble France
| | - Isabelle Baussanne
- Departement de Pharmacochimie Moléculaire; Université Grenoble Alpes, CNRS UMR5063; 38041 Grenoble France
| | - Cécile Moucheron
- Laboratoire de Chimie Organique et Photochimie; Université Libre de Bruxelles; 1050 Bruxelles Belgium
| | - Martine Demeunynck
- Departement de Pharmacochimie Moléculaire; Université Grenoble Alpes, CNRS UMR5063; 38041 Grenoble France
| | - David Monchaud
- Institut de Chimie Moléculaire; ICMUB CNRS UMR6302, UBFC; 21078 Dijon France
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Real-time and quantitative fluorescent live-cell imaging with quadruplex-specific red-edge probe (G4-REP). Biochim Biophys Acta Gen Subj 2016; 1861:1312-1320. [PMID: 27956241 DOI: 10.1016/j.bbagen.2016.11.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 02/01/2023]
Abstract
The development of quadruplex-directed molecular diagnostic and therapy rely on mechanistic insights gained at both cellular and tissue levels by fluorescence imaging. This technique is based on fluorescent reporters that label cellular DNA and RNA quadruplexes to spatiotemporally address their complex cell biology. The photophysical characteristics of quadruplex probes usually dictate the modality of cell imaging by governing the selection of the light source (lamp, LED, laser), the optical light filters and the detection modality. Here, we report the characterizations of prototype from a new generation of quadruplex dye termed G4-REP (for quadruplex-specific red-edge probe) that provides fluorescence responses regardless of the excitation wavelength and modality (owing to the versatility gained through the red-edge effect), thus allowing for diverse applications and most imaging facilities. This is demonstrated by cell images (and associated quantifications) collected through confocal and multiphoton microscopy as well as through real-time live-cell imaging system over extended period, monitoring both non-cancerous and cancerous human cell lines. Our results promote a new way of designing versatile, efficient and convenient quadruplex-reporting dyes for tracking these higher-order nucleic acid structures in living human cells. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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