1
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Pipier A, Devaux A, Lavergne T, Adrait A, Couté Y, Britton S, Calsou P, Riou JF, Defrancq E, Gomez D. Constrained G4 structures unveil topology specificity of known and new G4 binding proteins. Sci Rep 2021; 11:13469. [PMID: 34188089 PMCID: PMC8241873 DOI: 10.1038/s41598-021-92806-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.
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Affiliation(s)
- A Pipier
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - A Devaux
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - T Lavergne
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - A Adrait
- CEA, INSERM, IRIG, BGE, Université Grenoble Alpes, 38000, Grenoble, France
| | - Y Couté
- CEA, INSERM, IRIG, BGE, Université Grenoble Alpes, 38000, Grenoble, France
| | - S Britton
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - P Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France
| | - J F Riou
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS, INSERM, CP 26, 75005, Paris, France
| | - E Defrancq
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Grenoble Alpes, 38058, Grenoble, France
| | - D Gomez
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
- Equipe Labellisée Ligue Contre Le Cancer 2018, Toulouse, France.
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2
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Kharel P, Becker G, Tsvetkov V, Ivanov P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res 2020; 48:12534-12555. [PMID: 33264409 PMCID: PMC7736831 DOI: 10.1093/nar/gkaa1126] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.
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Affiliation(s)
- Prakash Kharel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gertraud Becker
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Tsvetkov
- Computational Oncology Group, I. M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Federal Research and Clinical Center for Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 117912, Russia
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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3
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Berlyoung AS, Armitage BA. Assembly and Characterization of RNA/DNA Hetero-G-Quadruplexes. Biochemistry 2020; 59:4072-4080. [PMID: 33048532 DOI: 10.1021/acs.biochem.0c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transient association of guanine-rich RNA and DNA in the form of hetero-G-quadruplexes (RDQs) has emerged as an important mechanism for regulating genome transcription and replication but relatively little is known about the structure and biophysical properties of RDQs compared with DNA and RNA homo-G-quadruplexes. Herein, we report the assembly and characterization of three RDQs based on sequence motifs found in human telomeres and mitochondrial nucleic acids. Stable RDQs were assembled using a duplex scaffold, which prevented segregation of the DNA and RNA strands into separate homo-GQs. Each of the RDQs exhibited UV melting temperatures above 50 °C in 100 mM KCl and predominantly parallel morphologies, evidently driven by the RNA component. The fluorogenic dye thioflavin T binds to each RDQ with low micromolar KD values, similar to its binding to RNA and DNA homo-GQs. These results establish a method for assembling RDQs that should be amenable to screening compounds and libraries to identify selective RDQ-binding small molecules, oligonucleotides, and proteins.
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Affiliation(s)
- April S Berlyoung
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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4
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Devaux A, Bonnat L, Lavergne T, Defrancq E. Access to a stabilized i-motif DNA structure through four successive ligation reactions on a cyclopeptide scaffold. Org Biomol Chem 2020; 18:6394-6406. [DOI: 10.1039/d0ob01311k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Four successive chemical ligations were used for the assembly of a sophisticated biomolecular system allowing the formation of a stabilized i-motif DNA at pH 7.
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Affiliation(s)
- Alexandre Devaux
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Laureen Bonnat
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Thomas Lavergne
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Eric Defrancq
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
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5
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Bonnat L, Dautriche M, Saidi T, Revol-Cavalier J, Dejeu J, Defrancq E, Lavergne T. Scaffold stabilization of a G-triplex and study of its interactions with G-quadruplex targeting ligands. Org Biomol Chem 2019; 17:8726-8736. [PMID: 31549116 DOI: 10.1039/c9ob01537j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-triplex nucleic acid structures (G3) have been conjectured to form in vivo but little is known about their physiological functions. The identification of ligands capable of specific binding to G3 structures is therefore highly appealing but remains elusive. Here we report on the assembly of a DNA conjugate which folds into a stable G3 structure. The structural mimic was used to probe the interactions between a G3 ligand and first-in-class G4 ligands, revealing signification binding promiscuity.
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Affiliation(s)
- Laureen Bonnat
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Maelle Dautriche
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Taous Saidi
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Johana Revol-Cavalier
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Jérôme Dejeu
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Eric Defrancq
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Thomas Lavergne
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
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6
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Weynand J, Bonnet H, Loiseau F, Ravanat JL, Dejeu J, Defrancq E, Elias B. Targeting G-Rich DNA Structures with Photoreactive Bis-Cyclometallated Iridium(III) Complexes. Chemistry 2019; 25:12730-12739. [PMID: 31290208 DOI: 10.1002/chem.201902183] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/02/2019] [Indexed: 01/19/2023]
Abstract
The synthesis and characterisation of three novel iridium(III) bis-cyclometallated complexes is reported. Their photophysics have been fully characterised by classical methods and revealed charge-transfer (CT) and ligand-centred (LC) transitions. Their ability to selectively interact with G-quadruplex telomeric DNA over duplex DNA has been studied by circular dichroism (CD), bio-layer interferometry (BLI) and surface plasmon resonance (SPR) analyses. Interestingly, one of the complexes was able to promote photoinduced electron transfer (PET) with the guanine DNA base, which in turn led to oxidative damage (such as the formation of 8-oxoguanine) to the telomeric sequence. To the best of our knowledge, this is the first study of highly photo-oxidising bis-cyclometallated iridium(III) complexes with G-quadruplex telomeric DNA.
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Affiliation(s)
- Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium.,CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Hughes Bonnet
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | | | - Jean-Luc Ravanat
- CEA, CNRS, INAC-SyMMES, Université Grenoble Alpes, 17 rue des martyrs, 38054, Grenoble CEDEX 9, France
| | - Jérôme Dejeu
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Eric Defrancq
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
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7
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Weynand J, Diman A, Abraham M, Marcélis L, Jamet H, Decottignies A, Dejeu J, Defrancq E, Elias B. Towards the Development of Photo‐Reactive Ruthenium(II) Complexes Targeting Telomeric G‐Quadruplex DNA. Chemistry 2018; 24:19216-19227. [DOI: 10.1002/chem.201804771] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/22/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Justin Weynand
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Aurélie Diman
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Michaël Abraham
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Lionel Marcélis
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Hélène Jamet
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Eric Defrancq
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Benjamin Elias
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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8
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Prado E, Bonnat L, Bonnet H, Lavergne T, Van der Heyden A, Pratviel G, Dejeu J, Defrancq E. Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13057-13064. [PMID: 30293430 DOI: 10.1021/acs.langmuir.8b02942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.
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Affiliation(s)
- E Prado
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - L Bonnat
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - H Bonnet
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - T Lavergne
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | | | - G Pratviel
- CNRS, Laboratoire de Chimie de Coordination , 205 route de Narbonne, BP44099 , F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT , Toulouse , France
| | - J Dejeu
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - E Defrancq
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
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9
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Haase L, Dickerhoff J, Weisz K. DNA–RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies. Chemistry 2018; 24:15365-15371. [DOI: 10.1002/chem.201803367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/05/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Linn Haase
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Jonathan Dickerhoff
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
- Present address: Department of Medicinal Chemistry and Molecular PharmacologyCollege of PharmacyPurdue University West Lafayette IN 47907 USA
| | - Klaus Weisz
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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10
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Piraux G, Bar L, Abraham M, Lavergne T, Jamet H, Dejeu J, Marcélis L, Defrancq E, Elias B. New Ruthenium-Based Probes for Selective G-Quadruplex Targeting. Chemistry 2017; 23:11872-11880. [PMID: 28609545 DOI: 10.1002/chem.201702076] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Indexed: 01/13/2023]
Abstract
Telomeric regions containing G-quadruplex (G4) structures play a pivotal role in the development of cancers. The development of specific binders for G4s is thus of great interest in order to gain a deeper understanding of the role of these structures, and to ultimately develop new anticancer drug candidates. For several years, RuII complexes have been studied as efficient probes for DNA. Interest in these complexes stems mainly from the tunability of their structures and properties, and the possibility of using light excitation as a tool to probe their environment or to selectively trigger their reaction with a biological target. Herein, we report on the synthesis and thorough study of new RuII complexes based on a novel dipyrazino[2,3-a:2',3'-h]phenazine ligand (dph), obtained through a Chichibabin-like reaction. Luminescence experiments, surface plasmon resonance (SPR), and computational studies have demonstrated that these complexes behave as selective probes for G-quadruplex structures.
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Affiliation(s)
- Guillaume Piraux
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Laure Bar
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Michaël Abraham
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Thomas Lavergne
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Hélène Jamet
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Jérôme Dejeu
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Lionel Marcélis
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Eric Defrancq
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
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11
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Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine. Sci Rep 2017; 7:6695. [PMID: 28751647 PMCID: PMC5532209 DOI: 10.1038/s41598-017-07050-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.
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12
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Bonnat L, Bar L, Génnaro B, Bonnet H, Jarjayes O, Thomas F, Dejeu J, Defrancq E, Lavergne T. Template-Mediated Stabilization of a DNA G-Quadruplex formed in the HIV-1 Promoter and Comparative Binding Studies. Chemistry 2017; 23:5602-5613. [PMID: 28264144 DOI: 10.1002/chem.201700417] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Indexed: 02/06/2023]
Abstract
G-rich DNA oligonucleotides derived from the promoter region of the HIV-1 long terminal repeat (LTR) were assembled onto an addressable cyclopeptide platform through sequential oxime ligation, a thiol-iodoacetamide SN2 reaction, and copper-catalyzed azide-alkyne cycloaddition reactions. The resulting conjugate was shown to fold into a highly stable antiparallel G4 architecture as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. The binding affinities of six state-of-the-art G4-binding ligands toward the HIV-G4 structure were compared to those obtained with a telomeric G4 structure and a hairpin structure. Surface plasmon resonance binding analysis provides new insights into the binding mode of broadly exploited G4 chemical probes and further suggests that potent and selective recognition of viral G4 structures of functional significance might be achieved.
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Affiliation(s)
- Laureen Bonnat
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France.,Univ. Grenoble Alpes, CNRS, DPM UMR-5063, 38000, Grenoble, France
| | - Laure Bar
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Béatrice Génnaro
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Hugues Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Olivier Jarjayes
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Fabrice Thomas
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Thomas Lavergne
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
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13
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Dickerhoff J, Appel B, Müller S, Weisz K. Zuckerseitige Wechselwirkungen in einem DNA-RNA-G-Quadruplex: Hinweise auf sequentielle C−H⋅⋅⋅O-Wasserstoffbrücken als Beitrag zur RNA-Quadruplex-Faltung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
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Dickerhoff J, Appel B, Müller S, Weisz K. Sugar-Edge Interactions in a DNA-RNA G-Quadruplex: Evidence of Sequential C-H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding. Angew Chem Int Ed Engl 2016; 55:15162-15165. [PMID: 27860177 DOI: 10.1002/anie.201608275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/29/2016] [Indexed: 11/11/2022]
Abstract
DNA G-quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti-dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA-RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3'-side within the quadruplex core strongly suggest the presence of C8-H⋅⋅⋅O hydrogen-bonding interactions with the O2' position of the C2'-endo ribonucleotide. A geometric analysis of reported high-resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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