1
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Bonnet C, Dian AL, Espie-Caullet T, Fabbri L, Lagadec L, Pivron T, Dutertre M, Luco R, Navickas A, Vagner S, Verga D, Uguen P. Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics. Bull Cancer 2024; 111:782-790. [PMID: 38824069 DOI: 10.1016/j.bulcan.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 06/03/2024]
Abstract
A better understanding of the RNA biology and chemistry is necessary to then develop new RNA therapeutic strategies. This review is the synthesis of a series of conferences that took place during the 6th international course on post-transcriptional gene regulation at Institut Curie. This year, the course made a special focus on RNA chemistry.
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Affiliation(s)
- Clara Bonnet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Tristan Espie-Caullet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucilla Fabbri
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucie Lagadec
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Thibaud Pivron
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Reini Luco
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Albertas Navickas
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, Inserm U1196, Chemistry and Modelling for the Biology of Cancer, Institut Curie, université Paris-Saclay, 91405 Orsay, France
| | - Patricia Uguen
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
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2
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Qin G, Liu Z, Yang J, Liao X, Zhao C, Ren J, Qu X. Targeting specific DNA G-quadruplexes with CRISPR-guided G-quadruplex-binding proteins and ligands. Nat Cell Biol 2024; 26:1212-1224. [PMID: 38961283 DOI: 10.1038/s41556-024-01448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Despite the demonstrated importance of DNA G-quadruplexes (G4s) in health and disease, technologies to readily manipulate specific G4 folding for functional analysis and therapeutic purposes are lacking. Here we employ G4-stabilizing protein/ligand in conjunction with CRISPR to selectively facilitate single or multiple targeted G4 folding within specific genomic loci. We demonstrate that fusion of nucleolin with a catalytically inactive Cas9 can specifically stabilize G4s in the promoter of oncogene MYC and muscle-associated gene Itga7 as well as telomere G4s, leading to cell proliferation arrest, inhibition of myoblast differentiation and cell senescence, respectively. Furthermore, CRISPR can confer intra-G4 selectivity to G4-binding compounds pyridodicarboxamide and pyridostatin. Compared with traditional G4 ligands, CRISPR-guided biotin-conjugated pyridodicarboxamide enables a more precise investigation into the biological functionality of de novo G4s. Our study provides insights that will enhance understanding of G4 functions and therapeutic interventions.
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Affiliation(s)
- Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Zhenqi Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Xiaofeng Liao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China.
- University of Science and Technology of China, Hefei, P. R. China.
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3
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Laigre E, Bonnet H, Beauvineau C, Lavergne T, Verga D, Defrancq E, Dejeu J, Teulade-Fichou MP. Systematic Evaluation of Benchmark G4 Probes and G4 Clinical Drugs using three Biophysical Methods: A Guideline to Evaluate Rapidly G4-Binding Affinity. Chembiochem 2024; 25:e202400210. [PMID: 38619969 DOI: 10.1002/cbic.202400210] [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: 04/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
G-quadruplex DNA structures (G4) are proven to interfere with most genetic and epigenetic processes. Small molecules binding these structures (G4 ligands) are invaluable tools to probe G4-biology and address G4-druggability in various diseases (cancer, viral infections). However, the large number of reported G4 ligands (>1000) could lead to confusion while selecting one for a given application. Herein we conducted a systematic affinity ranking of 11 popular G4 ligands vs 5 classical G4 sequences using FRET-melting, G4-FID assays and SPR. Interestingly SPR data globally align with the rankings obtained from the two semi-quantitative assays despite discrepancies due to limits and characteristics of each assay. In the whole, PhenDC3 emerges as the most potent binder irrespective of the G4 sequence. Immediately below PDS, PDC-360A, BRACO19, TMPyP4 and RHPS4 feature strong to medium binding again with poor G4 topology discrimination. More strikingly, the G4 drugs Quarfloxin, CX5461 and c-PDS exhibit weak affinity with all G4s studied. Finally, NMM and Cu-ttpy showed heterogeneous behaviors due, in part, to their physicochemical particularities poorly compatible with screening conditions. The remarkable properties of PhenDC3 led us to propose its use for benchmarking FRET-melting and G4-FID assays for rapid G4-affinity evaluation of newly developed ligands.
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Affiliation(s)
- E Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - H Bonnet
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - C Beauvineau
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - T Lavergne
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - D Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - E Defrancq
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - J Dejeu
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
- SUPMICROTECH, Université Franche-Comté, CNRS, Institut FEMTO-ST, 25000, Besançon, France
| | - M-P Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
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4
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Robinson J, Stenspil SG, Maleckaite K, Bartlett M, Di Antonio M, Vilar R, Kuimova MK. Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy. J Am Chem Soc 2024; 146:1009-1018. [PMID: 38151240 PMCID: PMC10786036 DOI: 10.1021/jacs.3c11908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.
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Affiliation(s)
- Jenna Robinson
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Stine G. Stenspil
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Karolina Maleckaite
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Molly Bartlett
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Marco Di Antonio
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Ramon Vilar
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
| | - Marina K. Kuimova
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
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5
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Lejault P, Prudent L, Terrier MP, Perreault JP. Small molecule chaperones facilitate the folding of RNA G-quadruplexes. Biochimie 2023; 214:83-90. [PMID: 37666291 DOI: 10.1016/j.biochi.2023.08.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/21/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
RNA G-quadruplexes (rG4) have recently emerged as major regulatory elements in both mRNA and non-coding RNA. In order to investigate the biological roles of rG4 structures, chemists have developed a variety of highly specific and potent ligands. All of these ligands bind to the rG4s by stacking on top of them. The binding specificity is demonstrated by comparison to other structures such as duplex or three-way junctions. It remains unclear whether rG4-ligands merely stabilize fully formed rG4 structures, or if they actively participate in the folding of the rG4 structure through their association with an unfolded RNA sequence. In order to elucidate the innate steps of ligand-rG4 associations and mechanisms robust in vitro techniques, including FRET, electrophoretic mobility shift assays and reverse transcriptase stalling assays, were used to examine the capacity of five well-known G4 ligands to induce rG4 structures derived from either long non-coding RNAs or from synthetic RNAs. It was found that both PhenDC3 and PDS induce rG4 formation in single RNA strands. This discovery has important implications for the interpretation of RNA-seq experiments. Overall, in vitro data that can assist biochemists in selecting the optimal G4-ligands for their RNA cellular experiments are presented, and the effects induced by these ligands on the rG4s are also considered.
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Affiliation(s)
- Pauline Lejault
- Department of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
| | - Louis Prudent
- Department of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michel-Pierre Terrier
- Department of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry and Functional Genomics, Pavillon de Recherche Appliquée sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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6
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Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
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Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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7
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Feng Y, He Z, Luo Z, Sperti FR, Valverde IE, Zhang W, Monchaud D. Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs. iScience 2023; 26:106846. [PMID: 37250775 PMCID: PMC10212998 DOI: 10.1016/j.isci.2023.106846] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
The search for G-quadruplex (G4)-forming sequences across the genome is motivated by their involvement in key cellular processes and their putative roles in dysregulations underlying human genetic diseases. Sequencing-based methods have been developed to assess the prevalence of DNA G4s genome wide, including G4-seq to detect G4s in purified DNA (in vitro) using the G4 stabilizer PDS, and G4 chromatin immunoprecipitation sequencing (G4 ChIP-seq) to detect G4s in in situ fixed chromatin (in vivo) using the G4-specific antibody BG4. We recently reported on G4-RNA precipitation and sequencing (G4RP-seq) to assess the in vivo prevalence of RNA G4 landscapes transcriptome wide using the small molecule BioTASQ. Here, we apply this technique for mapping DNA G4s in plants (rice) and compare the efficiency of this new technique, G4-DNA precipitation and sequencing, G4DP-seq, to that of BG4-DNA-IP-seq that we developed for mapping of DNA G4s in rice using BG4. By doing so, we compare the G4 capture ability of small-sized ligands (BioTASQ and BioCyTASQ) versus the antibody BG4.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
| | - Ibai E. Valverde
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, Nanjing, P.R. China
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR 6302, Université de Bourgogne, Dijon, France
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8
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Holden L, Gkika KS, Burke CS, Long C, Keyes TE. Selective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex. Inorg Chem 2023; 62:2213-2227. [PMID: 36703307 PMCID: PMC9906756 DOI: 10.1021/acs.inorgchem.2c03903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sensors capable of transducing G-quadruplex DNA binding are important both in solution and for imaging and interrogation in cellulo. Ru(II)-based light switches incorporating dipyridylphenazine (dppz) ligands are effective probes for recognition and imaging of DNA and its polymorphs including G-quadruplex, although selectivity is a limitation. While the majority of Ru(II)-based light switches reported to date, stabilize the quadruplex, imaging/theranostic probes that can disrupt G4s are of potentially enormous value in study and therapy for a range of disease states. We report here, on a Ru(II) complex (Ru-PDC3) that assembles the light switch capability of a Ru(II) dipyridylphenazine complex with the well-known G4-selective ligand Phen-DC3, into a single structure. The complex shows the anticipated light switch effect and strong affinity for G4 structures. Affinity depended on the G4 topology and sequence, but across all structures bar one, it was roughly an order of magnitude greater than for duplex or single-stranded DNA. Moreover, photophysical and Raman spectral data showed clear discrimination between duplex DNA and G4-bound structures offering the prospect of discrimination in imaging as well as in solution. Crucially, unlike the constituent components of the probe, Ru-PDC3 is a powerful G4 disrupter. From circular dichroism (CD), a reduction of ellipticity of the G4 between 70 and 95% was observed depending on topology and in many cases was accompanied by an induced CD signal for the metal complex. The extent of change in ellipticity is amongst the largest reported for small-molecule ligand G4 binding. While a promising G4 probe, without modification, the complex is fully water-soluble and readily permeable to live cells.
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9
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Reznichenko O, Leclercq D, Franco Pinto J, Mouawad L, Gabelica V, Granzhan A. Optimization of G-Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones). Chemistry 2023; 29:e202202427. [PMID: 36286608 PMCID: PMC10099395 DOI: 10.1002/chem.202202427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/06/2022]
Abstract
G-quadruplexes (G4s), secondary structures adopted by guanine-rich DNA and RNA sequences, are implicated in numerous biological processes and have been suggested as potential drug targets. Accordingly, there is an increasing interest in developing high-throughput methods that allow the generation of congeneric series of G4-targeting molecules ("ligands") and investigating their interactions with the targets. We have developed an operationally simple method of parallel synthesis to generate "ready-to-screen" libraries of cationic acylhydrazones, a motif that we have previously identified as a promising scaffold for potent, biologically active G4 ligands. Combined with well-established screening techniques, such as fluorescence melting, this method enables the rapid synthesis and screening of combinatorial libraries of potential G4 ligands. Following this protocol, we synthesized a combinatorial library of 90 bis(acylhydrazones) and screened it against five different nucleic acid structures. This way, we were able to analyze the structure-activity relationships within this series of G4 ligands, and identified three novel promising ligands whose interactions with G4-DNAs of different topologies were studied in detail by a combination of several biophysical techniques, including native mass spectrometry, and molecular modeling.
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Affiliation(s)
- Oksana Reznichenko
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Denis Leclercq
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Jaime Franco Pinto
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Liliane Mouawad
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Valérie Gabelica
- Univ. BordeauxCNRS, INSERM, ARNAUMR 5320, U1212, IECB33600PessacFrance
| | - Anton Granzhan
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
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10
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Lu X, Wu X, Kuang S, Lei C, Nie Z. Visualization of Deep Tissue G-quadruplexes with a Novel Large Stokes-Shifted Red Fluorescent Benzothiazole Derivative. Anal Chem 2022; 94:10283-10290. [PMID: 35776781 DOI: 10.1021/acs.analchem.2c02049] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-quadruplex (G4) is a noncanonical nucleic acid secondary structure that has implications for various physiological and pathological processes and is thus essential to exploring new approaches to G4 detection in live cells. However, the deficiency of molecular imaging tools makes it challenging to visualize the G4 in ex vivo tissue samples. In this study, we established a G4 probe design strategy and presented a red fluorescent benzothiazole derivative, ThT-NA, to detect and image G4 structures in living cells and tissue samples. By enhancing the electron-donating group of thioflavin T (ThT) and optimizing molecular structure, ThT-NA shows excellent photophysical properties, including red emission (610 nm), a large Stokes shift (>100 nm), high sensitivity selectivity toward G4s (1600-fold fluorescence turn-on ratio) and robust two-photon fluorescence emission. Therefore, these features enable ThT-NA to reveal the endogenous RNA G4 distribution in living cells and differentiate the cell cycle by monitoring the changes of RNA G4 folding. Significantly, to the best of our knowledge, ThT-NA is the first benzothiazole-derived G4 probe that has been developed for imaging G4s in ex vivo cancer tissue samples by two-photon microscopy techniques.
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Affiliation(s)
- Xu Lu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Xianhua Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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