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Michael Sabo T, Trent JO, Chaires JB, Monsen RC. Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination. Methods 2024; 230:9-20. [PMID: 39032720 DOI: 10.1016/j.ymeth.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/22/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.
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Affiliation(s)
- T Michael Sabo
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States.
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2
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Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
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Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
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3
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Attanayake K, Mahmud S, Banerjee C, Sharif D, Rahman M, Majuta S, DeBastiani A, Sultana MN, Foroushani SH, Li C, Li P, Valentine SJ. Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 499:117231. [PMID: 38854816 PMCID: PMC11156224 DOI: 10.1016/j.ijms.2024.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.
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Affiliation(s)
- Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Chandrima Banerjee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sandra Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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4
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Brundridge NM, Fritz JM, Dickerhoff J, Yang D, McLuckey SA. Negative Electron Transfer Collision-Induced Dissociation of G-Quadruplexes: Uncovering the Guanine Radical Anion Loss Pathway. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:756-766. [PMID: 38456425 PMCID: PMC11022967 DOI: 10.1021/jasms.3c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
G-quadruplex (G4) DNA can form highly stable secondary structures in the presence of metal cations, and research has shown its potential as a transcriptional regulator for oncogenes in the human genome. In order to explore the interactions of DNA with metal cations using mass spectrometry, employing complementary fragmentation methods can enhance structural information. This study explores the use of ion-ion reactions for sequential negative electron transfer collision-induced dissociation (nET-CID) as a complement to traditional ion-trap CID (IT-CID). The resulting nET-CID data for G4 anions with and without metal cations show an increase in fragment ion type diversity and yield of structurally informative ions relative to IT-CID. The nET-CID yields greater sequence coverage by virtue of fragmentation at the 3'-side of thymine residues, which is lacking with IT-CID. Potassium adductions to backbone fragments in IT-CID and nET-CID spectra were nearly identical. Of note is a prominent fragment resulting from a loss of a 149 Da anion seen in nET-CID of large, G-rich sequences, proposed to be radical anion guanine loss. Neutral loss of neutral guanine (151 Da) and deprotonated nucleobase loss (150 Da) have been previously reported, but this is the first report of radical anion guanine loss (149 Da). Confirmation of the identity of the 149 Da anion results from the examination of the homonucleobase sequence 5'-GGGGGGGG-3'. Loss of a charged adenine radical anion at much lower relative abundance was also noted for the sequence 5'-AAAAAAAA-3'. DFT modeling indicates that the loss of a nucleobase as a radical anion from odd-electron nucleic acid anions is a thermodynamically favorable fragmentation pathway for G.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jordan M Fritz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W. Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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5
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Di Carluccio C, Cerofolini L, Moreira M, Rosu F, Padilla-Cortés L, Gheorghita GR, Xu Z, Santra A, Yu H, Yokoyama S, Gray TE, St. Laurent CD, Manabe Y, Chen X, Fukase K, Macauley MS, Molinaro A, Li T, Bensing BA, Marchetti R, Gabelica V, Fragai M, Silipo A. Molecular Insights into O-Linked Sialoglycans Recognition by the Siglec-Like SLBR-N (SLBR UB10712) of Streptococcus gordonii. ACS CENTRAL SCIENCE 2024; 10:447-459. [PMID: 38435526 PMCID: PMC10906241 DOI: 10.1021/acscentsci.3c01598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/05/2024]
Abstract
Streptococcus gordonii is a Gram-positive bacterial species that typically colonizes the human oral cavity, but can also cause local or systemic diseases. Serine-rich repeat (SRR) glycoproteins exposed on the S. gordonii bacterial surface bind to sialylated glycans on human salivary, plasma, and platelet glycoproteins, which may contribute to oral colonization as well as endocardial infections. Despite a conserved overall domain organization of SRR adhesins, the Siglec-like binding regions (SLBRs) are highly variable, affecting the recognition of a wide range of sialoglycans. SLBR-N from the SRR glycoprotein of S. gordonii UB10712 possesses the remarkable ability to recognize complex core 2 O-glycans. We here employed a multidisciplinary approach, including flow cytometry, native mass spectrometry, isothermal titration calorimetry, NMR spectroscopy from both protein and ligand perspectives, and computational methods, to investigate the ligand specificity and binding preferences of SLBR-N when interacting with mono- and disialylated core 2 O-glycans. We determined the means by which SLBR-N preferentially binds branched α2,3-disialylated core 2 O-glycans: a selected conformation of the 3'SLn branch is accommodated into the main binding site, driving the sTa branch to further interact with the protein. At the same time, SLBR-N assumes an open conformation of the CD loop of the glycan-binding pocket, allowing one to accommodate the entire complex core 2 O-glycan. These findings establish the basis for the generation of novel tools for the detection of specific complex O-glycan structures and pave the way for the design and development of potential therapeutics against streptococcal infections.
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Affiliation(s)
- Cristina Di Carluccio
- Department
of Chemical Sciences, University of Naples
Federico II, Naples 80138, Italy
| | - Linda Cerofolini
- Magnetic
Resonance Centre (CERM), CIRMMP, and Department of Chemistry “Ugo
Schiff”, University of Florence, Sesto Fiorentino 50019, Italy
| | - Miguel Moreira
- Department
of Chemical Sciences, University of Naples
Federico II, Naples 80138, Italy
| | - Frédéric Rosu
- IECB
Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Luis Padilla-Cortés
- Magnetic
Resonance Centre (CERM), CIRMMP, and Department of Chemistry “Ugo
Schiff”, University of Florence, Sesto Fiorentino 50019, Italy
| | - Giulia Roxana Gheorghita
- Magnetic
Resonance Centre (CERM), CIRMMP, and Department of Chemistry “Ugo
Schiff”, University of Florence, Sesto Fiorentino 50019, Italy
- Giotto
Biotech s.r.l., Sesto Fiorentino 50019, Italy
| | - Zhuojia Xu
- Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Abhishek Santra
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Hai Yu
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Shinji Yokoyama
- Graduate
School of Science, Osaka University, Osaka 565-0871, Japan
| | - Taylor E. Gray
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Chris D. St. Laurent
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yoshiyuki Manabe
- Graduate
School of Science, Osaka University, Osaka 565-0871, Japan
| | - Xi Chen
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Koichi Fukase
- Graduate
School of Science, Osaka University, Osaka 565-0871, Japan
| | - Matthew S. Macauley
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Antonio Molinaro
- Department
of Chemical Sciences, University of Naples
Federico II, Naples 80138, Italy
- Graduate
School of Science, Osaka University, Osaka 565-0871, Japan
| | - Tiehai Li
- Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Barbara A. Bensing
- San
Francisco Veterans Affairs Medical Center and University of California, San Francisco, California 94121, United States
| | - Roberta Marchetti
- Department
of Chemical Sciences, University of Naples
Federico II, Naples 80138, Italy
| | - Valérie Gabelica
- IECB
Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Marco Fragai
- Magnetic
Resonance Centre (CERM), CIRMMP, and Department of Chemistry “Ugo
Schiff”, University of Florence, Sesto Fiorentino 50019, Italy
| | - Alba Silipo
- Department
of Chemical Sciences, University of Naples
Federico II, Naples 80138, Italy
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6
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Largy E, Ranz M, Gabelica V. A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA. J Am Chem Soc 2023; 145:26843-26857. [PMID: 38044563 DOI: 10.1021/jacs.3c09365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging, because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize the G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in the inner and outer tetrads. We also established relationships among exchange rates, numbers of tetrads and bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.
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Affiliation(s)
- Eric Largy
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Matthieu Ranz
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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7
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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8
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Brundridge NM, Dickerhoff J, Yang D, McLuckey SA. Gas-Phase Fragmentation as a Probe of G-Quadruplex Formation. Anal Chem 2023; 95:15057-15067. [PMID: 37774231 PMCID: PMC11022955 DOI: 10.1021/acs.analchem.3c03143] [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] [Indexed: 10/01/2023]
Abstract
G-quadruplex (G4) DNA is found in oncogene promoters and human telomeres and is an attractive anticancer target. Stable G4 structures form in guanine-rich sequences in the presence of metal cations and can stabilize further with specific ligand adduction. To explore the preservation and stability of this secondary structure with mass spectrometry, gas-phase collision-induced dissociation kinetics of G4-like and non-G4-like ion structures were determined in a linear quadrupole ion trap. This study focused on a sequence from the promoter of the MYC oncogene, MycG4, and a mutant non-G4-forming sequence, MycNonG4. At relatively high ion activation energies, the backbone fragmentation patterns of the MycG4 and MycNonG4 are similar, while potassium ion-stabilized G4-folded [MycG4 + 2K-7H]5- and counterpart [MycG4-5H]5- ions are essentially indistinguishable, indicating that high-energy fragmentation is not sensitive to the G4 structure. At low energies, the backbone fragmentation patterns of MycG4 and MycNonG4 are significantly different. For MycG4, fragmentation over time differed significantly between the potassium-bound and free structures, reflecting the preservation of the G4 structure in the gas phase. Kinetic measurements revealed the [MycG4 + 2K-7H]5- ions to fragment two to three times more slowly than the [MycG4-5H]5-. Results for the control MycNonG4 indicated that the phenomena noted for [MycG4 + 2K-7H]5- ions are specific to G4-folding. Therefore, our data show that gentle activation conditions can lead to fragmentation behavior that is sensitive to G-quadruplex structure, revealing differences in kinetic stabilities of isomeric structures as well as the regions of the sequence that are directly involved in forming these structures.
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Affiliation(s)
- Nicole M Brundridge
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Danzhou Yang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, 575 W Stadium Avenue, West Lafayette, Indiana 47904, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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9
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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: 4.0] [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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10
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Binacchi F, Elia C, Cirri D, Van de Griend C, Zhou XQ, Messori L, Bonnet S, Pratesi A, Biver T. A biophysical study of the interactions of palladium(II), platinum(II) and gold(III) complexes of aminopyridyl-2,2'-bipyridine ligands with RNAs and other nucleic acid structures. Dalton Trans 2023; 52:598-608. [PMID: 36562298 DOI: 10.1039/d2dt03483b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal compounds form an attractive class of ligands for a variety of nucleic acids. Five metal complexes bearing aminopyridyl-2,2'-bipyridine tetradentate ligands and possessing a quasi-planar geometry were challenged toward different types of nucleic acid molecules including RNA polynucleotides in the duplex or triplex form, an RNA Holliday four-way junction, natural double helix DNA and a DNA G-quadruplex. The binding process was monitored comparatively using different spectroscopic and melting methods. The binding preferences that emerge from our analysis are discussed in relation to the structural features of the metal complexes.
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Affiliation(s)
- Francesca Binacchi
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Cassandra Elia
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Damiano Cirri
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Corjan Van de Griend
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Xue-Quan Zhou
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands
| | - Alessandro Pratesi
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Tarita Biver
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, 56124 Pisa, Italy.
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11
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van Dyck JF, Burns JR, Le Huray KIP, Konijnenberg A, Howorka S, Sobott F. Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility. Nat Commun 2022; 13:3610. [PMID: 35750666 PMCID: PMC9232653 DOI: 10.1038/s41467-022-31029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.
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Affiliation(s)
- Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK
| | - Kyle I P Le Huray
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium.,Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium. .,School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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12
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Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT. Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex. Biochem Biophys Res Commun 2022; 613:153-158. [DOI: 10.1016/j.bbrc.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022]
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13
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Marlton SJP, Trevitt A. Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers. Chem Commun (Camb) 2022; 58:9451-9467. [DOI: 10.1039/d2cc02101c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...
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