1
|
Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
Collapse
Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| |
Collapse
|
2
|
Malina J, Kostrhunova H, Scott P, Brabec V. Fe II Metallohelices Stabilize DNA G-Quadruplexes and Downregulate the Expression of G-Quadruplex-Regulated Oncogenes. Chemistry 2021; 27:11682-11692. [PMID: 34048082 DOI: 10.1002/chem.202101388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Indexed: 12/15/2022]
Abstract
DNA G-quadruplexes (G4s) have been identified within the promoter regions of many proto-oncogenes. Thus, G4s represent attractive targets for cancer therapy, and the design and development of new drugs as G4 binders is a very active field of medicinal chemistry. Here, molecular biophysics and biology methods were employed to investigate the interaction of chiral metallohelices with a series of four DNA G4s (hTelo, c-myc, c-kit1, c-kit2) that are formed by the human telomeric sequence (hTelo) and in the promoter regions of c-MYC and c-KIT proto-oncogenes. We show that the investigated water-compatible, optically pure metallohelices, which are made by self-assembly of simple nonpeptidic organic components around FeII ions and exhibit bioactivity emulating the natural systems, bind with high affinity to G4 DNA and much lower affinity to duplex DNA. Notably, both enantiomers of a metallohelix containing a m-xylenyl bridge (5 b) were found to effectively inhibit primer elongation catalyzed by Taq DNA polymerase by stabilizing G4 structures formed in the template strands containing c-myc and c-kit2 G4-forming sequences. Moreover, both enantiomers of 5 b downregulated the expression of c-MYC and c-KIT oncogenes in human embryonic kidney cells at mRNA and protein levels. As metallohelices also bind alternative nucleic acid structures, they hold promise as potential multitargeted drugs.
Collapse
Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Hana Kostrhunova
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| |
Collapse
|
3
|
Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| |
Collapse
|
4
|
Sasaki S, Ma Y, Ishizuka T, Bao HL, Hirokawa T, Xu Y, Tera M, Nagasawa K. Linear consecutive hexaoxazoles as G4 ligands inducing chair-type anti-parallel topology of a telomeric G-quadruplex. RSC Adv 2020; 10:43319-43323. [PMID: 35519695 PMCID: PMC9058415 DOI: 10.1039/d0ra09413g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
G-quadruplex structures (G4s) in guanine-rich regions of DNA play critical roles in various biological phenomena, including replication, translation, and gene expression. There are three types of G4 topology, i.e., parallel, anti-parallel, and hybrid, and ligands that selectively interact with or stabilize a specific topology have been extensively explored to enable studies of topology-related functions. Here, we describe the synthesis of a new series of G4 ligands based on 6LCOs (6-linear consecutive oxazoles), i.e., L2H2-2M2EA-6LCO (2), L2A2-2M2EAc-6LCO (3), and L2G2-2M2EG-6LCO (4), which bear four aminoalkyl, acetamidealkyl, and guanidinylalkyl side chains, respectively. Among them, ligand 2 stabilized telomeric G4 and induced anti-parallel topology independently of the presence of cations. The anti-parallel topology induced by 2 was identified as chair-type by means of 19F NMR spectroscopy and fluorescence experiments with 2-aminopurine-labeled DNA.
Collapse
Affiliation(s)
- Shogo Sasaki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Hong-Liang Bao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Division of Biomedical Science, University of Tsukuba 1-1-1 Tennodai Tsukuba, 305-8575 Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ward Tokyo 135-0064 Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazak 5200 Kihara, Kiyotake Miyazaki 889-1692 Japan
| | - Masayuki Tera
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho, Koganei Tokyo 184-8588 Japan
| |
Collapse
|
5
|
Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
|
6
|
Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
7
|
Schmidt OP, Benz AS, Mata G, Luedtke NW. HgII binds to C-T mismatches with high affinity. Nucleic Acids Res 2018; 46:6470-6479. [PMID: 29901748 PMCID: PMC6061796 DOI: 10.1093/nar/gky499] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/04/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.
Collapse
Affiliation(s)
- Olivia P Schmidt
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Andrea S Benz
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Guillaume Mata
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Nathan W Luedtke
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| |
Collapse
|
8
|
Simple G-quadruplex-based 2-aminopurine fluorescence probe for highly sensitive and amplified detection of microRNA-21. Talanta 2018; 178:974-979. [DOI: 10.1016/j.talanta.2017.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 01/12/2023]
|
9
|
Peng P, Du Y, Sun Y, Liu S, Mi L, Li T. Probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine for label-free switchable molecular sensing. Analyst 2018; 143:3814-3820. [DOI: 10.1039/c8an00914g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a novel ligand-free signal readout mechanism for probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine.
Collapse
Affiliation(s)
- Pai Peng
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| | - Yi Du
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| | - Yudie Sun
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| | - Shuangna Liu
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| | - Lan Mi
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| | - Tao Li
- Department of Chemistry
- University of Science and Technology of China
- Hefei
- P.R. China
| |
Collapse
|
10
|
Ihmels H, Löhl K, Paululat T, Uebach S. NMR-spectroscopic investigation of the complex between tetraazoniapentapheno[6,7-h]pentaphene and quadruplex DNA Tel26. NEW J CHEM 2018. [DOI: 10.1039/c8nj01931b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tetraazoniapentapheno[6,7-h]pentaphene binds to the hybrid-1 quadruplex structure of the oligonucleotide Tel26 by terminal π stacking, likely on top of the A3–A9–A21 triplet.
Collapse
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Katharina Löhl
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Thomas Paululat
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Sandra Uebach
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| |
Collapse
|
11
|
Lee CY, Park KS, Park HG. Pyrrolo-dC modified duplex DNA as a novel probe for the sensitive assay of base excision repair enzyme activity. Biosens Bioelectron 2017; 98:210-214. [DOI: 10.1016/j.bios.2017.06.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/07/2017] [Accepted: 06/25/2017] [Indexed: 01/13/2023]
|
12
|
Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
Collapse
Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| |
Collapse
|
13
|
del Mundo I, Zewail-Foote M, Kerwin SM, Vasquez KM. Alternative DNA structure formation in the mutagenic human c-MYC promoter. Nucleic Acids Res 2017; 45:4929-4943. [PMID: 28334873 PMCID: PMC5416782 DOI: 10.1093/nar/gkx100] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/31/2017] [Accepted: 02/07/2017] [Indexed: 01/08/2023] Open
Abstract
Mutation 'hotspot' regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood. To address this issue, we investigated the folding preferences of oligonucleotides from a chromosomal breakpoint hotspot in the human c-MYC oncogene containing both potential G4-forming and H-DNA-forming elements. We characterized the structures formed in the presence of G4-DNA-stabilizing K+ ions or H-DNA-stabilizing Mg2+ ions using multiple techniques. We found that under conditions favorable for H-DNA formation, a stable intramolecular triplex DNA structure predominated; whereas, under K+-rich, G4-DNA-forming conditions, a plurality of unfolded and folded species were present. Thus, within a limited region containing sequences with the potential to adopt multiple structures, only one structure predominates under a given condition. The predominance of H-DNA implicates this structure in the instability associated with the human c-MYC oncogene.
Collapse
Affiliation(s)
- Imee Marie A. del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX 78723, USA
| | - Maha Zewail-Foote
- Department of Chemistry and Biochemistry, Southwestern University, 1001 E University Ave, Georgetown, TX 78626, USA
| | - Sean M. Kerwin
- Department of Chemistry and Biochemistry, Texas State University, 601 University Dr., San Marcos, TX 78666, USA
| | - Karen M. Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. Austin, TX 78723, USA
| |
Collapse
|
14
|
Gao Y, Guang T, Ye X. Sedimentation velocity analysis of TMPyP4-induced dimer formation of human telomeric G-quadruplex. RSC Adv 2017. [DOI: 10.1039/c7ra07758k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Analytical ultracentrifugation sedimentation velocity (AUC-SV) was used to study the interactions between TMPyP4 and AGGG(TTAGGG)3 (Tel22) and the TMPyP4-induced dimer formation of G-quadruplex.
Collapse
Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Tianlei Guang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| |
Collapse
|
15
|
Schmidt OP, Mata G, Luedtke NW. Fluorescent Base Analogue Reveals T-HgII-T Base Pairs Have High Kinetic Stabilities That Perturb DNA Metabolism. J Am Chem Soc 2016; 138:14733-14739. [DOI: 10.1021/jacs.6b09044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Olivia P. Schmidt
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Guillaume Mata
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
16
|
Mandal PK, Baptiste B, Langlois d'Estaintot B, Kauffmann B, Huc I. Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State. Chembiochem 2016; 17:1911-1914. [DOI: 10.1002/cbic.201600281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Pradeep K. Mandal
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Benoît Baptiste
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Béatrice Langlois d'Estaintot
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| | - Brice Kauffmann
- University of Bordeaux; IECB; UMS 3033); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; IECB; UMS 3033); 2 rue Escarpit 33600 Pessac France
- INSERM; IECB; US001); 2 rue Escarpit 33600 Pessac France
| | - Ivan Huc
- University of Bordeaux; CBMN; UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
- Bordeaux Institut National Polytechnique; CBMN; UMR 5248); 2 rue Escarpit 33600 Pessac France
| |
Collapse
|
17
|
Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
Collapse
Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| |
Collapse
|
18
|
Tanpure AA, Srivatsan SG. Conformation-sensitive nucleoside analogues as topology-specific fluorescence turn-on probes for DNA and RNA G-quadruplexes. Nucleic Acids Res 2015. [PMID: 26202965 PMCID: PMC4678839 DOI: 10.1093/nar/gkv743] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Development of probes that can discriminate G-quadruplex (GQ) structures and indentify efficient GQ binders on the basis of topology and nucleic acid type is highly desired to advance GQ-directed therapeutic strategies. In this context, we describe the development of minimally perturbing and environment-sensitive pyrimidine nucleoside analogues, based on a 5-(benzofuran-2-yl)uracil core, as topology-specific fluorescence turn-on probes for human telomeric DNA and RNA GQs. The pyrimidine residues of one of the loop regions (TTA) of telomeric DNA and RNA GQ oligonucleotide (ON) sequences were replaced with 5-benzofuran-modified 2′-deoxyuridine and uridine analogues. Depending on the position of modification the fluorescent nucleoside analogues distinguish antiparallel, mixed parallel-antiparallel and parallel stranded DNA and RNA GQ topologies from corresponding duplexes with significant enhancement in fluorescence intensity and quantum yield. Further, these GQ sensors enabled the development of a simple fluorescence binding assay to quantify topology- and nucleic acid-specific binding of small molecule ligands to GQ structures. Together, our results demonstrate that these nucleoside analogues are useful GQ probes, which are anticipated to provide new opportunities to study and discover efficient G-quadruplex binders of therapeutic potential.
Collapse
Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|
19
|
Le DD, Di Antonio M, Chan LKM, Balasubramanian S. G-quadruplex ligands exhibit differential G-tetrad selectivity. Chem Commun (Camb) 2015; 51:8048-50. [PMID: 25864836 DOI: 10.1039/c5cc02252e] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A rapid and simple equilibrium-binding assay mediated by ligand-induced fluorescence quenching of fluorophore-labelled G-quadruplex (G4) structures enabled quantitative interrogation of mutually exclusive ligand binding interactions at opposed G-tetrads. This technique revealed that the ligands TmPyP4, PhenDC3, and PDS have differential chemotype-specific binding preferences for individual G-tetrads of a model genomic G4 structure.
Collapse
Affiliation(s)
- D D Le
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | | | | | | |
Collapse
|
20
|
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Collapse
|
21
|
Lee CY, Park KS, Park HG. A fluorescent G-quadruplex probe for the assay of base excision repair enzyme activity. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc05010c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A G-quadruplex probe incorporating 2-AP is utilized to develop a novel strategy to accurately determine UDG activity. The excision reaction promoted by UDG is designed to trigger the formation of G-quadruplex structure with significant fluorescence enhancement of 2-AP within the probe. By employing this strategy, UDG activity can be reliably determined with high sensitivity and specificity.
Collapse
Affiliation(s)
- Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK21 + Program)
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
| | - Ki Soo Park
- Department of Chemical and Biomolecular Engineering (BK21 + Program)
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 + Program)
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 305-701
- Republic of Korea
| |
Collapse
|
22
|
Mohapatra B, Verma S. Crystallographic Studies of Modified 2-Aminopurine Nucleobase with Transition Metal Ions. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2014. [DOI: 10.1007/s40010-014-0147-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
23
|
Abstract
This review summarizes the results of structural studies carried out with analogs of G-quadruplexes built from natural nucleotides. Several dozens of base-, sugar-, and phosphate derivatives of the biological building blocks have been incorporated into more than 50 potentially quadruplex forming DNA and RNA oligonucleotides and the stability and folding topology of the resultant intramolecular, bimolecular and tetramolecular architectures characterized. The TG4T, TG5T, the 15 nucleotide-long thrombin binding aptamer, and the human telomere repeat AG3(TTAG3)3 sequences were modified in most cases, and four guanine analogs can be noted as being particularly useful in structural studies. These are the fluorescent 2-aminopurine, the 8-bromo-, and 8-methylguanines, and the hypoxanthine. The latter three analogs stabilize a given fold in a mixture of structures making possible accurate structural determinations by circular dichroism and nuclear magnetic resonance measurements.
Collapse
Affiliation(s)
- Janos Sagi
- a Rimstone Laboratory , RLI, 29 Lancaster Way, Cheshire , CT , 06410 , USA
| |
Collapse
|
24
|
Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | | | | |
Collapse
|
25
|
Buscaglia R, Jameson DM, Chaires JB. G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots. Nucleic Acids Res 2012; 40:4203-15. [PMID: 22241767 PMCID: PMC3351194 DOI: 10.1093/nar/gkr1286] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/17/2022] Open
Abstract
The use of time-resolved fluorescence measurements in studies of telomeric G-quadruplex folding and stability has been hampered by the complexity of fluorescence lifetime distributions in solution. The application of phasor diagrams to the analysis of time-resolved fluorescence measurements, collected from either frequency-domain or time-domain instrumentation, allows for rapid characterization of complex lifetime distributions. Phasor diagrams are model-free graphical representations of transformed time-resolved fluorescence results. Simplification of complex fluorescent decays by phasor diagrams is demonstrated here using a 2-aminopurine substituted telomeric G-quadruplex sequence. The application of phasor diagrams to complex systems is discussed with comparisons to traditional non-linear regression model fitting. Phasor diagrams allow for the folding and stability of the telomeric G-quadruplex to be monitored in the presence of either sodium or potassium. Fluorescence lifetime measurements revealed multiple transitions upon folding of the telomeric G-quadruplex through the addition of potassium. Enzymatic digestion of the telomeric G-quadruplex structure, fluorescence quenching and Förster resonance energy transfer were also monitored through phasor diagrams. This work demonstrates the sensitivity of time-resolved methods for monitoring changes to the telomeric G-quadruplex and outlines the phasor diagram approach for analysis of complex time-resolved results that can be extended to other G-quadruplex and nucleic acid systems.
Collapse
Affiliation(s)
- Robert Buscaglia
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - David M. Jameson
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| |
Collapse
|
26
|
Collie GW, Parkinson GN. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 2011; 40:5867-92. [PMID: 21789296 DOI: 10.1039/c1cs15067g] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).
Collapse
Affiliation(s)
- Gavin W Collie
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London, UK WC1N 1AX
| | | |
Collapse
|
27
|
Dumas A, Luedtke NW. Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA. Chembiochem 2011; 12:2044-51. [PMID: 21786378 DOI: 10.1002/cbic.201100214] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 12/24/2022]
Abstract
Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.
Collapse
Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | | |
Collapse
|
28
|
Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
29
|
Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011; 50:8046-50. [DOI: 10.1002/anie.201101759] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/30/2011] [Indexed: 12/18/2022]
|
30
|
Dumas A, Luedtke NW. Highly fluorescent guanosine mimics for folding and energy transfer studies. Nucleic Acids Res 2011; 39:6825-34. [PMID: 21551219 PMCID: PMC3159459 DOI: 10.1093/nar/gkr281] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Guanosines with substituents at the 8-position can provide useful fluorescent probes that effectively mimic guanine residues even in highly demanding model systems such as polymorphic G-quadruplexes and duplex DNA. Here, we report the synthesis and photophysical properties of a small family of 8-substituted-2′-deoxyguanosines that have been incorporated into the human telomeric repeat sequence using phosphoramidite chemistry. These include 8-(2-pyridyl)-2′-deoxyguanosine (2PyG), 8-(2-phenylethenyl)-2′-deoxyguanosine (StG) and 8-[2-(pyrid-4-yl)-ethenyl]-2′-deoxyguanosine (4PVG). On DNA folding and stability, 8-substituted guanosines can exhibit context-dependent effects but were better tolerated by G-quadruplex and duplex structures than pyrimidine mismatches. In contrast to previously reported fluorescent guanine analogs, 8-substituted guanosines exhibit similar or even higher quantum yields upon their incorporation into nucleic acids (Φ = 0.02–0.45). We have used these highly emissive probes to quantify energy transfer efficiencies from unmodified DNA nucleobases to 8-substituted guanosines. The resulting DNA-to-probe energy transfer efficiencies (ηt) are highly structure selective, with ηt(duplex) < ηt(single-strand) < ηt(G-quadruplex). These trends were independent of the exact structural features and thermal stabilities of the G-quadruplexes or duplexes containing them. The combination of efficient energy transfer, high probe quantum yield, and high molar extinction coefficient of the DNA provides a highly sensitive and reliable readout of G-quadruplex formation even in highly diluted sample solutions of 0.25 nM.
Collapse
Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | |
Collapse
|
31
|
Dumas A, Luedtke NW. Cation-Mediated Energy Transfer in G-Quadruplexes Revealed by an Internal Fluorescent Probe. J Am Chem Soc 2010; 132:18004-7. [DOI: 10.1021/ja1079578] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Switzerland
| | - Nathan W. Luedtke
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Switzerland
| |
Collapse
|
32
|
Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| |
Collapse
|
33
|
Gray RD, Petraccone L, Trent JO, Chaires JB. Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence. Biochemistry 2010; 49:179-94. [PMID: 19961180 DOI: 10.1021/bi901357r] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Human telomeric DNA consists of tandem repeats of the DNA sequence d(GGGTTA). Oligodeoxynucleotide telomere models such as d[A(GGGTTA)(3)GGG] (Tel22) fold in a cation-dependent manner into quadruplex structures consisting of stacked G-quartets linked by d(TTA) loops. NMR has shown that in Na(+) solutions Tel22 forms a "basket" topology of four antiparallel strands; in contrast, Tel22 in K(+) solutions consists of a mixture of unknown topologies. Our previous studies on the mechanism of folding of Tel22 and similar telomere analogues utilized changes in UV absorption between 270 and 325 nm that report primarily on G-quartet formation and stacking showed that quadruplex formation occurs within milliseconds upon mixing with an appropriate cation. In this study, we assess the dynamics and equilibria of folding of specific loops by using Tel22 derivatives in which the dA residues were serially substituted with the fluorescent reporter base, 2-aminopurine (2-AP). Tel22 folding induced by Na(+) or K(+) assessed by changes in 2-AP fluorescence consists of at least three kinetic steps with time constants spanning a range from milliseconds to several hundred seconds. Na(+)-dependent equilibrium titrations of Tel22 folding could be approximated as a cooperative two-state process. In contrast, K(+)-dependent folding curves were biphasic, revealing that different conformational ensembles are present in 1 and 30 mM K(+). This conclusion was confirmed by (1)H NMR. Molecular dynamics simulations revealed a K(+) binding pocket in Tel22 located near dA1 that is specific for the so-called hybrid-1 conformation in which strand 1 is in a parallel arrangement. The possible presence of this topologically specific binding site suggests that K(+) may play an allosteric role in regulating telomere conformation and function by modulating quadruplex tertiary structure.
Collapse
Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, USA
| | | | | | | |
Collapse
|
34
|
Mendez MA, Szalai VA. Fluorescence of unmodified oligonucleotides: A tool to probe G-quadruplex DNA structure. Biopolymers 2009; 91:841-50. [PMID: 19548317 DOI: 10.1002/bip.21268] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fluorescence of unmodified oligonucleotides has not been exploited for guanine-quadruplex (G-quadruplex) characterization. We observe that G-rich sequences fluoresce more strongly than duplex or single-stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G-quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5'-T(4)G(n)T(4)-3' (n = 4-10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5'-GGGT-3', which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan-Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5'-TGGG-3', the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G-rich sequences can be probed using fluorescence signatures of unmodified oligonucleotides.
Collapse
Affiliation(s)
- Miguel Angel Mendez
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | | |
Collapse
|
35
|
Lang K, Rieder R, Micura R. Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res 2007; 35:5370-8. [PMID: 17693433 PMCID: PMC2018614 DOI: 10.1093/nar/gkm580] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Riboswitches are genetic control elements within non-coding regions of mRNA. They consist of a metabolite-sensitive aptamer and an adjoining expression platform. Here, we describe ligand-induced folding of a thiamine pyrophosphate (TPP) responsive riboswitch from Escherichia coli thiM mRNA, using chemically labeled variants. Referring to a recent structure determination of the TPP/aptamer complex, each variant was synthesized with a single 2-aminopurine (AP) nucleobase replacement that was selected to monitor formation of tertiary interactions of a particular region during ligand binding in real time by fluorescence experiments. We have determined the rate constants for conformational adjustment of the individual AP sensors. From the 7-fold differentiation of these constants, it can be deduced that tertiary contacts between the two parallel helical domains (P2/J3-2/P3/L3 and P4/P5/L5) that grip the ligand's ends in two separate pockets, form significantly faster than the function-critical three-way junction with stem P1 fully developed. Based on these data, we characterize the process of ligand binding by an induced fit of the RNA and propose a folding model of the TPP riboswitch aptamer. For the full-length riboswitch domain and for shorter constructs that represent transcriptional intermediates, we have additionally evaluated ligand-induced folding via AP-modified variants and provide insights into the sequential folding pathway that involves a finely balanced equilibrium of secondary structures.
Collapse
Affiliation(s)
| | | | - Ronald Micura
- *To whom correspondence should be addressed. +43 512 507 5210+43 512 507 2892
| |
Collapse
|