1
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Yao LY, Qin L, Chen Z, Lam J, Yam VWW. Assembly of Luminescent Chiral Gold(I)-Sulfido Clusters via Chiral Self-Sorting. Angew Chem Int Ed Engl 2024; 63:e202316200. [PMID: 38009456 DOI: 10.1002/anie.202316200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Due to the ubiquity of chirality in nature, chiral self-assembly involving self-sorting behaviors has remained as one of the most important research topics of interests. Herein, starting from a racemic mixture of SEG-based (SEG=SEGPHOS) chlorogold(I) precursors, a unique chiral butterfly-shape hexadecanuclear gold(I) cluster (Au16 ) with different ratios of RSEG and SSEG ligands is obtained via homoleptic and heterochiral self-sorting. More interestingly, by employing different chlorogold(I) precursors of opposite chirality (such as RSEG -Au2 and SBIN -Au2 (BIN=BINAP)), an unprecedented heteroleptic and heterochiral self-sorting strategy has been developed to give a series of heteroleptic chiral decanuclear gold(I) clusters (Au10 ) with propellor-shape structures. Heterochiral and heteroleptic self-sorting have also been observed between enantiomers of homoleptic chiral Au10 clusters to result in the heteroleptic chiral Au10 clusters via cluster-to-cluster transformation. Incorporation of heteroleptic ligands is found to decrease the symmetry from S4 of homoleptic meso Au10 to C2 of heteroleptic chiral Au10 clusters. The chirality has been transferred from the axial chiral ligands and stored in the heteroleptic gold(I) clusters.
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Affiliation(s)
- Liao-Yuan Yao
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
- MOE Key Laboratory of Cluster Sciences, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 8 Liangxiang East Road, Beijing, 102488, P. R. China
| | - Lin Qin
- MOE Key Laboratory of Cluster Sciences, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 8 Liangxiang East Road, Beijing, 102488, P. R. China
| | - Ziyong Chen
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Jonathan Lam
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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2
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Schumann SL, Kotnig S, Kutin Y, Drosou M, Stratmann LM, Streltsova Y, Schnegg A, Pantazis DA, Clever GH, Kasanmascheff M. Structure and Flexibility of Copper-Modified DNA G-Quadruplexes Investigated by 19 F ENDOR Experiments at 34 GHz. Chemistry 2023; 29:e202302527. [PMID: 37602522 DOI: 10.1002/chem.202302527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
DNA G-quadruplexes (GQs) are of great interest due to their involvement in crucial biological processes such as telomerase maintenance and gene expression. Furthermore, they are reported as catalytically active DNAzymes and building blocks in bio-nanotechnology. GQs exhibit remarkable structural diversity and conformational heterogeneity, necessitating precise and reliable tools to unravel their structure-function relationships. Here, we present insights into the structure and conformational flexibility of a unimolecular GQ with high spatial resolution via electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. These findings showcase the successful application of the 19 F-ENDOR methodology at 34 GHz, overcoming the limitations posed by the complexity and scarcity of higher-frequency spectrometers. Importantly, our approach retains both sensitivity and orientational resolution. This integrated study not only enhances our understanding of GQs but also expands the methodological toolbox for studying other macromolecules.
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Affiliation(s)
- Simon L Schumann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Simon Kotnig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Maria Drosou
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Lukas M Stratmann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yana Streltsova
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Alexander Schnegg
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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3
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Sasaki S, Ma Y, Hirokawa T, Ikebukuro K, Tera M, Nagasawa K. Regulation of thrombin activity by ligand-induced topological alteration in a thrombin-binding aptamer. Chem Commun (Camb) 2023. [PMID: 37377065 DOI: 10.1039/d3cc02308g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Thrombin-binding aptamer (TBA), which forms a G-quadruplex (G4) structure with anti-parallel topology, interacts with thrombin to inhibit its enzymatic activity. Here we show that the G4-topology-altering ligand L2H2-2M2EA-6LCO (6LCO) changes the anti-parallel topology of TBA G4 to the parallel topology, thereby abrogating the thrombin-inhibitory activity of TBA. This finding suggests that G4 ligands that alter topology may be promising drug candidates for diseases involving G4-binding proteins.
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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 Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Research Core Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takatsugu Hirokawa
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, 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.
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4
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Lefringhausen N, Seiffert V, Erbacher C, Karst U, Müller J. Chiral-at-Metal Silver-Mediated Base Pairs: Metal-Centred Chirality versus DNA Helical Chirality. Chemistry 2023; 29:e202202630. [PMID: 36219466 PMCID: PMC10098492 DOI: 10.1002/chem.202202630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/23/2022]
Abstract
When covalently incorporating ligands capable of forming chiral metal complexes into a DNA oligonucleotide duplex, an enantiospecific formation of metal-mediated base pairs is possible. We have been investigating the chirality of the silver-mediated base pair P-AgI -P (P, 1H-imidazo[4,5-f][1,10]phenanthroline) depending on the number of consecutive P : P pairs within a series of duplexes. Towards this end, both enantiomers of the nucleoside analogue 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-1-yl)propane-1,2-diol comprising an acyclic backbone were introduced into DNA duplexes, resulting in diastereomeric metal-mediated base pairs. The same chiral-at-metal complex is formed inside the duplex for up to five neighbouring P-AgI -P pairs, irrespective of whether (S)-P or (R)-P is used. With six silver-mediated base pairs, the chirality of the metal complex is inverted for (S)-P but not for (R)-P. This indicates an intricate balance of what determines the configuration of the metal complex, the intrinsically preferred metal-centred chirality or the DNA helical chirality.
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Affiliation(s)
- Nils Lefringhausen
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Victoria Seiffert
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Catharina Erbacher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstr. 28/30, 48149, Münster, Germany
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5
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Human telomeric G-quadruplex DNA enabled preferential recognition of copper (II) and Iron (III) ions sensed by a red emissive probe. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Algar JL, Findlay JA, Preston D. Roles of Metal Ions in Foldamers and Other Conformationally Flexible Supramolecular Systems. ACS ORGANIC & INORGANIC AU 2022; 2:464-476. [PMID: 36855532 PMCID: PMC9955367 DOI: 10.1021/acsorginorgau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
Conformational control is a key prerequisite for much molecular function. As chemists seek to create complex molecules that have applications beyond the academic laboratory, correct spatial positioning is critical. This is particularly true of flexible systems. Conformationally flexible molecules show potential because they resemble in many cases naturally occurring analogues such as the secondary structures found in proteins and peptides such as α-helices and β-sheets. One of the ways in which conformation can be controlled in these molecules is through interaction with or coordination to metal ions. This review explores how secondary structure (i.e., controlled local conformation) in foldamers and other conformationally flexible systems can be enforced or modified through coordination to metal ions. We hope to provide examples that illustrate the power of metal ions to influence this structure toward multiple different outcomes.
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7
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Heddinga MH, Müller J. Modulating aptamer function by copper(II)-mediated base pair formation. Org Biomol Chem 2022; 20:4787-4793. [PMID: 35640171 DOI: 10.1039/d2ob00788f] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two aptamers, one for ATP and one for arginine, were modified using an artificial 2'-dexoyribonucleoside based on the nucleobase surrogate imidazole-4-carboxylate. This synthetic nucleoside substitute does not engage in hydrogen bonding but is capable of forming Cu(II)-mediated base pairs instead. Hence, the addition of Cu(II) can be used to influence the ability of the aptamer derivatives to adopt the correct fold necessary for binding their respective target molecule. As a result, aptamer function can be modulated via the addition of Cu(II). The extent of modulation ability depends on the identity of the aptamer and on the exact location of the artificial nucleosides within the oligonucleotide sequence.
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Affiliation(s)
- Marius H Heddinga
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany. .,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstraße 28/30, 48149 Münster, Germany
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8
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Buchanan JS, Preston D. A Catalogue of Orthogonal Complementary Ligand Pairings for Palladium(II) Complexes. Chem Asian J 2022; 17:e202200272. [PMID: 35362213 PMCID: PMC9324840 DOI: 10.1002/asia.202200272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/29/2022] [Indexed: 11/23/2022]
Abstract
Molecular recognition is a form of information transfer, seen in the base pairing in DNA which is derived from the identity (acceptor or donor) and number of hydrogen bond sites within each base. Here we report bis‐ligand palladium(II) complexes that exhibit similar complementarity. Pd(II) has square planar four‐coordinate geometry, giving control over ligand orientation and denticity. Pairings were developed using ligand denticity (3 : 1 or 2 : 2), and hydrogen bond capability (AA:DD or AD:DA) or lack thereof. Five pairings were investigated, with two sets of four being found fully orthogonal. The two 3 : 1 pairings exhibited limited ligand exchange. The extent of this exchange varied dependant on solvent from 2 : 1 (desired to undesired) to 6 : 1. A reliable and varied set of ligand pairs have therefore been developed for bis‐ligand coordination sphere engineering in pursuit of sorting for complex molecular architectures and molecular‐level information storage and transfer events.
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Affiliation(s)
- Jason S Buchanan
- Australian National University, Research School of Chemistry, AUSTRALIA
| | - Dan Preston
- Australian National University, Research School of Chemistry, Building 137, Sullivan Creek Road, 26010, Australia, 9200, Canberra, AUSTRALIA
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9
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Yum JH, Sugiyama H, Park S. Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives. CHEM REC 2022; 22:e202100333. [PMID: 35312235 DOI: 10.1002/tcr.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan.,Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Japan
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10
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Takezawa Y, Sakakibara S, Shionoya M. Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting. Chemistry 2021; 27:16626-16633. [PMID: 34623721 DOI: 10.1002/chem.202102977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 11/12/2022]
Abstract
DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, Ubpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand NiII (bpy)3 complex at the junction core (ΔTm =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside Ubpy -2, the degree of the NiII -mediated stabilization observed with Ubpy -3 was comparable to that of Ubpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of NiII ions. Furthermore, NiII -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of NiII (bpy)3 complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shiori Sakakibara
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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11
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Nishiyama K, Mori K, Takezawa Y, Shionoya M. Metal-responsive reversible binding of triplex-forming oligonucleotides with 5-hydroxyuracil nucleobases. Chem Commun (Camb) 2021; 57:2487-2490. [PMID: 33616595 DOI: 10.1039/d1cc00553g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-responsive triplex-forming oligonucleotides (TFOs) were synthesised by incorporating 5-hydroxyuracil (UOH) nucleobases as metal recognition sites. Binding of the UOH-containing TFO to the target natural DNA duplexes was reversibly regulated by the addition and removal of GdIII ions under isothermal conditions.
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Affiliation(s)
- Kotaro Nishiyama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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12
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Punt PM, Langenberg MD, Altan O, Clever GH. Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity. J Am Chem Soc 2021; 143:3555-3561. [PMID: 33630569 DOI: 10.1021/jacs.0c13251] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Marie D Langenberg
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Okan Altan
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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13
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Stratmann LM, Kutin Y, Kasanmascheff M, Clever GH. Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:4939-4947. [PMID: 33063395 PMCID: PMC7984025 DOI: 10.1002/anie.202008618] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/12/2020] [Indexed: 12/20/2022]
Abstract
DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine)4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu2+ -Cu2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates.
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Affiliation(s)
- Lukas M. Stratmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Strasse 644227DortmundGermany
| | - Yury Kutin
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Strasse 644227DortmundGermany
| | - Müge Kasanmascheff
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Strasse 644227DortmundGermany
| | - Guido H. Clever
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Strasse 644227DortmundGermany
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14
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Gholamjani Moghaddam K, Giudetti G, Sipma W, Faraji S. Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex. Phys Chem Chem Phys 2020; 22:26944-26954. [PMID: 33206064 DOI: 10.1039/d0cp04392c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.
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15
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Stratmann LM, Kutin Y, Kasanmascheff M, Clever GH. Präzise Abstandsmessungen in DNA‐G‐Quadruplex‐Dimeren und Sandwichkomplexen über gepulste dipolare EPR‐Spektroskopie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lukas M. Stratmann
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Yury Kutin
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Müge Kasanmascheff
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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16
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Heddinga MH, Müller J. Incorporation of a metal-mediated base pair into an ATP aptamer - using silver(I) ions to modulate aptamer function. Beilstein J Org Chem 2020; 16:2870-2879. [PMID: 33299485 PMCID: PMC7705865 DOI: 10.3762/bjoc.16.236] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.
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Affiliation(s)
- Marius H Heddinga
- Institut für Anorganische und Analytische Chemie & Cells in Motion Interfaculty Center, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie & Cells in Motion Interfaculty Center, Westfälische Wilhelms-Universität Münster, Corrensstr. 28/30, 48149 Münster, Germany
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17
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Deore PS, Manderville RA. Ratiometric fluorescent sensing of the parallel G-quadruplex produced by PS2.M: implications for K + detection. Analyst 2020; 145:1288-1293. [PMID: 31895357 DOI: 10.1039/c9an02122a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent ligands that selectively bind to a specific G-quadruplex (GQ) topology (antiparallel, hybrid or parallel) are highly sought after for aptasensor development and nanodevice construction. The coumarin-benzothiazole hybrid (BnBtC) is an internal charge transfer (ICT) ratiometric fluorescent probe, which displays two well-resolved emission bands at ∼450 nm for the coumarin component and ∼650 nm for the ICT band. The red ICT emission of BnBtC displays turn-on responses to protic solvent polarity and upon binding GQ structures, especially those produced by the hemin binding aptamer (PS2.M). In the present work, BnBtC was found to exhibit enhanced ICT emission upon binding the parallel GQ topology of PS2.M that is selectively produced in the presence of K+. This ability to discriminate K+ from other cationic metal ions through a turn-on ratiometric fluorescent response demonstrates the potential utility of the BnBtC probe for biosensor applications.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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18
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Luteran EM, Kahn JD, Paukstelis PJ. Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif. Biophys J 2020; 119:1580-1589. [PMID: 32966760 DOI: 10.1016/j.bpj.2020.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and antiparallel unimolecular hairpin in a pH-dependent manner. Here, we evaluate the thermodynamic stability and nuclease sensitivity of oligonucleotides composed of the d(CGA) motif and several structurally related sequence variants. These results show that the structural transition resulting from decreasing the pH is accompanied by both a significant energetic stabilization and decreased nuclease sensitivity as unimolecular hairpin structures are converted to parallel-stranded homo-base paired duplexes. Furthermore, the stability of the parallel-stranded duplex form can be altered by changing the 5'-nucleobase of the d(CGA) triplet and the frequency and position of the altered triplets within long stretches of d(CGA) triplets. This work offers insight into the stability and versatility of the d(CGA) triplet repeat motif and provides constraints for using this pH-adaptive structural motif for creating DNA-based nanomaterials.
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Affiliation(s)
- Emily M Luteran
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland
| | - Jason D Kahn
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland
| | - Paul J Paukstelis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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19
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Lai L, Xiong Z, Ma L, Chen T. Smart Microenvironment-Responsive Organocopper(II) Supramolecular Polymers to Regulate the Stability and Anticancer Efficacy by Different Substituents. ACS APPLIED MATERIALS & INTERFACES 2020; 12:40013-40020. [PMID: 32805979 DOI: 10.1021/acsami.0c09919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The search for chemotherapeutic drugs with a high efficiency and low toxicity continues to be a challenge in tumor treatment for scientists. Organometallic supramolecular polymers are an attractive option to achieve this goal, not only due to the fact that they possess both advantages of metal complexes and nanostructures but also because they are usually sensitive to pH. Here, we report the design and synthesis of a series novel smart microenvironment-responsive organocopper(II) supramolecular polymers with various substituted ligands to regulate their stability and anticancer efficacy. The investigation of the possible mechanisms revealed that the organocopper(II) polymers enter cancer cells through endocytosis and then induce apoptosis of cancer cells. Furthermore, the in vivo anticancer efficacy study demonstrated that these organocopper(II) polymers inhibited the tumor growth effectively without damage to the major organs. Overall, the organocopper(II) supramolecular polymers present a promising pathway to achieve high-efficiency and low-toxicity chemotherapy.
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Affiliation(s)
- Lanhai Lai
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Zushuang Xiong
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Li Ma
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China
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20
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Berrocal-Martin R, Sanchez-Cano C, Chiu CKC, Needham RJ, Sadler PJ, Magennis SW. Metallation-Induced Heterogeneous Dynamics of DNA Revealed by Single-Molecule FRET. Chemistry 2020; 26:4980-4987. [PMID: 31999015 DOI: 10.1002/chem.202000458] [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: 01/27/2020] [Indexed: 11/09/2022]
Abstract
The metallation of nucleic acids is key to wide-ranging applications, from anticancer medicine to nanomaterials, yet there is a lack of understanding of the molecular-level effects of metallation. Here, we apply single-molecule fluorescence methods to study the reaction of an organo-osmium anticancer complex and DNA. Individual metallated DNA hairpins are characterised using Förster resonance energy transfer (FRET). Although ensemble measurements suggest a simple two-state system, single-molecule experiments reveal an underlying heterogeneity in the oligonucleotide dynamics, attributable to different degrees of metallation of the GC-rich hairpin stem. Metallated hairpins display fast two-state transitions with a two-fold increase in the opening rate to ≈2 s-1 , relative to the unmodified hairpin, and relatively static conformations with long-lived open (and closed) states of 5 to ≥50 s. These studies show that a single-molecule approach can provide new insight into metallation-induced changes in DNA structure and dynamics.
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Affiliation(s)
- Raul Berrocal-Martin
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Carlos Sanchez-Cano
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Cookson K C Chiu
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Russell J Needham
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
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21
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Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA. J Biol Inorg Chem 2020; 25:647-654. [PMID: 32277288 PMCID: PMC7239801 DOI: 10.1007/s00775-020-01788-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Metal-mediated base pairs involving artificial nucleobases have emerged as a promising means for the site-specific functionalization of nucleic acids with metal ions. In this context, a GNA-appended (GNA: glycol nucleic acid) nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) has already been applied successfully in a variety of homo- and heteroleptic metal-mediated base pairs, mainly involving Ag(I) ions. Herein, we report a thorough investigation of the Hg(II)-binding properties of P when incorporated into antiparallel-stranded DNA duplexes. The artificial nucleobase P is able to form Hg(II)-mediated homoleptic base pairs of the type P-Hg(II)-P with a [2 + 2] coordination environment. In addition, the heteroleptic P-Hg(II)-T pair was investigated. The addition of a stoichiometric amount of Hg(II) to a duplex comprising either a P:P pair or a P:T pair stabilizes the DNA duplex by 4.3 °C and 14.5 °C, respectively. The P-Hg(II)-T base pair, hence, represents the most stabilizing non-organometallic Hg(II)-mediated base pair reported to date. The formation of the Hg(II)-mediated base pairs was investigated by means of temperature-dependent UV spectroscopy and CD spectroscopy.
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22
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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23
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Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
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24
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Punt PM, Stratmann LM, Sevim S, Knauer L, Strohmann C, Clever GH. Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes. Front Chem 2020; 8:26. [PMID: 32064249 PMCID: PMC7000376 DOI: 10.3389/fchem.2020.00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/09/2020] [Indexed: 12/28/2022] Open
Abstract
The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides LI. Here, we expand this modular system to more complex, heteroleptic coordination environments by combining LI with a new benzoate ligandoside LB within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of LB results in strong destabilization expressed in lower thermal denaturation temperatures Tm. While no transition metal cations could be bound by G-quadruplexes containing only LB, heteroleptic derivatives containing both LI and LB were found to complex CuII, NiII, and ZnII. Especially in case of CuII we found strong stabilizations of up to ΔTm = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lukas M Stratmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Sinem Sevim
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lena Knauer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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25
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020; 59:4091-4098. [DOI: 10.1002/anie.201913956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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26
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Ma Y, Iida K, Nagasawa K. Topologies of G-quadruplex: Biological functions and regulation by ligands. Biochem Biophys Res Commun 2020; 531:3-17. [PMID: 31948752 DOI: 10.1016/j.bbrc.2019.12.103] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/20/2019] [Accepted: 12/28/2019] [Indexed: 01/06/2023]
Abstract
G-Quadruplex (G4) is one of the higher-order structures occurring in guanine-rich sequences of nucleic acids, and plays critical roles in biological processes. The G4-forming sequences can generate three kinds of topologies, i.e., parallel, anti-parallel, and hybrid, and these polymorphic structures have an important influence on G4-related biological functions. In this review, we highlight variety of structures generated by G4s containing various sequences and under diverse conditions. We also discuss the G4 ligands which induce specific topologies and/or conversion between different topologies.
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Affiliation(s)
- Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Japan.
| | - Keisuke Iida
- Department of Chemistry, Chiba University, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Japan.
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27
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Naskar S, Müller J. Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs. Chemistry 2019; 25:16214-16218. [PMID: 31682036 PMCID: PMC6972992 DOI: 10.1002/chem.201903789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Indexed: 12/16/2022]
Abstract
By applying caged thymidine residues, DNA duplexes were created in which HgII -mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal-mediated base pairs was achieved.
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Affiliation(s)
- Shuvankar Naskar
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische ChemieCorrensstr. 3048149MünsterGermany
| | - Jens Müller
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische ChemieCorrensstr. 3048149MünsterGermany
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28
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Takezawa Y, Nakama T, Shionoya M. Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides. J Am Chem Soc 2019; 141:19342-19350. [PMID: 31731834 DOI: 10.1021/jacs.9b08955] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a CuII-mediated base pair (H-CuII-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-CuII-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of CuII ions. Furthermore, metal-dependent orthogonal activation of a CuII-responsive H-DNAzyme and a HgII-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-CuII-H as well as widely explored T-HgII-T base pairs. These results suggest that the incorporation of H-CuII-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
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29
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Punt PM, Clever GH. Tailored Transition-Metal Coordination Environments in Imidazole-Modified DNA G-Quadruplexes. Chemistry 2019; 25:13987-13993. [PMID: 31468606 PMCID: PMC6899475 DOI: 10.1002/chem.201903445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Indexed: 12/18/2022]
Abstract
Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G‐quadruplexes. The modified oligonucleotides were shown to complex a range of different transition‐metal cations including NiII, CuII, ZnII and CoII, as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine‐tuned metal affinities. It is shown that CuII, which is typically square‐planar coordinated, has a higher affinity for systems offering four ligands, whereas NiII prefers G‐quadruplexes with six ligands. Likewise, the positioning of ligands in a square‐planar versus tetrahedral fashion affects binding affinities of CuII and ZnII cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition‐metal‐modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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30
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Deore PS, Gray MD, Chung AJ, Manderville RA. Ligand-Induced G-Quadruplex Polymorphism: A DNA Nanodevice for Label-Free Aptasensor Platforms. J Am Chem Soc 2019; 141:14288-14297. [PMID: 31436972 DOI: 10.1021/jacs.9b06533] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
G-Quadruplexes (GQs) serve as popular recognition elements for DNA aptasensors and are incorporated into a DNA nanodevice capable of controlled conformational changes to activate a sensing mechanism. Herein we highlight the utility of a GQ-GQ nanodevice fueled by GQ-specific ligands as a label-free aptasensor detection strategy. The concept was first illustrated utilizing the prototypical polymorphic human telomeric repeat sequence (H-Telo22, d[AG3(T2AG3)3]) that can undergo ligand-induced topology changes between antiparallel, parallel, or hybrid GQ structures. The H-Telo22-ligand interactions served as a model of the GQ-GQ nanodevice. The utility of the device in a real aptasensor platform was then highlighted utilizing the ochratoxin A (OTA) binding aptamer (OTABA) that folds into an antiparallel GQ in the absence and presence of target OTA. Three cationic fluorogenic ligands served as GQ-specific light-up probes and as potential fuel for the GQ-GQ nanodevice by producing an inactive GQ topology (parallel or hybrid) of OTABA. Our findings demonstrate efficient OTA-mediated dye displacement with excellent emission sensitivity for OTA detection when the fluorogenic dyes induce a topology change in OTABA (parallel or hybrid). However, when the fluorogenic dye fails to induce a conformational change in the antiparallel fold of OTABA, subsequent additions of OTA to the aptamer-dye complex results in poor dye displacement with weak emission response for OTA detection. These results are the first to exemplify a ligand-induced GQ-GQ nanodevice as an aptasensor mechanism and demonstrate diagnostic applications for topology-specific GQ binders.
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Affiliation(s)
- Prashant S Deore
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Micaela D Gray
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Andrew J Chung
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Richard A Manderville
- Departments of Chemistry and Toxicology , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
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31
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A Gold Quartet Framework with Reversible Anisotropic Structural Transformation Accompanied by Luminescence Response. Chem 2019. [DOI: 10.1016/j.chempr.2019.06.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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Zhu J, Haynes CJE, Kieffer M, Greenfield JL, Greenhalgh RD, Nitschke JR, Keyser UF. Fe II4L 4 Tetrahedron Binds to Nonpaired DNA Bases. J Am Chem Soc 2019; 141:11358-11362. [PMID: 31283214 PMCID: PMC7007224 DOI: 10.1021/jacs.9b03566] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A water-soluble self-assembled supramolecular FeII4L4 tetrahedron binds to single stranded DNA, mismatched DNA base pairs, and three-way DNA junctions. Binding of the coordination cage quenches fluorescent labels on the DNA strand, which provides an optical means to detect the interaction and allows the position of the binding site to be gauged with respect to the fluorescent label. Utilizing the quenching and binding properties of the coordination cage, we developed a simple and rapid detection method based on fluorescence quenching to detect unpaired bases in double-stranded DNA.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Cally J E Haynes
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Marion Kieffer
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Jake L Greenfield
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ryan D Greenhalgh
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jonathan R Nitschke
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
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35
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O'Hagan MP, Morales JC, Galan MC. Binding and Beyond: What Else Can G-Quadruplex Ligands Do? European J Org Chem 2019. [DOI: 10.1002/ejoc.201900692] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”; Consejo Superior de Investigaciones Científicas (CSIC); PTS Granada; Avenida del Conocimiento 17 18016 Armilla, Granada Spain
| | - M. Carmen Galan
- School of Chemistry; University of Bristol; Cantock's Close BS8 1TS UK
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Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J. Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine. J Biol Inorg Chem 2019; 24:693-702. [DOI: 10.1007/s00775-019-01682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023]
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Askari MS, Lachance-Brais C, Rizzuto FJ, Toader V, Sleiman H. Remote control of charge transport and chiral induction along a DNA-metallohelicate. NANOSCALE 2019; 11:11879-11884. [PMID: 31184682 DOI: 10.1039/c9nr03212f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Herein we present a new strategy to achieve chiral induction and redox switching along the backbone of metallohelicate architectures, wherein a DNA duplex directs the handedness and charge transport properties of a metal-organic assembly more than 60 bonds away (a distance of >10 nm). The quantitative and site-specific binding of copper(i) ions to DNA-templated coordination sites imparts enhanced thermodynamic stability to the assembly, while the DNA duplex transfers its natural right-handed helicity to the proximal and distal metal centers of the helicates. When copper(ii) ions are employed instead of copper(i) ions, spontaneous DNA-mediated reduction occurs, which we propose is followed by a slower change in coordination environment (from pentacoordinate CuII to tetrahedral CuI) to generate copper(i) helicates. We demonstrate that the reduction of the adjacent and distal bis-phenanthroline sites is dependent on their proximity to DNA guanine bases (which act as the electron source). The kinetics of helical charge transport can thus be tuned based on guanine-CuII separation, resulting in a sequence- and distance-dependent redox switch that transfers electronic information from DNA to multiple linearly-arranged metal centers.
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Affiliation(s)
- Mohammad S Askari
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, Quebec, Canada.
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38
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Ali A, Bullen GA, Cross B, Dafforn TR, Little HA, Manchester J, Peacock AFA, Tucker JHR. Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer. Chem Commun (Camb) 2019; 55:5627-5630. [PMID: 31025680 DOI: 10.1039/c9cc01540j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The reversible photocontrol of an enzyme governing blood coagulation is demonstrated. The thrombin binding aptamer (TBA), was rendered photochromic by modification with two anthracene groups. Light-triggered anthracene photodimerisation distorts its structure, inhibiting binding of the enzyme thrombin, which in turn triggers catalysis and the resulting clotting process.
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Affiliation(s)
- Aysha Ali
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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39
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Importance of Chiral Recognition in Designing Metal-Free Ligands for G-Quadruplex DNA. Molecules 2019; 24:molecules24081473. [PMID: 30991655 PMCID: PMC6514905 DOI: 10.3390/molecules24081473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 01/26/2023] Open
Abstract
Four pairs of amino acid-functionalized naphthalenediimide enantiomers (d- and l-lysine derived NDIs) were screened toward G-quadruplex forming sequences in telomeres (h-TELO) and oncogene promoters: c-KIT1, c-KIT2, k-RAS and BCL-2. This is the first study to address the effect of point chirality toward G-quadruplex DNA stabilization using purely small organic molecules. Enantioselective behavior toward the majority of ligands was observed, particularly in the case of parallel conformations of c-KIT2 and k-RAS. Additionally, Nε-Boc-l-Lys-NDI and Nε-Boc-d-Lys-NDI discriminate between quadruplexes with parallel and hybrid topologies, which has not previously been observed with enantiomeric ligands.
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40
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O'Hagan MP, Haldar S, Duchi M, Oliver TAA, Mulholland AJ, Morales JC, Galan MC. A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA. Angew Chem Int Ed Engl 2019; 58:4334-4338. [PMID: 30682233 PMCID: PMC6563076 DOI: 10.1002/anie.201900740] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Indexed: 11/14/2022]
Abstract
The polymorphic nature of G-quadruplex (G4) DNA structures points to a range of potential applications in nanodevices and an opportunity to control G4 in biological settings. Light is an attractive means for the regulation of oligonucleotide structure as it can be delivered with high spatiotemporal precision. However, surprisingly little attention has been devoted towards the development of ligands for G4 that allow photoregulation of G4 folding. We report a novel G4-binding chemotype derived from stiff-stilbene. Surprisingly however, whilst the ligand induces high stabilization in the potassium form of human telomeric DNA, it causes the unfolding of the same G4 sequence in sodium buffer. This effect can be reversed on demand by irradiation with 400 nm light through deactivation of the ligand by photo-oxidation. By fuelling the system with the photolabile ligand, the conformation of G4 DNA was switched five times.
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Affiliation(s)
| | - Susanta Haldar
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
| | - Marta Duchi
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”Consejo Superior de Investigaciones Científicas (CSIC)PTS GranadaAvenida del Conocimiento 1718016ArmillaGranadaSpain
| | - M. Carmen Galan
- School of ChemistryUniversity of BristolCantock's CloseBS8 1TSUK
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41
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Facile detection of melamine by a FAM-aptamer-G-quadruplex construct. Anal Bioanal Chem 2019; 411:2521-2530. [PMID: 30863884 DOI: 10.1007/s00216-019-01688-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/26/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022]
Abstract
The development of a novel method for melamine detection that uses a FAM-aptamer-G-quadruplex construct due to the efficient quenching ability of an aptamer-linked G-quadruplex is reported herein. The construct, which is labeled with the fluorescent dye 6-carboxyfluorescein (FAM), consists of two parts: a melamine-binding aptamer and a G-rich sequence that can form a G-quadruplex structure. Because of the specific recognition of melamine by the T-rich aptamer, this aptamer folds into a hairpin structure in the presence of melamine, which draws the G-quadruplex closer to the FAM fluorophore, leading to the quenching of the fluorescence of FAM. Thus, a highly sensitive and selective fluorescence strategy for assaying melamine was established. Under optimal conditions, the fluorescence quenching is proportional to the concentration of melamine within the range 10-90 nM, and the method has a detection limit of 6.32 nM. Further application of the method to plastic cup samples suggested that it permitted recoveries of between 97.15% ± 1.02 and 101.92% ± 2.07. The detected amounts of melamine spiked into the plastic cup samples and the corresponding amounts measured by HPLC were in good accordance, indicating that this fluorescent method is reliable and practical. Owing to its high sensitivity, excellent selectivity, and convenient procedure, this strategy represents a promising alternative method of melamine screening. Graphical abstract.
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42
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O'Hagan MP, Haldar S, Duchi M, Oliver TAA, Mulholland AJ, Morales JC, Galan MC. A Photoresponsive Stiff‐Stilbene Ligand Fuels the Reversible Unfolding of G‐Quadruplex DNA. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900740] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Susanta Haldar
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
| | - Marta Duchi
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
| | | | | | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”Consejo Superior de Investigaciones Científicas (CSIC)PTS Granada Avenida del Conocimiento 17 18016 Armilla Granada Spain
| | - M. Carmen Galan
- School of ChemistryUniversity of Bristol Cantock's Close BS8 1TS UK
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43
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Metal-mediated base pairing in DNA involving the artificial nucleobase imidazole-4-carboxylate. J Inorg Biochem 2019; 191:85-93. [DOI: 10.1016/j.jinorgbio.2018.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
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44
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Punt PM, Clever GH. Imidazole-modified G-quadruplex DNA as metal-triggered peroxidase. Chem Sci 2019; 10:2513-2518. [PMID: 30931097 PMCID: PMC6399679 DOI: 10.1039/c8sc05020a] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/31/2018] [Indexed: 12/30/2022] Open
Abstract
Four imidazoles, serving as metalloprotein-inspired ligands for complexing a range of transition metal cations, were incorporated into tetramolecular G-quadruplex DNA structures. Modified quadruplexes were found to complex Cu(ii), Ni(ii), Zn(ii) and Co(ii) in a 1 : 1 ratio with unprecedented strong thermal stabilizations of up to ΔT 1/2 = +51 °C. Furthermore, addition of Cu(ii) was found to lead to extraordinarily fast G-quadruplex association rates with k on values being ∼100 times higher compared to unmodified G-quadruplexes. This is ascribed to a template effect of Cu(ii), preorganizing the four single strands via coordination, followed by rapid formation of hydrogen-bonded G-quartets. Native electrospray ionization mass spectrometry (ESI), coupled with trapped ion-mobility spectrometry (timsTOF), supports the proposed 1 : 1 G-quadruplex-metal complexes and could further disclose their ability to bind the iron-porphyrin complex hemin in a 1 : 1 stoichiometry. DNA sequence design allowed us to equip this G-quadruplex-hemin complex, known to function as a horseradish peroxidase mimic, with a metal-dependent trigger. A competitive screen of transition metals revealed a high selectivity for Cu(ii), even in mixtures of several divalent metal cations. Once formed, the Cu(ii)-carrying DNAzyme was shown to be preserved in the presence of EDTA, attributed to its remarkable kinetic stability. Stimuli-responsive G-quadruplexes promise application in DNAzymes with switchable activity, adaptive sensors and dynamic DNA origami constructs.
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Affiliation(s)
- Philip M Punt
- TU Dortmund University , Faculty for Chemistry and Chemical Biology , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Guido H Clever
- TU Dortmund University , Faculty for Chemistry and Chemical Biology , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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45
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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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46
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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47
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Engelhard DM, Meyer A, Berndhäuser A, Schiemann O, Clever GH. Di-copper(ii) DNA G-quadruplexes as EPR distance rulers. Chem Commun (Camb) 2018; 54:7455-7458. [DOI: 10.1039/c8cc04053b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Paramagnetic Cu(ii) complexes, immobilized via four-point-attachment to both ends of G-quadruplexes, serve as EPR-based distance rulers for studying DNA structure.
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Affiliation(s)
- David M. Engelhard
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Andreas Meyer
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Andreas Berndhäuser
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Guido H. Clever
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
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48
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Engelhard DM, Stratmann LM, Clever GH. Structure-Property Relationships in Cu II -Binding Tetramolecular G-Quadruplex DNA. Chemistry 2017; 24:2117-2125. [PMID: 29139578 DOI: 10.1002/chem.201703409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Indexed: 12/29/2022]
Abstract
A series of artificial metal-base tetrads composed of a CuII cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [LA-D d(G4 )]4 (LA-D =ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)4 ] complex behaves analogously to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1-5 atoms) and thus demonstrating the robustness of the chosen ligand design. Only at long linker lengths, the stabilizing effect of copper binding is compensated by the loss of conformational freedom. A previously reported ligand LE with chiral backbone enables incorporation at any oligonucleotide position. We show that ligand chirality distinctly steers CuII -induced G-quadruplex stabilization. 5'-End formation of two metal-base tetrads by tetramolecular G-quadruplex [LE2 d(G)4 ]4 shows that stabilization in the presence of CuII is not additive. All results are based on UV/Vis thermal denaturation, thermal difference, circular dichroism experiments and molecular dynamics simulations.
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Affiliation(s)
- David M Engelhard
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Lukas M Stratmann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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49
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Müller J. Metal-mediated base pairs in parallel-stranded DNA. Beilstein J Org Chem 2017; 13:2671-2681. [PMID: 29564004 PMCID: PMC5753045 DOI: 10.3762/bjoc.13.265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 01/03/2023] Open
Abstract
In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.
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Affiliation(s)
- Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
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50
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Jash B, Müller J. Metal-Mediated Base Pairs: From Characterization to Application. Chemistry 2017; 23:17166-17178. [PMID: 28833684 DOI: 10.1002/chem.201703518] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/11/2022]
Abstract
The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.
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Affiliation(s)
- Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
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