1
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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: 1] [Impact Index Per Article: 1.0] [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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2
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Vianney YM, Schröder N, Jana J, Chojetzki G, Weisz K. Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect. J Am Chem Soc 2023; 145:22194-22205. [PMID: 37751488 DOI: 10.1021/jacs.3c08336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G3-G3-G2-G4-G3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Gregor Chojetzki
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
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3
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Ghosh A, Trajkovski M, Teulade‐Fichou M, Gabelica V, Plavec J. Phen-DC 3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl 2022; 61:e202207384. [PMID: 35993443 PMCID: PMC9826182 DOI: 10.1002/anie.202207384] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 01/11/2023]
Abstract
Human telomeric G-quadruplex DNA structures are attractive anticancer drug targets, but the target's polymorphism complicates the drug design: different ligands prefer different folds, and very few complexes have been solved at high resolution. Here we report that Phen-DC3 , one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG)3 to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex.
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Affiliation(s)
- Anirban Ghosh
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECBUniversité de Bordeaux33600PessacFrance
| | - Marko Trajkovski
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia
| | | | - Valérie Gabelica
- CNRS, INSERM, ARNA, UMR 5320, U1212, IECBUniversité de Bordeaux33600PessacFrance
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 191000LjubljanaSlovenia
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana1000LjubljanaSlovenia
- EN-FIST, Centre of Excellence1000LjubljanaSlovenia
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4
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Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J. Phen‐DC3 Induces Refolding of Human Telomeric DNA into a Chair‐type Antiparallel G‐quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anirban Ghosh
- IECB: Institut Europeen de Chimie et Biologie ARNA FRANCE
| | - Marko Trajkovski
- National Institute of Chemistry Slovenia: Kemijski institut Slovenian NMR centre SLOVENIA
| | | | | | - Janez Plavec
- National Institute of Chemistry NMR centre Hajdrihova 19 SI-1001 Ljubljana SLOVENIA
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5
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Wang KB, Dickerhoff J, Yang D. Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter. J Am Chem Soc 2021; 143:16549-16555. [PMID: 34586799 PMCID: PMC8626096 DOI: 10.1021/jacs.1c06200] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The G-quadruplexes (G4s) formed in the PDGFR-β gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-β gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.
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6
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Das P, Winnerdy FR, Maity A, Mechulam Y, Phan AT. A novel minimal motif for left-handed G-quadruplex formation. Chem Commun (Camb) 2021; 57:2527-2530. [PMID: 33690751 DOI: 10.1039/d0cc08146a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A recent study on the left-handed G-quadruplex (LHG4) DNA revealed a 12-nt minimal motif GTGGTGGTGGTG with the ability to independently form an LHG4 and to drive an adjacent sequence to LHG4 formation. Here we have identified a second LHG4-forming motif, GGTGGTGGTGTG, and determined the X-ray crystal structure of an LHG4 involving this motif. Our structural analysis indicated the role of split guanines and single thymine loops in promoting LHG4 formation.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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7
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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8
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Reddy Sannapureddi RK, Mohanty MK, Gautam AK, Sathyamoorthy B. Characterization of DNA G-quadruplex Topologies with NMR Chemical Shifts. J Phys Chem Lett 2020; 11:10016-10022. [PMID: 33179931 DOI: 10.1021/acs.jpclett.0c02969] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
G-quadruplexes are nucleic acid motifs formed by stacking of guanosine-tetrad pseudoplanes. They perform varied biological roles, and their distinctive structural features enable diverse applications. High-resolution structural characterization of G-quadruplexes is often time-consuming and expensive, calling for effective methods. Herein, we develop NMR chemical shifts and machine learning-based methodology that allows direct, rapid, and reliable analysis of canonical three-plane DNA G-quadruplexes sans isotopic enrichment. We show, for the first time, that each unique topology enforces a specific distribution of glycosidic torsion angles. Newly acquired carbon chemical shifts are exquisite probes for the dihedral angle distribution and provide immediate and unambiguous backbone topology assignment. The support vector machine learning methodology aids resonance assignment by providing plane indices for tetrad-forming guanosines. We further demonstrate the robustness by successful application of the methodology to a sequence that folds in two dissimilar topologies under different ionic conditions, providing its first atomic-level characterization.
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Affiliation(s)
| | - Manish Kumar Mohanty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Anoop Kumar Gautam
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
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9
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Haase L, Weisz K. Locked nucleic acid building blocks as versatile tools for advanced G-quadruplex design. Nucleic Acids Res 2020; 48:10555-10566. [PMID: 32890406 PMCID: PMC7544228 DOI: 10.1093/nar/gkaa720] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/20/2020] [Indexed: 01/21/2023] Open
Abstract
A hybrid-type G-quadruplex is modified with LNA (locked nucleic acid) and 2′-F-riboguanosine in various combinations at the two syn positions of its third antiparallel G-tract. LNA substitution in the central tetrad causes a complete rearrangement to either a V-loop or antiparallel structure, depending on further modifications at the 5′-neighboring site. In the two distinct structural contexts, LNA-induced stabilization is most effective compared to modifications with other G surrogates, highlighting a potential use of LNA residues for designing not only parallel but various more complex G4 structures. For instance, the conventional V-loop is a structural element strongly favored by an LNA modification at the V-loop 3′-end in contrast with an alternative V-loop, clearly distinguishable by altered conformational properties and base-backbone interactions as shown in a detailed analysis of V-loop structures.
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Affiliation(s)
- Linn Haase
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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10
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Smirnov IP, Kolganova NA, Surzhikov SA, Grechishnikova IV, Novikov RA, Timofeev EN. Folding topology, structural polymorphism, and dimerization of intramolecular DNA G-quadruplexes with inverted polarity strands and non-natural loops. Int J Biol Macromol 2020; 162:1972-1981. [PMID: 32800956 DOI: 10.1016/j.ijbiomac.2020.08.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 01/27/2023]
Abstract
Synthetically modified DNA G-quadruplexes (GQs) have great potential in the development of designer molecules for a wide range of applications. Identification of the role of various structural elements in the folding and final topology of artificial GQs is necessary to predict their secondary structure. We report here the results of spectroscopic and electrophoretic studies of GQ scaffolds formed by G-rich sequences comprising four G3-tracts of different polarity connected by either a single-nucleotide thymine loop or a non-natural tetraethyleneglycol loop. Depending on G-strand polarities, loop arrangement and the presence of extra 5'-base G-rich oligonucleotides form monomeric, dimeric, or multimeric species of different topologies. In most cases, oligonucleotides were able to fold into stable parallel or hybrid GQs. However, certain specific arrangements of loops and G-tracts resulted in a diverse mixture of low stable structures. Comparative analysis of topology, stability, and structural heterogeneity of different G-rich sequences suggests the important role of loop type and arrangement, G3-tract polarities, and the presence of 5'-capping residues in the outcome of the folding process. The results also imply that the formation of anti-parallel G-hairpin intermediates is a key event in major favourable folding pathways.
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Affiliation(s)
- Igor P Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Natalia A Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina V Grechishnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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11
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Wang ZF, Li MH, Chu IT, Winnerdy FR, Phan AT, Chang TC. Cytosine epigenetic modification modulates the formation of an unprecedented G4 structure in the WNT1 promoter. Nucleic Acids Res 2020; 48:1120-1130. [PMID: 31912153 PMCID: PMC7026657 DOI: 10.1093/nar/gkz1207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/09/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
Time-resolved imino proton nuclear magnetic resonance spectra of the WT22m sequence d(GGGCCACCGGGCAGTGGGCGGG), derived from the WNT1 promoter region, revealed an intermediate G-quadruplex G4(I) structure during K+-induced conformational transition from an initial hairpin structure to the final G4(II) structure. Moreover, a single-base C-to-T mutation at either position C4 or C7 of WT22m could lock the intermediate G4(I) structure without further conformational change to the final G4(II) structure. Surprisingly, we found that the intermediate G4(I) structure is an atypical G4 structure, which differs from a typical hybrid G4 structure of the final G4(II) structure. Further studies of modified cytosine analogues associated with epigenetic regulation indicated that slight modification on a cytosine could modulate G4 structure. A simplified four-state transition model was introduced to describe such conformational transition and disclose the possible mechanism for G4 structural selection caused by cytosine modification.
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Affiliation(s)
- Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C
| | - Ming-Hao Li
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C
| | - I-Te Chu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, R.O.C
| | - Fernaldo R Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh T Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan, R.O.C.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, R.O.C
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12
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Wang KB, Dickerhoff J, Wu G, Yang D. PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. J Am Chem Soc 2020; 142:5204-5211. [PMID: 32101424 DOI: 10.1021/jacs.9b12770] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.
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13
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Haase L, Dickerhoff J, Weisz K. Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops. Chemistry 2020; 26:524-533. [PMID: 31609483 PMCID: PMC6973071 DOI: 10.1002/chem.201904044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/10/2019] [Indexed: 01/04/2023]
Abstract
A DNA G-quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti-favoring 2'-deoxy-2'-fluoro-riboguanosine (F rG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5'-terminal G residue located in the central tetrad and the two modified residues linked by a V-shaped zero-nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the F rG analogue preceding the V-loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3'-endo sugar pucker within the V-loop architecture outweighs the propensity of the F rG analogue to adopt an anti glycosidic conformation. Refolding into a V-loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2'-F-arabinoguanosine analogues with their favored south-east sugar conformation do not support formation of the V-loop topology. Examination of known G-quadruplexes with a V-shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.
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Affiliation(s)
- Linn Haase
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
| | - Jonathan Dickerhoff
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
- Present address: Department of Medicinal Chemistry and Molecular PharmacologyCollege of PharmacyPurdue UniversityWest LafayetteIN47907USA
| | - Klaus Weisz
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417487GreifswaldGermany
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14
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Karg B, Mohr S, Weisz K. Duplex‐Guided Refolding into Novel G‐Quadruplex (3+1) Hybrid Conformations. Angew Chem Int Ed Engl 2019; 58:11068-11071. [DOI: 10.1002/anie.201905372] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Beatrice Karg
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Swantje Mohr
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Klaus Weisz
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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15
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Karg B, Mohr S, Weisz K. Duplex‐gesteuerte Umfaltung in neuartige G‐Quadruplex‐(3+1)‐ Hybridkonformationen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Beatrice Karg
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Swantje Mohr
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für BiochemieUniversität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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16
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Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52. Molecules 2019; 24:molecules24071294. [PMID: 30987050 PMCID: PMC6479982 DOI: 10.3390/molecules24071294] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 11/17/2022] Open
Abstract
The potential to affect gene expression via G-quadruplex stabilization has been extended to all domains of life, including viruses. Here, we investigate the polymorphism and structures of G-quadruplexes of the human papillomavirus type 52 with UV, CD and NMR spectroscopy and gel electrophoresis. We show that oligonucleotide with five G-tracts folds into several structures and that naturally occurring single nucleotide polymorphisms (SNPs) have profound effects on the structural polymorphism in the context of G-quadruplex forming propensity, conformational heterogeneity and folding stability. With help of SNP analysis, we were able to select one of the predominant forms, formed by G-rich sequence d(G₃TAG₃CAG₄ACACAG₃T). This oligonucleotide termed HPV52(1-4) adopts a three G-quartet snap back (3 + 1) type scaffold with four syn guanine residues, two edgewise loops spanning the same groove, a no-residue V loop and a propeller type loop. The first guanine residue is incorporated in the central G-quartet and all four-guanine residues from G4 stretch are included in the three quartet G-quadruplex core. Modification studies identified several structural elements that are important for stabilization of the described G-quadruplex fold. Our results expand set of G-rich targets in viral genomes and address the fundamental questions regarding folding of G-rich sequences.
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17
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Haase L, Karg B, Weisz K. Manipulating DNA G-Quadruplex Structures by Using Guanosine Analogues. Chembiochem 2019; 20:985-993. [PMID: 30511814 DOI: 10.1002/cbic.201800642] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/22/2022]
Abstract
The ability to control the folding topology of DNA G-quadruplexes allows for rational design of quadruplex-based scaffolds for potential use in various therapeutic and technological applications. By exploiting the distinct conformational properties of some base- and sugar-modified guanosine surrogates, conformational transitions can be induced through their judicious incorporation at specific sites in the quadruplex core. Changes may involve tetrad polarity inversions with conservation of the global fold or complete refolding to new topologies. Reliable predictions relating to low-energy conformers formed upon specific chemical perturbations of the system and the rational design of modified sequences suffer from our still limited understanding of the subtle interplay of various favorable and unfavorable interactions within a particular quadruplex scaffold. However, aided by an increasing number of systematic substitution experiments and high-resolution structures of modified quadruplex variants, critical interactions, in addition to glycosidic bond angle propensities, are starting to emerge as important contributors to modification-driven quadruplex refolding.
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Affiliation(s)
- Linn Haase
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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18
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Bielskutė S, Plavec J, Podbevšek P. Impact of Oxidative Lesions on the Human Telomeric G-Quadruplex. J Am Chem Soc 2019; 141:2594-2603. [PMID: 30657306 PMCID: PMC6727377 DOI: 10.1021/jacs.8b12748] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Telomere
attrition is closely associated with cell aging and exposure
to reactive oxygen species (ROS). While oxidation products of nucleotides
have been studied extensively in the past, the underlying secondary/tertiary
structural changes in DNA remain poorly understood. In this work,
we systematically probed guanine positions in the human telomeric
oligonucleotide sequence (hTel) by substitutions with the major product
of ROS, 8-oxo-7,8-dihydroguanine (oxoG), and evaluated
the G-quadruplex forming ability of such oligonucleotides. Due to
reduced hydrogen-bonding capability caused by oxoG, a loss
of G-quadruplex structure was observed for most oligonucleotides containing
oxidative lesions. However, some positions in the hTel sequence were
found to tolerate substitutions with oxoG. Due to oxoG’s preference for the syn conformation, distinct responses were observed when replacing guanines
with different glycosidic conformations. Accommodation of oxoG at sites originally in syn or anti in nonsubstituted hTel G-quadruplex requires a minor structural
rearrangement or a major conformational shift, respectively. The system
responds by retaining or switching to a fold where oxoG
is in syn conformation. Most importantly, these G-quadruplex
structures are still stable at physiological temperatures and should
be considered detrimental in higher-order telomere structures.
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Affiliation(s)
- Stasė Bielskutė
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Janez Plavec
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia
| | - Peter Podbevšek
- Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia
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19
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Filitcheva J, Edwards PJB, Norris GE, Filichev VV. α-2′-Deoxyguanosine can switch DNA G-quadruplex topologies from antiparallel to parallel. Org Biomol Chem 2019; 17:4031-4042. [DOI: 10.1039/c9ob00360f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-2′-Deoxyguanosine (α-dG) converts antiparallel, dimeric G-quadruplex DNA into a parallel, tetramolecular complex.
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Affiliation(s)
- Jana Filitcheva
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
| | | | - Gillian E. Norris
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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20
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Lenarčič Živković M, Rozman J, Plavec J. Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex. Angew Chem Int Ed Engl 2018; 57:15395-15399. [PMID: 30222243 PMCID: PMC6563693 DOI: 10.1002/anie.201809328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Indexed: 12/15/2022]
Abstract
A G-rich sequence found in the regulatory region of the RANKL gene, which is associated with homeostasis of bone metabolism, folds into a two-quartet basket-type G-quadruplex stabilized by A⋅G⋅A and G⋅G⋅G base-triads. Perusal of local structural features together with G/A-to-T modifications uncovered the critical role of A5 for the formation of a distinct antiparallel two-quartet topology and not the three-quartet topology that would be expected based on the sequence with four GGG-tracts alone. The structural changes induced by the A5-to-T5 modification include a switch in orientation and relative positions of G-strands that together with anti to syn reorientation of G12 provide insights into the complexity of the interactions that influence the folding of G-rich DNA. Understanding the impact of loop residues on the stability and formation of G-quadruplexes advances our knowledge and ability to predict structures adopted by G-rich sequences, which are involved in regulatory mechanisms in the cell, and may also facilitate drug design.
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Affiliation(s)
| | - Jan Rozman
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 9LjubljanaSlovenia
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 9LjubljanaSlovenia
- EN- FIST Centre of ExcellenceTrg OF 13LjubljanaSlovenia
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVečna pot 113LjubljanaSlovenia
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21
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Lenarčič Živković M, Rozman J, Plavec J. Adenine‐Driven Structural Switch from a Two‐ to Three‐Quartet DNA G‐Quadruplex. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Jan Rozman
- Slovenian NMR CentreNational Institute of Chemistry Hajdrihova 9 Ljubljana Slovenia
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of Chemistry Hajdrihova 9 Ljubljana Slovenia
- EN- FIST Centre of Excellence Trg OF 13 Ljubljana Slovenia
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
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22
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Haase L, Dickerhoff J, Weisz K. DNA–RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies. Chemistry 2018; 24:15365-15371. [DOI: 10.1002/chem.201803367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/05/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Linn Haase
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Jonathan Dickerhoff
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
- Present address: Department of Medicinal Chemistry and Molecular PharmacologyCollege of PharmacyPurdue University West Lafayette IN 47907 USA
| | - Klaus Weisz
- Institute of BiochemistryUniversity of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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23
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Karg B, Weisz K. Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes. Chemistry 2018; 24:10246-10252. [PMID: 29756658 DOI: 10.1002/chem.201801851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/12/2018] [Indexed: 01/24/2023]
Abstract
A G-quadruplex forming sequence from the MYC promoter region was modified with syn-favoring 8-bromo-2'-deoxyguanosine residues. Depending on the number and position of modifications in the intramolecular parallel G-quadruplex, substitutions with the bromoguanosine analogue at the 5'-tetrad induce conformational rearrangements with concerted all-anti to all-syn transitions for all residues of the modified G-quartet. No unfavorable steric interactions of the C8-substituents in the medium grooves are apparent in the high-resolution structure as determined for a tetrasubstituted MYC quadruplex that exclusively forms the all-syn isomer. In contrast, considerable steric clashes with 5'-phosphate oxygen atoms for those analogues that follow a less flexible 1-nucleotide loop in the native all-anti conformation seem to constitute the major driving force for the tetrad inversion and allow for the rational design of appropriately substituted sequences. Correlations found between the population of species subjected to a tetrad flip and melting temperatures indicate that more effective conformational transitions are compromised by lower thermal stabilities of the modified parallel quadruplexes.
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Affiliation(s)
- Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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24
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Dickerhoff J, Weisz K. Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway. Chembiochem 2018; 19:927-930. [PMID: 29460996 DOI: 10.1002/cbic.201800099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Indexed: 12/23/2022]
Abstract
A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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25
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Moriou C, Da Silva AD, Vianelli Prado MJ, Denhez C, Plashkevych O, Chattopadhyaya J, Guillaume D, Clivio P. C2′-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level. J Org Chem 2018; 83:2473-2478. [DOI: 10.1021/acs.joc.7b03186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette 91198 Cedex, France
| | - Adilson D. Da Silva
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Marcos Joel Vianelli Prado
- Departamento
de Quimica, ICE, Universidade Federal de Juiz de Fora, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Clément Denhez
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
- Université
de Reims Champagne Ardenne, Multiscale Molecular Modelling Platform, UFR Sciences Exactes et Naturelles, Reims F-51687 Cedex 2, France
| | - Oleksandr Plashkevych
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Jyoti Chattopadhyaya
- Institute of Cell & Molecular Biology, Program of Chemical Biology, Box 581, Biomedical Center, University of Uppsala, S-75123 Uppsala, Sweden
| | - Dominique Guillaume
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
| | - Pascale Clivio
- Université
de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51 rue Cognacq-Jay, Reims 51096 Cedex, France
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26
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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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27
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Dickerhoff J, Weisz K. Nonconventional C-H···F Hydrogen Bonds Support a Tetrad Flip in Modified G-Quadruplexes. J Phys Chem Lett 2017; 8:5148-5152. [PMID: 28976755 DOI: 10.1021/acs.jpclett.7b02428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A G-quadruplex adopting a (3 + 1)-hybrid structure was substituted at its 5'-tetrad by 2'-deoxy-2'-fluoro-arabinoguanosine (FaraG) analogs. Incorporation of anti-favoring FaraG at syn-positions of the 5'-outer tetrad induced a reversal of the tetrad polarity without noticeably compromising the quadruplex stability. This conformational change is shown to be promoted by nonconventional C-H···F hydrogen bonds acting within the anti-FaraG residues.
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Affiliation(s)
- Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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28
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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29
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Dickerhoff J, Haase L, Langel W, Weisz K. Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes. ACS Chem Biol 2017; 12:1308-1315. [PMID: 28318229 DOI: 10.1021/acschembio.6b01096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A human telomere sequence that folds into an intramolecular (3 + 1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines (FG) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a FG-substituted (3 + 1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal. Two out of the three FG analogs in both modified quadruplexes adopt an S-type sugar pucker, challenging a sole contribution of N-type sugars in enforcing an anti glycosidic torsion angle associated with the tetrad flip. NMR restrained three-dimensional structures of the two substituted quadruplexes reveal a largely conserved overall fold but significant rearrangements of the overhang and loop nucleotides capping the flipped tetrad. Sugar pucker preferences of the FG analogs may be rationalized by different orientations of the fluorine atom and its resistance to be positioned within the narrow groove with its highly negative electrostatic potential and spine of water molecules.
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Affiliation(s)
- Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Walter Langel
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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30
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Karg B, Haase L, Funke A, Dickerhoff J, Weisz K. Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes. Biochemistry 2016; 55:6949-6955. [PMID: 27951645 DOI: 10.1021/acs.biochem.6b00925] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (BrG) analogues in one of its outer G-tetrads. The propensity of the BrG analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues with BrG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (kex) of 0.2 s-1 is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disruption of the corresponding outer G-tetrad but not of the whole quadruplex core during the tetrad flip. Conformational syn-anti isomers with homopolar and heteropolar stacking interactions are nearly isoenergetic with a transition enthalpy of 18.2 kJ/mol in favor of the all-syn isomer.
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Affiliation(s)
- Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Andrea Funke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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31
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Dickerhoff J, Appel B, Müller S, Weisz K. Zuckerseitige Wechselwirkungen in einem DNA-RNA-G-Quadruplex: Hinweise auf sequentielle C−H⋅⋅⋅O-Wasserstoffbrücken als Beitrag zur RNA-Quadruplex-Faltung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
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32
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Dickerhoff J, Appel B, Müller S, Weisz K. Sugar-Edge Interactions in a DNA-RNA G-Quadruplex: Evidence of Sequential C-H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding. Angew Chem Int Ed Engl 2016; 55:15162-15165. [PMID: 27860177 DOI: 10.1002/anie.201608275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/29/2016] [Indexed: 11/11/2022]
Abstract
DNA G-quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti-dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA-RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3'-side within the quadruplex core strongly suggest the presence of C8-H⋅⋅⋅O hydrogen-bonding interactions with the O2' position of the C2'-endo ribonucleotide. A geometric analysis of reported high-resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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Effects of metal ions and cosolutes on G-quadruplex topology. J Inorg Biochem 2016; 166:190-198. [PMID: 27665315 DOI: 10.1016/j.jinorgbio.2016.09.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/31/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022]
Abstract
Topologies of G-quadruplexes depend on oligonucleotide sequences and on environmental factors, and the diversity of G-quadruplex topologies complicates investigation of functions of these nucleic acid structures. To investigate how metal ions and cosolutes regulate topologies of G-quadruplexes, we stabilized the antiparallel conformation by insertion of 2'-deoxyxanthosine and 8-oxo-2'-deoxyguanosine into selected positions of an oligonucleotide. Thermodynamic analyses of the oligonucleotide revealed that Na+ stabilized the antiparallel G-quadruplex, whereas K+ destabilized this topology. This result suggests that metal ions selectively stabilize G-quadruplex topologies with cavities between G-quartet planes of certain sizes. In the presence of KCl in 20wt% poly(ethylene glycol) with average molecular weight of 200, the antiparallel basket-type G-quadruplex conformation was not stabilized compared with the dilute condition. In the presence of NaCl, the cosolute did stabilize the G-quadruplex with respect to the dilute condition. The presented data show that metal ions and cosolutes regulate topologies of G-quadruplexes through mechanisms that depend on sizes of metal ion cavities and hydration states.
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Luo D, Mu Y. Computational Insights into the Stability and Folding Pathways of Human Telomeric DNA G-Quadruplexes. J Phys Chem B 2016; 120:4912-26. [DOI: 10.1021/acs.jpcb.6b01919] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Di Luo
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuguang Mu
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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35
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Cheong VV, Lech CJ, Heddi B, Phan AT. Inverting the G-Tetrad Polarity of a G-Quadruplex by Using Xanthine and 8-Oxoguanine. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Cheong VV, Lech CJ, Heddi B, Phan AT. Inverting the G-Tetrad Polarity of a G-Quadruplex by Using Xanthine and 8-Oxoguanine. Angew Chem Int Ed Engl 2015; 55:160-3. [PMID: 26563582 DOI: 10.1002/anie.201507034] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/04/2015] [Indexed: 01/24/2023]
Abstract
G-quadruplexes are four-stranded nucleic acid structures that are built from consecutively stacked guanine tetrad (G-tetrad) assemblies. The simultaneous incorporation of two guanine base lesions, xanthine (X) and 8-oxoguanine (O), within a single G-tetrad of a G-quadruplex was recently shown to lead to the formation of a stable G⋅G⋅X⋅O tetrad. Herein, a judicious introduction of X and O into a human telomeric G-quadruplex-forming sequence is shown to reverse the hydrogen-bond polarity of the modified G-tetrad while preserving the original folding topology. The control exerted over G-tetrad polarity by joint X⋅O modification will be valuable for the design and programming of G-quadruplex structures and their properties.
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Affiliation(s)
- Vee Vee Cheong
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore)
| | - Christopher Jacques Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore)
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore)
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore).
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