1
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El-Khoury R, Cabrero C, Movilla S, Kaur H, Friedland D, Domínguez A, Thorpe JD, Roman M, Orozco M, González C, Damha MJ. Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions. Nucleic Acids Res 2024:gkae508. [PMID: 38874502 DOI: 10.1093/nar/gkae508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 05/06/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
Recent findings in cell biology have rekindled interest in Z-DNA, the left-handed helical form of DNA. We report here that two minimally modified nucleosides, 2'F-araC and 2'F-riboG, induce the formation of the Z-form under low ionic strength. We show that oligomers entirely made of these two nucleosides exclusively produce left-handed duplexes that bind to the Zα domain of ADAR1. The effect of the two nucleotides is so dramatic that Z-form duplexes are the only species observed in 10 mM sodium phosphate buffer and neutral pH, and no B-form is observed at any temperature. Hence, in contrast to other studies reporting formation of Z/B-form equilibria by a preference for purine glycosidic angles in syn, our NMR and computational work revealed that sequential 2'F…H2N and intramolecular 3'H…N3' interactions stabilize the left-handed helix. The equilibrium between B- and Z- forms is slow in the 19F NMR time scale (≥ms), and each conformation exhibited unprecedented chemical shift differences in the 19F signals. This observation led to a reliable estimation of the relative population of B and Z species and enabled us to monitor B-Z transitions under different conditions. The unique features of 2'F-modified DNA should thus be a valuable addition to existing techniques for specific detection of new Z-binding proteins and ligands.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Cristina Cabrero
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Santiago Movilla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Harneesh Kaur
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - David Friedland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Arnau Domínguez
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
- IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - James D Thorpe
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Morgane Roman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Carlos González
- Instituto de Química Física Blas Cabrera, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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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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i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. Commun Chem 2023; 6:31. [PMID: 36797370 PMCID: PMC9935537 DOI: 10.1038/s42004-023-00831-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC5 normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC5 to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.
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4
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Devi G, Winnerdy FR, Ang JCY, Lim KW, Phan AT. Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold. ACS NANO 2022; 16:533-540. [PMID: 34927423 DOI: 10.1021/acsnano.1c07630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.
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Affiliation(s)
- Gitali Devi
- 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
| | - Jason Cheng Yu Ang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- 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
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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5
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El-Khoury R, Damha MJ. 2'-Fluoro-arabinonucleic Acid (FANA): A Versatile Tool for Probing Biomolecular Interactions. Acc Chem Res 2021; 54:2287-2297. [PMID: 33861067 DOI: 10.1021/acs.accounts.1c00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Account highlights the structural features that render 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology.The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2'F-H8(purine) pseudohydrogen bonding interactions. We have shown that FANA/RNA hybrids are substrates of RNase H and Ago2, both implicated in the mechanism of action of antisense oligonucleotides (ASOs) and siRNA, respectvely. This knowledge has helped us study the conformational preferences of ASOs and siRNA as well as crRNA in CRISPR-associated Cas9, thereby revealing structural features crucial to biochemical activity.Additionally, FANA is of particular use in stabilizing noncanonical DNA structures. For instance, we have taken advantage of the anti N-glycosidic bond conformation of FANA monomers to induce a parallel topology in telomeric G-quadruplexes. Subsequent single-molecule FRET studies elucidated the mechanism by which these parallel G-quadruplexes are recognized and extended by telomerase. Similarly, we have utilized FANA to stabilize elusive telomeric i-motifs in the presence of concomitant parallel G-quadruplexes and under physiological conditions, thereby reinforcing their potential relevance to telomere biology. In another study, we adapted microarray technology and used FANA substitutions to enhance the binding affinity of the G-quadruplex thrombin-binding aptamer to its thrombin target.Finally, we discovered that DNA polymerases can synthesize FANA strands from DNA templates. On the basis of this property, other groups demonstrated that FANA, like DNA, can store hereditary information. They did so by engineering polymerases to efficiently transfer genetic information from DNA to FANA and retrieve it back into DNA. Subsequent studies showed that FANA could be evolved to acquire ribozyme-like endonuclease or ligase activity and to form high-affinity aptamers.Overall, the implications of these studies are remarkable because they promise a deeper understanding of human biochemistry for innovative therapeutic avenues. This Account summarizes past achievements and provides an outlook for inspiring the increased use of FANA in biological applications and fostering interdisciplinary collaborations.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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6
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Müller D, Bessi I, Richter C, Schwalbe H. The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021; 60:10895-10901. [PMID: 33539622 PMCID: PMC8252441 DOI: 10.1002/anie.202100280] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Indexed: 01/23/2023]
Abstract
We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K+‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
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Affiliation(s)
- Diana Müller
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany.,Present address: Julius-Maximilians-University Würzburg, Institute of Organic Chemistry, Am Hubland 16, 97074, Würzburg, Germany
| | - Christian Richter
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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7
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The Folding Landscapes of Human Telomeric RNA and DNA G‐Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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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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9
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Amato J, Mashima T, Kamatari YO, Kuwata K, Novellino E, Randazzo A, Giancola C, Katahira M, Pagano B. Improved Anti-Prion Nucleic Acid Aptamers by Incorporation of Chemical Modifications. Nucleic Acid Ther 2020; 30:414-421. [PMID: 32991255 DOI: 10.1089/nat.2020.0899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nucleic acid aptamers are innovative and promising candidates to block the hallmark event in the prion diseases, that is the conversion of prion protein (PrP) into an abnormal form; however, they need chemical modifications for effective therapeutic activity. This communication reports on the development and biophysical characterization of a small library of chemically modified G-quadruplex-forming aptamers targeting the cellular PrP and the evaluation of their anti-prion activity. The results show the possibility of enhancing anti-prion aptamer properties through straightforward modifications.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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10
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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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11
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Li Q, Chen J, Trajkovski M, Zhou Y, Fan C, Lu K, Tang P, Su X, Plavec J, Xi Z, Zhou C. 4′-Fluorinated RNA: Synthesis, Structure, and Applications as a Sensitive 19F NMR Probe of RNA Structure and Function. J Am Chem Soc 2020; 142:4739-4748. [DOI: 10.1021/jacs.9b13207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pingping Tang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China
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12
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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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13
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Haase L, Weisz K. Switching the type of V-loop in sugar-modified G-quadruplexes through altered fluorine interactions. Chem Commun (Camb) 2020; 56:4539-4542. [DOI: 10.1039/d0cc01285h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interplay of specific fluoro interactions determines conformational features of G-quadruplexes with two different 2′-fluoro-substituted residues.
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Affiliation(s)
- Linn Haase
- Institut für Biochemie
- Universität Greifswald
- D-17489 Greifswald
- Germany
| | - Klaus Weisz
- Institut für Biochemie
- Universität Greifswald
- D-17489 Greifswald
- Germany
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14
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Brcic J, Plavec J. NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism. Nucleic Acids Res 2019; 46:11605-11617. [PMID: 30277522 PMCID: PMC6265483 DOI: 10.1093/nar/gky886] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), is a largely increased number of d(G4C2)n•(G2C4)n repeats located in the non-coding region of C9orf72 gene. Non-canonical structures, including G-quadruplexes, formed within expanded repeats have been proposed to drive repeat expansion and pathogenesis of ALS and FTD. Oligonucleotide d[(G4C2)3G4], which represents the shortest oligonucleotide model of d(G4C2) repeats with the ability to form a unimolecular G-quadruplex, forms two major G-quadruplex structures in addition to several minor species which coexist in solution with K+ ions. Herein, we used solution-state NMR to determine the high-resolution structure of one of the major G-quadruplex species adopted by d[(G4C2)3G4]. Structural characterization of the G-quadruplex named AQU was facilitated by a single substitution of dG with 8Br-dG at position 21 and revealed an antiparallel fold composed of four G-quartets and three lateral C-C loops. The G-quadruplex exhibits high thermal stability and is favored kinetically and under slightly acidic conditions. An unusual structural element distinct from a C-quartet is observed in the structure. Two C•C base pairs are stacked on the nearby G-quartet and are involved in a dynamic equilibrium between symmetric N3-amino and carbonyl-amino geometries and protonated C+•C state.
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Affiliation(s)
- Jasna Brcic
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana SI-1000, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana SI-1000, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana SI-1000, Slovenia.,EN-FIST Center of Excellence, Ljubljana SI-1000, Slovenia
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15
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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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16
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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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17
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He XY, Wang J, Lu DD, Wang SQ. Synthesis and Antisense Properties of 2'β-F-Arabinouridine Modified Oligonucleotides with 4'- C-OMe Substituent. Molecules 2018; 23:molecules23092374. [PMID: 30227644 PMCID: PMC6225415 DOI: 10.3390/molecules23092374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/16/2022] Open
Abstract
A novel 2′-F,4′-C-OMe–arabinouridine (araU) was successfully synthesized and introduced into oligonucleotides. The oligonucleotide containing 2′-F,4′-C-OMe–araU exhibited improved nuclease resistance and RNA hybridizing selective ability relative to 2′-F–araU. In particular, when 2′-F,4′-C-OMe–araU inserted into C–H⋯F–C bonding-favorable 5′–uridine–purine–3′ steps, the modified oligonucleotide showed remarkable binding affinity and selectivity to RNA complements. Thus, 2′-F,4′-C-OMe–araU has valuable antisense properties and can be used as novel chemical modification for antisense therapeutic strategy.
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Affiliation(s)
- Xiao-Yang He
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jing Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Dan-Dan Lu
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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18
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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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19
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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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20
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Sacre L, O'Flaherty DK, Archambault P, Copp W, Peslherbe GH, Muchall HM, Wilds CJ. O 4 -Alkylated-2-Deoxyuridine Repair by O 6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification. Chembiochem 2018; 19:575-582. [PMID: 29243336 DOI: 10.1002/cbic.201700660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Oligonucleotides containing various adducts, including ethyl, benzyl, 4-hydroxybutyl and 7-hydroxyheptyl groups, at the O4 atom of 5-fluoro-O4 -alkyl-2'-deoxyuridine were prepared by solid-phase synthesis. UV thermal denaturation studies demonstrated that these modifications destabilised the duplex by approximately 10 °C, relative to the control containing 5-fluoro-2'-deoxyuridine. Circular dichroism spectroscopy revealed that these modified duplexes all adopted a B-form DNA structure. O6 -Alkylguanine DNA alkyltransferase (AGT) from humans (hAGT) was most efficient at repair of the 5-fluoro-O4 -benzyl-2'-deoxyuridine adduct, whereas the thymidine analogue was refractory to repair. The Escherichia coli AGT variant (OGT) was also efficient at removing O4 -ethyl and benzyl adducts of 5-fluoro-2-deoxyuridine. Computational assessment of N1-methyl analogues of the O4 -alkylated nucleobases revealed that the C5-fluorine modification had an influence on reducing the electron density of the O4 -Cα bond, relative to thymine (C5-methyl) and uracil (C5-hydrogen). These results reveal the positive influence of the C5-fluorine atom on the repair of larger O4 -alkyl adducts to expand knowledge of the range of substrates able to be repaired by AGT.
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Affiliation(s)
- Lauralicia Sacre
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Derek K O'Flaherty
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada.,Present address: Howard Hughes Medical Institute, Department of Molecular Biology and, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Philippe Archambault
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - William Copp
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Gilles H Peslherbe
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Heidi M Muchall
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
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21
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Presa A, Vázquez G, Barrios LA, Roubeau O, Korrodi-Gregório L, Pérez-Tomás R, Gamez P. Photoactivation of the Cytotoxic Properties of Platinum(II) Complexes through Ligand Photoswitching. Inorg Chem 2018. [PMID: 29543468 DOI: 10.1021/acs.inorgchem.8b00146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of photoactivatable metal complexes with potential anticancer properties is a topical area of current investigation. Photoactivated chemotherapy using coordination compounds is typically based on photochemical processes occurring at the metal center. In the present study, an innovative approach is applied that takes advantage of the remarkable photochemical properties of diarylethenes. Following a proof-of-concept study with two complexes, namely, C1 and C2, a series of additional platinum(II) complexes from dithienylcyclopentene-based ligands was designed and prepared. Like C1 and C2, these new coordination compounds exhibit two thermally stable, interconvertible photoisomers that display distinct properties. The photochemical behavior of ligands L3-L7 has been analyzed by 1H NMR and UV-vis spectroscopies. Subsequently, the corresponding platinum(II) complexes C3-C7 were synthesized and fully characterized, including by single-crystal X-ray diffraction for some of them. Next, the interaction of each photoisomer (i.e., containing the open or closed ligand) of the metal complexes with DNA was examined thoroughly using various techniques, revealing their distinct DNA-binding modes and affinities, as observed for the earlier compounds C1 and C2. The antiproliferative activity of the two forms of the complexes was then assessed with five cancer cell lines and compared with that of C1 and C2, which supported the use of such diarylethene-based systems for the generation of a new class of potential photochemotherapeutic metallodrugs.
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Affiliation(s)
- Andreu Presa
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
| | - Guillem Vázquez
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
| | - Leoní A Barrios
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain
| | - Olivier Roubeau
- Instituto de Ciencia de Materiales de Aragón , CSIC and Universidad de Zaragoza , Plaza San Francisco s/n , 50009 Zaragoza , Spain
| | - Luís Korrodi-Gregório
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine , University of Barcelona, Campus Bellvitge , Feixa Llarga s/n , 08907 L'Hospitalet de Llobregat , Spain
| | - Ricardo Pérez-Tomás
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine , University of Barcelona, Campus Bellvitge , Feixa Llarga s/n , 08907 L'Hospitalet de Llobregat , Spain
| | - Patrick Gamez
- Department of Inorganic and Organic Chemistry, Inorganic Chemistry Section , University of Barcelona , Martí i Franquès 1-11 , 08028 Barcelona , Spain.,Catalan Institution for Research and Advanced Studies , Passeig Lluís Companys 23 , 08010 Barcelona , Spain.,Institute of Nanoscience and Nanotechnology , Martí i Franquès 1-11 , 08028 Barcelona , Spain
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22
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Guo F, Li Q, Zhou C. Synthesis and biological applications of fluoro-modified nucleic acids. Org Biomol Chem 2018; 15:9552-9565. [PMID: 29086791 DOI: 10.1039/c7ob02094e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Owing to the unique physical properties of a fluorine atom, incorporating fluoro-modifications into nucleic acids offers striking biophysical and biochemical features, and thus significantly extends the breadth and depth of biological applications of nucleic acids. In this review, fluoro-modified nucleic acids that have been synthesized through either solid phase synthesis or the enzymatic approach are briefly summarised, followed by a section describing their biomedical applications in nucleic acid-based therapeutics, 18F PET imaging and mechanistic studies of DNA modifying enzymes. In the last part, the utility of 19F NMR and MRI for probing the structure, dynamics and molecular interactions of fluorinated nucleic acids is reviewed.
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Affiliation(s)
- Fengmin Guo
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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23
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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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24
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Ishizuka T, Yamashita A, Asada Y, Xu Y. Studying DNA G-Quadruplex Aptamer by 19F NMR. ACS OMEGA 2017; 2:8843-8848. [PMID: 30023592 PMCID: PMC6045382 DOI: 10.1021/acsomega.7b01405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
In this study, we demonstrated that 19F NMR can be used to study the thrombin-binding aptamer (TBA) DNA G-quadruplex, widely used as a model structure for studying G-quadruplex aptamers. We systematically examined the structural feature of the TBA G-quadruplex aptamer with fluorine-19 (19F) labels at all of the thymidine positions. We successfully observed the structural change between the G-quadruplex and the unstructured single strand by 19F NMR spectroscopy. The thermodynamic parameters of these DNA G-quadruplex aptamers were also determined from the 19F NMR signals. We further showed that the 19F NMR method can be used to observe the complex formed by TBA G-quadruplex and thrombin. Our results suggest that 19F NMR spectroscopy is a useful approach to study the aptamer G-quadruplex structure.
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Affiliation(s)
- Takumi Ishizuka
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Atsushi Yamashita
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yujiro Asada
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Division
of Chemistry, Department of Medical Sciences, Faculty of
Medicine and Department of Pathology, Division of Pathophysiology, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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25
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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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26
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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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27
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Lietard J, Abou Assi H, Gómez-Pinto I, González C, Somoza MM, Damha MJ. Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res 2017; 45:1619-1632. [PMID: 28100695 PMCID: PMC5389548 DOI: 10.1093/nar/gkw1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/28/2016] [Indexed: 01/13/2023] Open
Abstract
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.,Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | - Hala Abou Assi
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
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28
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Fluorine NMR spectroscopy and computational calculations for assessing intramolecular hydrogen bond involving fluorine and for characterizing the dynamic of a fluorinated molecule. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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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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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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31
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Mompeán M, Villalba M, Bruix M, Zamora-Carreras H. Insights into protein-carbohydrate recognition: A novel binding mechanism for CBM family 43. J Mol Graph Model 2017; 73:152-156. [PMID: 28279823 DOI: 10.1016/j.jmgm.2017.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 01/08/2023]
Abstract
Despite the growing number of carbohydrate-binding modules (CBMs) that are being uncovered, information on the structural determinants for the sugar-binding regions at atomic resolution is scarce. It is widely accepted that aromatic and H-bonding interactions govern these processes, and reported simulations and theoretical calculations are valuable tools to quantify and understand these interactions. We present here a computational model derived from experimental data that provide a unique atomistic picture of an uncharacterized binding mode of laminarin to the CBM family 43. The present study, which is among the first describing an isolated CBM with the bound carbohydrate, is complemented with quantum mechanical calculations. This allows us to attribute certain experimental observations (binding affinities) to key interactions (H-bonds and aromatic stacking), on the basis of NMR-driven docking structure.
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Affiliation(s)
- Miguel Mompeán
- Department of Biological Physical Chemistry, Institute of Physical Chemistry "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain.
| | - Mayte Villalba
- Department of Biochemistry and Molecular Biology I, Faculty of Chemistry, Complutense University, 28040, Madrid, Spain
| | - Marta Bruix
- Department of Biological Physical Chemistry, Institute of Physical Chemistry "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain
| | - Héctor Zamora-Carreras
- Department of Biological Physical Chemistry, Institute of Physical Chemistry "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain.
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32
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Graton J, Compain G, Besseau F, Bogdan E, Watts JM, Mtashobya L, Wang Z, Weymouth-Wilson A, Galland N, Le Questel JY, Linclau B. Influence of Alcohol β-Fluorination on Hydrogen-Bond Acidity of Conformationally Flexible Substrates. Chemistry 2016; 23:2811-2819. [DOI: 10.1002/chem.201604940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Jerome Graton
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Guillaume Compain
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Francois Besseau
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Elena Bogdan
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Joseph M. Watts
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Lewis Mtashobya
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Zhong Wang
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Alex Weymouth-Wilson
- Dextra Laboratories Ltd; The Science and Technology Centre; Earley Gate, Whiteknights Road Reading RG6 6BZ UK
| | - Nicolas Galland
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Bruno Linclau
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
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33
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Darré L, Ivani I, Dans PD, Gómez H, Hospital A, Orozco M. Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA. J Am Chem Soc 2016; 138:16355-16363. [DOI: 10.1021/jacs.6b09471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Leonardo Darré
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Ivan Ivani
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Pablo D. Dans
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Hansel Gómez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Joint
BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, 08028 Barcelona, Spain
- Department
of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
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34
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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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35
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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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36
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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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37
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Mompeán M, Nogales A, Ezquerra TA, Laurents DV. Complex System Assembly Underlies a Two-Tiered Model of Highly Delocalized Electrons. J Phys Chem Lett 2016; 7:1859-1864. [PMID: 27139835 DOI: 10.1021/acs.jpclett.6b00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Amyloid fibrils are exceptionally stable oligomeric structures with extensive, highly cooperative H-bonding networks whose physical origin remains elusive. While nonpolar systems benefit from both H-bonds and hydrophobic interactions, we found that highly polar sequences containing glutamine and asparagine amino acid residues form hyperpolarized H-bonds. This feature, observed by density functional theory calculations, encodes the origin of these polar oligomers' high stability. These results are explained in a theoretical model for complex amyloid assembly based on two different types of cooperative effects resulting from highly delocalized electrons, one of which is always present in both polar and hydrophobic systems. Experimental electric conductivity measurements, ThT fluorescence enhancement, and NMR spectroscopy support this proposal and reveal the conditions for disassembly.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano" (IQFR-CSIC) , Serrano 119, Madrid E-28006, Spain
| | - Aurora Nogales
- Instituto de Estructura de la Materia (IEM-CSIC) , Serrano 121, Madrid E-28006, Spain
| | - Tiberio A Ezquerra
- Instituto de Estructura de la Materia (IEM-CSIC) , Serrano 121, Madrid E-28006, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano" (IQFR-CSIC) , Serrano 119, Madrid E-28006, Spain
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38
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Assi HA, Harkness RW, Martin-Pintado N, Wilds CJ, Campos-Olivas R, Mittermaier AK, González C, Damha MJ. Stabilization of i-motif structures by 2'-β-fluorination of DNA. Nucleic Acids Res 2016; 44:4998-5009. [PMID: 27166371 PMCID: PMC4914123 DOI: 10.1093/nar/gkw402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Robert W Harkness
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - Christopher J Wilds
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | | | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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39
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Dalvit C, Vulpetti A. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening. Chemistry 2016; 22:7592-601. [DOI: 10.1002/chem.201600446] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Claudio Dalvit
- Faculty of Science University of Neuchâtel 2000 Neuchâtel Switzerland
- Sanofi, LG-CR/SDI/SBB 94403 Vitry-sur-Seine France
| | - Anna Vulpetti
- Novartis Institutes for Biomedical Research, Global Discovery Chemistry, CADD 4002 Basel Switzerland
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40
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Brčić J, Plavec J. G-quadruplex formation of oligonucleotides containing ALS and FTD related GGGGCC repeat. Front Chem Sci Eng 2016. [DOI: 10.1007/s11705-016-1556-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Revilla-López G, Bertran O, Casanovas J, Turon P, Puiggalí J, Alemán C. Effects of hydroxyapatite (0001) Ca2+/Mg2+ substitution on adsorbed d-ribose ring puckering. RSC Adv 2016. [DOI: 10.1039/c6ra10660a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Advanced Molecular Dynamics (MD) simulation protocols have been used to assess the ring puckering of cyclic d-ribose when the sugar is adsorbed on the most stable (0001) facet of calcium hydroxyapatite (HAp).
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Affiliation(s)
- Guillem Revilla-López
- Institut für Organische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
- Departament d'Enginyeria Química
| | - Oscar Bertran
- Departament de Física Aplicada
- EEI
- Universitat Politècnica de Catalunya
- 08700 Igualada
- Spain
| | - Jordi Casanovas
- Departament de Química
- Escola Politècnica Superior
- Universitat de Lleida
- Lleida E-25001
- Spain
| | | | - Jordi Puiggalí
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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42
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Abstract
We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
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43
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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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44
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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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45
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Cheong VV, Heddi B, Lech CJ, Phan AT. Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad. Nucleic Acids Res 2015; 43:10506-14. [PMID: 26400177 PMCID: PMC4666386 DOI: 10.1093/nar/gkv826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/28/2015] [Indexed: 01/31/2023] Open
Abstract
G-quadruplexes are four-stranded structures built from stacked G-tetrads (G·G·G·G), which are planar cyclical assemblies of four guanine bases interacting through Hoogsteen hydrogen bonds. A G-quadruplex containing a single guanine analog substitution, such as 8-oxoguanine (O) or xanthine (X), would suffer from a loss of a Hoogsteen hydrogen bond within a G-tetrad and/or potential steric hindrance. We show that a proper arrangement of O and X bases can reestablish the hydrogen-bond pattern within a G·G·X·O tetrad. Rational incorporation of G·G·X·O tetrads in a (3+1) G-quadruplex demonstrated a similar folding topology and thermal stability to that of the unmodified G-quadruplex. pH titration conducted on X·O-modified G-quadruplexes indicated a protonation-deprotonation equilibrium of X with a pKa ∼6.7. The solution structure of a G-quadruplex containing a G·G·X·O tetrad was determined, displaying the same folding topology in both the protonated and deprotonated states. A G-quadruplex containing a deprotonated X·O pair was shown to exhibit a more electronegative groove compared to that of the unmodified one. These differences are likely to manifest in the electronic properties of G-quadruplexes and may have important implications for drug targeting and DNA-protein interactions.
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Affiliation(s)
- Vee Vee Cheong
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Christopher Jacques Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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46
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Martínez-Montero S, Deleavey GF, Martín-Pintado N, Fakhoury JF, González C, Damha MJ. Locked 2'-Deoxy-2',4'-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity. ACS Chem Biol 2015; 10:2016-23. [PMID: 26053215 DOI: 10.1021/acschembio.5b00218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
2'-Deoxy-2',4'-difluorouridine (2',4'-diF-rU) was readily incorporated into DNA and RNA oligonucleotides via standard solid phase synthesis protocols. NMR and thermal denaturation (Tm) data of duplexes was consistent with the 2',4'-diF-rU nucleotides adopting a rigid North (RNA-like) sugar conformation, as previously observed for the nucleoside monomer. The impact of this modification on Tm is neutral when incorporated within RNA:RNA duplexes, mildly destabilizing when located in the RNA strand of a DNA:RNA duplex, and highly destabilizing when inserted in the DNA strand of DNA:RNA and DNA:DNA duplexes. Molecular dynamics calculations suggest that the destabilization effect in DNA:DNA and DNA:RNA duplexes is the result of structural distortions created by A/B junctions within the helical structures. Quantum mechanics calculations suggest that the "neutral" effect imparted to A-form duplexes is caused by alterations in charge distribution that compensate the stabilizing effect expected for a pure North-puckered furanose sugar. 2',4'-diF-RNA modified siRNAs were able to trigger RNA interference with excellent efficiency. Of note, incorporation of a few 2',4'-diF-rU residues in the middle of the guide (antisense) strand afforded siRNAs that were more potent than the corresponding siRNAs containing LNA and 2'-F-ANA modifications, and as active as the 2'-F-RNA modified siRNAs.
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Affiliation(s)
- Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Glen F. Deleavey
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Johans F. Fakhoury
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/. Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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Zhou P, Shi R, Yao JF, Sheng CF, Li H. Supramolecular self-assembly of nucleotide–metal coordination complexes: From simple molecules to nanomaterials. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.02.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Presa A, Brissos RF, Caballero AB, Borilovic I, Korrodi-Gregório L, Pérez-Tomás R, Roubeau O, Gamez P. Photoswitching the Cytotoxic Properties of Platinum(II) Compounds. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Presa A, Brissos RF, Caballero AB, Borilovic I, Korrodi-Gregório L, Pérez-Tomás R, Roubeau O, Gamez P. Photoswitching the Cytotoxic Properties of Platinum(II) Compounds. Angew Chem Int Ed Engl 2015; 54:4561-5. [DOI: 10.1002/anie.201412157] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/09/2015] [Indexed: 11/10/2022]
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50
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Garavís M, López-Méndez B, Somoza A, Oyarzabal J, Dalvit C, Villasante A, Campos-Olivas R, González C. Discovery of selective ligands for telomeric RNA G-quadruplexes (TERRA) through 19F-NMR based fragment screening. ACS Chem Biol 2014; 9:1559-66. [PMID: 24837572 DOI: 10.1021/cb500100z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Telomeric repeat-containing RNA (TERRA) is a novel and very attractive antitumoral target. Here, we report the first successful application of (19)F-NMR fragment-based screening to identify chemically diverse compounds that bind to an RNA molecule such as TERRA. We have built a library of 355 fluorinated fragments, and checked their interaction with a long telomeric RNA as a target molecule. The screening resulted in the identification of 20 hits (hit rate of 5.6%). For a number of binders, their interaction with TERRA was confirmed by (19)F- and (1)H NMR as well as by CD melting experiments. We have also explored the selectivity of the ligands for RNA G-quadruplexes and found that some of the hits do not interact with other nucleic acids such as tRNA and duplex DNA and, most importantly, favor the propeller-like parallel conformation in telomeric DNA G-quadruplexes. This suggests a selective recognition of this particular quadruplex topology and that different ligands may recognize specific sites in propeller-like parallel G-quadruplexes. Such features make some of the resulting binders promising lead compounds for fragment based drug discovery.
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Affiliation(s)
- Miguel Garavís
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
- Centro
de Biología Molecular “‘Severo Ochoa”’
(CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás
Cabrera1, Cantoblanco, 28049 Madrid, Spain
| | - Blanca López-Méndez
- Spectroscopy and
NMR Unit and Experimental Therapeutics Programme, Spanish National
Cancer Research Center (CNIO), Melchor
Fernández Almagro 3, 28029 Madrid, Spain
| | - Alvaro Somoza
- IMDEA Nanociencia
and CNB-CSIC-IMDEA Nanociencia Associated Unit ‘‘Unidad
de Nanobiotecnologia’’, C/Faraday 9, Cantoblanco, 28049 Madrid, Spain
| | - Julen Oyarzabal
- Spectroscopy and
NMR Unit and Experimental Therapeutics Programme, Spanish National
Cancer Research Center (CNIO), Melchor
Fernández Almagro 3, 28029 Madrid, Spain
| | - Claudio Dalvit
- Spectroscopy and
NMR Unit and Experimental Therapeutics Programme, Spanish National
Cancer Research Center (CNIO), Melchor
Fernández Almagro 3, 28029 Madrid, Spain
| | - Alfredo Villasante
- Centro
de Biología Molecular “‘Severo Ochoa”’
(CSIC-UAM), Universidad Autónoma de Madrid, c/ Nicolás
Cabrera1, Cantoblanco, 28049 Madrid, Spain
| | - Ramón Campos-Olivas
- Spectroscopy and
NMR Unit and Experimental Therapeutics Programme, Spanish National
Cancer Research Center (CNIO), Melchor
Fernández Almagro 3, 28029 Madrid, Spain
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
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