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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Hibiki Yoshioka
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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2
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Röthlisberger P, Levi-Acobas F, Leumann CJ, Hollenstein M. Enzymatic synthesis of biphenyl-DNA oligonucleotides. Bioorg Med Chem 2020; 28:115487. [PMID: 32284226 DOI: 10.1016/j.bmc.2020.115487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
The incorporation of nucleotides equipped with C-glycosidic aromatic nucleobases into DNA and RNA is an alluring strategy for a number of practical applications including fluorescent labelling of oligonucleotides, expansion of the genetic alphabet for the generation of aptamers and semi-synthetic organisms, or the modulation of excess electron transfer within DNA. However, the generation of C-nucleoside containing oligonucleotides relies mainly on solid-phase synthesis which is quite labor intensive and restricted to short sequences. Here, we explore the possibility of constructing biphenyl-modified DNA sequences using enzymatic synthesis. The presence of multiple biphenyl-units or biphenyl residues modified with electron donors and acceptors permits the incorporation of a single dBphMP nucleotide. Moreover, templates with multiple abasic sites enable the incorporation of up to two dBphMP nucleotides, while TdT-mediated tailing reactions produce single-stranded DNA oligonucleotides with four biphenyl residues appended at the 3'-end.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France.
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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Röthlisberger P, Levi-Acobas F, Sarac I, Ricoux R, Mahy JP, Herdewijn P, Marlière P, Hollenstein M. Incorporation of a minimal nucleotide into DNA. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Roethlisberger P, Kaliginediand V, Leumann CJ. Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates. Chemistry 2017; 23:2022-2025. [PMID: 27992671 DOI: 10.1002/chem.201605846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Indexed: 11/06/2022]
Abstract
The modulation of excess electron transfer (EET) within DNA containing a dimethylaminopyrene (C-AP) as an electron donor and 5-bromouracil (Br dU) as an electron acceptor through phenanthrenyl pairs (phen-R) could be achieved by modifying the phenanthrenyl base surrogates with electron withdrawing and donating groups. Arranging the phenanthrenyl units to form a descending LUMO gradient increased the EET efficiency compared to the electron transfer through uniform LUMOs or an ascending LUMO gradient.
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Affiliation(s)
- Pascal Roethlisberger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | | | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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Singleton DG, Hussain R, Siligardi G, Kumar P, Hrdlicka PJ, Berova N, Stulz E. Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling. Org Biomol Chem 2016; 14:149-57. [PMID: 26416024 PMCID: PMC4766578 DOI: 10.1039/c5ob01681a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/18/2015] [Indexed: 12/23/2022]
Abstract
Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.
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Affiliation(s)
- Daniel G. Singleton
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
| | - Rohanah Hussain
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Giuliano Siligardi
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Pawan Kumar
- Department of Chemistry , University of Idaho , Moscow , ID 83844 , USA
| | | | - Nina Berova
- Department of Chemistry , Columbia University , 3000 Broadway , New York , NY 10027 , USA
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
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Roethlisberger P, Istrate A, Marcaida Lopez MJ, Visini R, Stocker A, Reymond JL, Leumann CJ. X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair. Chem Commun (Camb) 2016; 52:4749-52. [DOI: 10.1039/c6cc00374e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties.
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Affiliation(s)
- P. Roethlisberger
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - A. Istrate
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | | | - R. Visini
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - A. Stocker
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - J.-L. Reymond
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - C. J. Leumann
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
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Robert-Burwell-Vorlesung über Katalyse: M. Neurock / Neuer Rektor der Universität Bern: C. Leumann / In die Nordrhein-Westfälische Akademie der Wissenschaften und der Künste gewählt: H. Braunschweig, P. R. Schreiner und K. Tatsumi. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Robert Burwell Lectureship in Catalysis: M. Neurock / Rector-Elect, University of Bern: C. Leumann / Elected to the Nordrhein-Westfälische Akademie der Wissenschaften und der Künste: H. Braunschweig, P. R. Schreiner, and K. Tatsumi. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201508043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bätzner E, Liang Y, Schweigert C, Unterreiner AN, Wagenknecht HA. Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs. Chemphyschem 2015; 16:1607-12. [PMID: 25784385 DOI: 10.1002/cphc.201500062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 02/05/2023]
Abstract
The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture.
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Affiliation(s)
- Effi Bätzner
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Yu Liang
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Caroline Schweigert
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany).
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany).
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Ikkanda BA, Samuel SA, Iverson BL. NDI and DAN DNA: nucleic acid-directed assembly of NDI and DAN. J Org Chem 2014; 79:2029-37. [PMID: 24502543 PMCID: PMC4272063 DOI: 10.1021/jo402704z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Two novel DNA base surrogate phosphoramidites 1 and 2, based upon relatively electron-rich 1,5-dialkoxynaphthalene (DAN) and relatively electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI), respectively, were designed, synthesized, and incorporated into DNA oligonucleotide strands. The DAN and NDI artificial DNA bases were inserted within a three-base-pair region within the interior of a 12-mer oligonucleotide duplex in various sequential arrangements and investigated with CD spectroscopy and UV melting curve analysis. The CD spectra of the modified duplexes indicated B-form DNA topology. Melting curve analyses revealed trends in DNA duplex stability that correlate with the known association of DAN and NDI moieties in aqueous solution as well as the known favorable interactions between NDI and natural DNA base pairs. This demonstrates that DNA duplex stability and specificity can be driven by the electrostatic complementarity between DAN and NDI. In the most favorable case, an NDI-DAN-NDI arrangement in the middle of the DNA duplex was found to be approximately as stabilizing as three A-T base pairs.
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Affiliation(s)
- Brian A Ikkanda
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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Nguyen T, Håkansson P, Edge R, Collison D, Goodman BA, Burns JR, Stulz E. EPR based distance measurement in Cu-porphyrin–DNA. NEW J CHEM 2014. [DOI: 10.1039/c4nj00673a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.
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Affiliation(s)
- ThaoNguyen Nguyen
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Pär Håkansson
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Ruth Edge
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - David Collison
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - Bernard A. Goodman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning 530005, China
| | - Jonathan R. Burns
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Eugen Stulz
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
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