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Sedghi Masoud S, Yamaoki Y, Ma Y, Marchand A, Winnerdy FR, Gabelica V, Phan AT, Katahira M, Nagasawa K. Analysis of Interactions between Telomeric i-Motif DNA and a Cyclic Tetraoxazole Compound. Chembiochem 2018; 19:2268-2272. [PMID: 30160816 DOI: 10.1002/cbic.201800425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 12/31/2022]
Abstract
The interaction of a macrocyclic tetraoxazole compound, L2H2-4OTD (1), with two aminoalkyl side chains and telomeric i-motif, was investigated by means of electrophoretic mobility shift assay, circular dichroism spectroscopy, mass spectrometry and NMR spectroscopy analyses. The results indicate that 1 interacts with the i-motif structure at two preferred binding sites.
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Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Yudai Yamaoki
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yue Ma
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Adrien Marchand
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Fernaldo Richtia Winnerdy
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Valérie Gabelica
- Université de Bordeaux, INSERM, CNRS, Acides Nucléiques, Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, SPMS PAP 05-04, 637371, Singapore, Singapore
| | - Masato Katahira
- Institute of Advanced Energy, Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
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Sakuma M, Ma Y, Tsushima Y, Iida K, Hirokawa T, Nagasawa K. Design and synthesis of unsymmetric macrocyclic hexaoxazole compounds with an ability to induce distinct G-quadruplex topologies in telomeric DNA. Org Biomol Chem 2016; 14:5109-16. [PMID: 27181296 DOI: 10.1039/c6ob00437g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New macrocyclic hexaoxazole compounds bearing two side chains on an unsymmetrical macrocyclic ring system, i.e., 4,2-L2H2-6OTD (2) and 5,1-L2H2-6OTD (3), were designed as candidate G-quadruplex (G4) ligands and synthesized. These G4 ligands 2 and 3 induced an anti-parallel topology and a hybrid-type topology of telomeric DNA, respectively, in contrast to the previously reported symmetrical macrocycle 3,3-L2H2-6OTD (1), which induces a typical anti-parallel structure. Molecular mechanics calculations and docking studies indicate that these differences arise from the different directions of the side chains in these L2H2-6OTD derivatives, and provide an explanation for the weaker stabilization of telomeric DNA by 2 and 3, compared with 1.
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Affiliation(s)
- Mai Sakuma
- Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo 184-8588, Japan.
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