Synthesis and application of a 19F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs

Wen Ann Wee; Ji Hye Yum; Shingo Hirashima; Hiroshi Sugiyama; Soyoung Park

doi:10.1039/D1CB00020A

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Synthesis and application of a ¹⁹F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs†

Wen Ann Wee,^a Ji Hye Yum,^a Shingo Hirashima,^a Hiroshi Sugiyama

*^ab and Soyoung Park

*^a

Author affiliations

* Corresponding authors

^a Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
E-mail: sugiyama.hiroshi.3s@kyoto-u.ac.jp, park.soyoung.3z@kyoto-u.ac.jp

^b Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan

Abstract

Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (^FPdC) that displays an unprecedented quantum yield and highly sensitive ¹⁹F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and ¹⁹F NMR spectroscopic DNA analysis. ^FPdC and ^FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and ¹⁹F chemical shift in response to i-motif formation. The utility of ^FPdC was exemplified through reversible fluorescence switching of an ^FPdC-containing i-motif oligonucleotide in the presence of Ag(I) and cysteine.

This article is part of the themed collection: RSC Chemical Biology Editors' Choice

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Article information

DOI: https://doi.org/10.1039/D1CB00020A
Article type: Paper
Submitted: 30 Jan 2021
Accepted: 04 Mar 2021
First published: 10 Mar 2021
This article is Open Access

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RSC Chem. Biol., 2021,2, 876-882

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Synthesis and application of a ¹⁹F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs

W. A. Wee, J. H. Yum, S. Hirashima, H. Sugiyama and S. Park, RSC Chem. Biol., 2021, 2, 876 DOI: 10.1039/D1CB00020A

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