ArticleNucleic acids research2020
5'-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 25 citations in OpenAlex.
- The Effect of 2'F-RNA on I-Motif Structure and Stability.Molecules (Basel, Switzerland) · 2025Article
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- Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsiveChemical science · 2024Article
- Advances in RNA Labeling with Trifluoromethyl Groups.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
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- Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy.Chemical science · 2023Article
- 4'-SCFAngewandte Chemie (International ed. in English) · 2022Article
- Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence andChembiochem : a European journal of chemical biology · 2022Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- A suite ofJournal of biomolecular NMR · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The high sensitivity of 19F nucleus to changes in the chemical environment has promoted the use of fluorine-labeled molecular probes to study structure and interactions of nucleic acids by 19F NMR. So far, most efforts have focused on incorporating the fluorine atom into nucleobase and ribose moieties using either monomer building blocks for solid-phase synthesis, or nucleoside triphosphates for enzymatic synthesis. Here, we report a simple and efficient synthesis of 5'-fluoromonophosphorylated and 5'-fluorodiphosphorylated oligodeoxyribonucleotides, which combines solid-phase and in-solution synthesis methods and requires only commercially available nucleoside phosphoramidites, followed by their evaluation as 19F NMR probes. We confirmed that the fluorine atom at the oligonucleotide 5' end did not alter the secondary structure of DNA fragments. Moreover, at the same time, it enabled real-time 19F NMR monitoring of various DNA-related biophysical processes, such as oligonucleotide hybridization (including mismatch identification), G-quadruplex folding/unfolding and its interactions with thrombin, as well as formation of an i-motif structure and its interaction with small-molecule ligands.
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