ArticleNucleic acids research2009
5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 87 citations in OpenAlex.
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- Observing nucleotide flipping in DNA using indirect 2'-F nucleotide probes and 19F NMR.Nucleic acids research · 2025Article
- NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity.Nature communications · 2024Article
- Controlling the incorporation of fluorinated amino acids in human cells and its structural impact.Protein science : a publication of the Protein Society · 2024Article
- Advances in RNA Labeling with Trifluoromethyl Groups.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry.Biochemistry · 2023Article
- Assessing the applicability ofJournal of biomolecular NMR · 2023Article
- Copper-promoted dehydrosulfurative carbon-nitrogen cross-coupling with concomitant aromatization for synthesis of 2-aminopyrimidines.RSC advances · 2022Article
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- A Small Molecule Exploits Hidden Structural Features within the RNA Repeat Expansion That Causes c9ALS/FTD and Rescues Pathological Hallmarks.ACS chemical neuroscience · 2021Article
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- Impact of 3-deazapurine nucleobases on RNA properties.Nucleic acids research · 2021Article
- In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells.Angewandte Chemie (International ed. in English) · 2021Article
- Review
- Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD.ACS chemical biology · 2020Article
- 2'-Chemical science · 2020Article
- AromaticAngewandte Chemie (International ed. in English) · 2020Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D (19)F and (1)H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis.
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