5′-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR

Marek R Baranowski, Marcin Warminski, Jacek Jemielity, and Joanna Kowalska

Nucleic Acids Res (2020), gkaa470. doi:10.1093/nar/gkaa470

This study describes the synthesis, characterization and application of oligonucleotides carrying 5′-fluoromonophosphate (FP) or 5′ fluorodiphosphate (FPP) moieties as 19F NMR probes of DNA structure and function. The authors synthesized several such labeled oligodeoxyribonucleotides using straightforward methods that avoid commercially unavailable phosphoramidite building blocks, and then validated their utility as molecular tools to: 1) probe duplex formation and distinguish 5′-terminal mismatches, 2) monitor G-quadruplex formation, 3) detect DNA-protein interactions and 4) monitor i-motif formation and its interactions with small molecule ligands.

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