4'-SCF3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA

Abstract

Fluorinated nucleotides are invaluable for ¹⁹ F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF₃ -thymidine (T ${}^{4{}^{\text{'}}\text{-}\mathrm{SCF}{}_3}$ ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF₃ group exhibited a flexible orientation in the minor groove of DNA duplexes and was well accommodated by various higher order DNA structures. The three magnetically equivalent fluorine atoms in 4'-SCF₃ -DNA constitute an isolated spin system, offering high ¹⁹ F NMR sensitivity and excellent resolution of the positioning of T ${}^{4{}^{\text{'}}\text{-}\mathrm{SCF}{}_3}$ within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T ${}^{4{}^{\text{'}}\text{-}\mathrm{SCF}{}_3}$ make it a valuable ¹⁹ F NMR probe for quantitatively distinguishing diverse DNA structures with single-nucleotide resolution and for monitoring the dynamics of interactions in the minor groove of double-stranded DNA.

Keywords: 19F NMR; DNA Structure; Fluorinated Nucleotides; Nucleic Acids.