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

Abstract

Fluorinated nucleotides are invaluable for 19F NMR studies of nucleic acid structure and function. Here, we synthesized 4′-SCF3-thymidine (T (Formula presented.)) 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 19F NMR sensitivity and excellent resolution of the positioning of T (Formula presented.) within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T (Formula presented.) make it a valuable 19F 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.