Abstract
Fluorinated nucleotides are invaluable for (19) F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF(3) -thymidine (T 4'-SCF3 ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF(3) 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'-SCF(3) -DNA constitute an isolated spin system, offering high (19) F NMR sensitivity and excellent resolution of the positioning of T 4'-SCF3 within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T 4'-SCF3 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.