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 4'-SCF3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ ) 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 19F NMR sensitivity and excellent resolution of the positioning of T 4'-SCF3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T 4'-SCF3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ 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.

Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes

“…In-cell 19 F NMR has become a powerful tool to study nucleic acid structures in cellular milieu, 37,[47][48][49] as uorine is 100% abundant, highly sensitive and importantly, absent in cellular systems (no background signal). [50][51][52][53][54][55] Furthermore, its signal does not undergo signicant line broadening in the heterogeneous cellular environment, which is very severe in the case of a proton signal. 56 To determine 19 F signatures of the longer LTR region and survey GQ and hairpin structures, ONs 13-15 labeled with FBFdU in the GQ domain or FdU in the hairpin domain were synthesized (Table 1, Fig.…”