Observing nucleotide flipping in DNA using indirect 2′-F nucleotide probes and 19F NMR

Many proteins that bind specifically to DNA and RNA employ a mechanism known as nucleotide flipping, whereby a nucleotide rotates out of the helical stack and into an active site. This conformational change can be monitored using spectroscopic methods, including fluorescence and nuclear magnetic resonance (NMR). We previously showed that flipping of a 2'-fluoroarabino-substituted nucleotide by thymine DNA glycosylase (TDG) can be directly monitored using 19F NMR. However, 2'-F-substituted phosphoramidites are typically readily available only for canonical nucleotides, posing an experimental limitation. Given the large conformational change associated with nucleotide flipping, we reasoned that it could be indirectly monitored by 2'-F nucleotides located at proximal sites in the target or complementary DNA strand. Indeed, we find that TDG flipping of deoxythymidine from a G⋅T mispair is robustly monitored by 2'-F probes at six of nine sites examined. Moreover, flipping of cadC (5-carboxyl-2'-deoxycytidine), paired with dG or dA, can be monitored with 2'-F probes in the complementary strand, revealing highly efficient cadC flipping by TDG. Notably, kinetic assays show that the 2'-F probes have a small or negligible effect on TDG activity. The results point to a general and experimentally accessible approach for studying nucleotide flipping and other conformational changes in nucleic acids.