Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 A ̊ ) of a KRAS G-quadruplex as a 5′-head-to-head dimer with extensive poly-A ﰀ-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A ﰀ-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indi- cated the poly-A loop was a binding site for these lig- ands in addition to the 5′-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of spe- cific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.
Ou, A., Schmidberger, J., Wilson, K., Evans, C., Hargreaves, J., Grigg, M., O'Mara, M., Swaminatha Iyer, K., Bond, C., & Smith, N. (2020). High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A π-stacking interactions for small-molecule recognition. Nucleic Acids Research, 48(10), 5766-5776. https://doi.org/10.1093/nar/gkaa262