Colchicine Selective Interaction with Oncogene RET G-quadruplex Revealed by NMR

G-quadruplexes (G4s) are frequently formed in the promoter regions of oncogenes, regulate their expression, and are considered as promising drug targets for anticancer therapy. Due to their high structural similarity, discovering ligands selectively interacting with only one G4 is full of challenges. Oncogene RET G4-DNA is a unique, parallel G4 with a G-tetrad at 5’-end, which is composed of four syn guanines. Here, by nuclear magnetic resonance (NMR) titration, one-dimensional 1H Carr-Purcell-Meiboom-Gill (CPMG) and saturation transfer difference (STD) experiments, we demonstrated that natural product colchicine selectively binds to RET G4-DNA. NMR solution structure of RET G4-colchicine complex at a mole ratio of 1:1 demonstrates that colchicine stacks with the outer G-tetrad at 3’-end, rather than the G-tetrad at 5’-end. Colchicine occupies the original position of base G14, and counteracts its roles in stabilizing RET G4-DNA conformation, which results in almost unchanged stability of RET G4-DNA. This unfoverable interaction might contribute to the binding selectivity of colchicine, as well as the 3’- flanking loops of RET G4-DNA. These data present molecular rationale of colchicine for its specific recognition of RET G4-DNA, advance the design of quadruplex-interacting small molecules to control expression of RET or other oncogenes.