Custom DNA microarrays reveal the selective recognition of BMVC to MYC promoter G-quadruplex: a large-scale assessment of ligand binding selectivity

G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. Here, we utilize high-throughput, large-scale custom DNA G4 microarrays to analyze the G4-binding selectivity of BMVC. BMVC preferentially binds to the parallel MycG4 and selectively recognizes flanking sequences of parallel G4s, especially the 3′-flanking thymine. Importantly, the microarray results are confirmed by orthogonal NMR and fluorescence binding analyses. Our study demonstrates the potential of custom G4 microarrays as a platform to broadly and unbiasedly assess the binding selectivity of G4-interactive ligands, and to help understand the properties that govern molecular recognition. Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting small molecules pyridostatin (PDS), BMVC. Briefly, the binding experiments involved incubating Cy5-conjugated PDS with unlabeled molecules (PDS and BMVC) to 180K feature Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine the binding preferences of the unlabelled molecules to G4-forming sequences.