Study of Binding of Triplex DNA with Flavone Derivatives Using Fluorescent Intercalator Displacement

Targeting duplex DNA using a triplex-forming oligonucleotide (TFO) in a sequence-specific manner is an attractive approach for anti-gene strategy. A TFO binds into the major groove of duplex DNA via Hoogsteen H-bonding. The formed non-canonical triplex structure can serve as a padlock on duplex DNA to regulate gene expression and replication and induce DNA damage and genomic instability. However, the triplex formation is thermodynamically unstable and kinetically unfavorable due to the repulsions between three negatively charged DNA strands. Anti-gene enhancers are small molecules that bind to triplex DNA specifically while having little effect on duplex DNA. Our lab has recently discovered and developed several classes of triplex binding ligands based on the flavone scaffold. These molecules bind to triplex DNA with high affinities via intercalation. In the present work, we investigated the relative binding specificity of these ligands with triplex DNA using a fluorescent intercalator displacement (FID). When thiazole orange (TO) binds to DNA, it fluoresces significantly. Adding a ligand into the TO-DNA solution can displace TO out of DNA and subsequently reduce the fluorescence of bound TO. Comparing the fluorescence signals as a function of ligand concentrations allows us to determine the relative binding strength of ligands. In this presentation, we will discuss the experimental setup and FID results.