Abstract 1942 Investigating Ligand-Induced Local Conformational Changes of Fluorescently Labeled G-Quadruplex Structures

DNA sequences rich in guanines readily fold to form quadruplex structures (GQs), which are bound by Hoogsteen-type hydrogen bonding of four guanine nucleotides (G4). GQs are important structural components in many physiological functions, including limiting telomerase activity seen in 85-90% of human tumor cells. Telomerase activity can be influenced by introducing small molecules that can interact with GQs. This interaction of small molecules can alter the stability and local conformations of the GQ at the guanine tetrad level, which in turn can affect the telomerase activity and cancer progression. To identify changes in the local conformations of the telomeric sequence upon interaction with small organic molecules, we incorporated 6-methylisoxanthopterine (6MI), a circular dichroism (CD)-active fluorescent base analogue of guanine in place of guanine at distinct positions in the human telomeric GQ sequence. Several variations of DNA sequences were used to monitor the conformational changes at different locations of the GQ structure using UV-Vis, CD, and fluorescence spectroscopic methods. Past studies investigated the binding of TmPyP4, a telomerase-inhibiting ligand, to the GQ but only addressed their interaction in a global conformational perspective. In this study, we used fluorescent base analogues to track the local conformation at individual G-tetrad levels using spectroscopic methods. The results demonstrated an initial stabilization followed by destabilization of the human telomeric DNA sequence with increasing ratios of TmPyP4, whereas the modified strands showed stabilization or destabilization depending on the position of the probe. The results suggest that site-specific fluorescent probes can monitor the global and local structure and stability changes in GQs upon ligand binding.