Benzo[b]Fluorenone as a Quadruplex Interactive Agent (Qia): Binding Studies and Quadruplex Formation with the Human Telomeric HT4 Sequence

Abstract

Many previously investigated agents capable of binding to and stabilizing G-quadruplex DNA conformations possess aromatic, planar chemical structures. Here, initial investigations on the interaction of benzo[b]fluorenone (BF) with the human telomeric forming oligonucleotide HT4 using circular dichroism (CD), thermal melting and steady-state fluorescence are reported. CD studies suggest that BF exhibits binding selectivity for G-quadruplex over model double-stranded DNA structures. BF binds to hybrid-mixed type quadruplex structures in the presence of physiological concentrations of K+ ions (100mM). However, even in the absence of salt, BF can induce an anti-parallel type quadruplex conformation. Thermal melting studies on quadruplex HT4 in the presence and absence of salt show BF has little effect on the melting temperature, suggesting that BF may associate with the G-quadruplex structure through a non-intercalating mode. As BF is known to be a solvatochromic fluorophore, steady state fluorescence emission spectra were taken for BF titrated with the HT4 quadruplex formed at 100mM K+, to explore the ability of BF to act as a potential probe of the environment of its binding site. Based on the red shift of BF emission, BF/quadruplex association appears to involve a relatively polar and hydrogen-bonded environment. This work was supported by NIH SCORE Grant S06 GM 060654.