Prevention of G-quadruplex folding by ligand-mediated stabilization of the G-triplex intermediate
Bracey, Harrison E.
G-quadruplex DNA is an extensively studied non-canonical DNA structure formed in guanine rich areas of the human genome. It is proposed that G-quadruplex structures play a role in telomere assembly, replication, and transcription. Experimental evidence has shown that an intermediate in the G-quadruplex folding pathway may exist as G-triplex DNA. The structure of G-triplex DNA is similar to that of G-quadruplex DNA. However, the G-triplex structure is unique in that it has a major groove. The goals of this project are to characterize different G-triplex structure topologies and to find small molecular weight ligands that can selectively bind to the major groove and stabilize the G-triplex intermediates to prevent G-quadruplex folding. To characterize G-triplex topology and stabilization, CD spectra and CD-derived melting temperatures (Tm) were compared to UV thermal difference spectra (TDS) and UV derived Tm of a collection of model G-triplex forming oligonucleotides. Potential ligands were identified by an in silico screen between truncated thrombin binding aptamer (T1) and 1.2 million compounds using molecular docking software, Autodock Vina, and a database of commercially available ligands, ZINC12. To determine if potential ligands bind to and stabilize TBA13, UV-vis spectroscopy melting assay and a FRET bound Tm assay employing a dual-labeled T1 oligonucleotide was performed.
DNA, G-quadruplex, G-triplex, DNA damage, Thermal difference spectra, FRET
Bracey, H. (2018). <i>Prevention of G-quadruplex folding by ligand-mediated stabilization of the G-triplex intermediate</i> (Unpublished thesis). Texas State University, San Marcos, Texas.