Prevention of G-quadruplex folding by ligand-mediated stabilization of the G-triplex intermediate
Date
2018-12
Authors
Bracey, Harrison E.
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Abstract
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.
Description
Keywords
DNA, G-quadruplex, G-triplex, DNA damage, Thermal difference spectra, FRET
Citation
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 (Unpublished thesis).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.