The goal of my project is to obtain information about the biophysical characteristics of a potentially biologically significant higher-order structural motif. We have been interested in structures of DNA quadruplexes whose core architecture is based on guanine quartets (G-quartets). It has been suggested that G-quartet structures may form at the natural eukaryotic chromosome ends (telomeres) and contribute to protein binding, regulation, or resistance to degradation. Telomeres are usually composed of simple tandem repeats of guanine-rich sequences associated with telomeric binding proteins. Telomeric sequences are typically found to be highly conserved across phylogenetically diverse organisms. More recently, however, many budding yeast telomeres have been shown to have more divergent sequences both in length and in base composition. Oligonucleotides having one to two repeats of the yeast telomeric sequences are usually less stable thermodynamically compared to those with more conserved sequences, such as ones from ciliate protozoa. My thesis project involves the characterization of several quadruplex-forming guanine-rich oligonucleotides from budding yeast telomeric and related sequences. Solution nuclear magnetic resonance (NMR) and other spectroscopic methods are used to understand their physical chemical features, the factors contributing to the stability of the complexes, and to determine high resolution solution structures of those oligonucleotides. So far, we have use MIDAS to visualize crystal/NMR structures of related DNA oligonucleotide sequences from the Brookhaven Protein Database. The starting model structures of tetra-stranded parallel quadruplexes were created using MIDAS for NMR structural calculations. To grasp distance violation, we have also visualized the proton-proton distances (mardishow, noeshow) calculated by MARDIGRAS (Matrix Analysis of Relaxation for DIscerning the Geometry of an Aqueous Structure) from NMR cross-peak intensities measured from 2D NOE experiments (SPARKY). The conformational changes made during the energy minimization precesses (AMBER) and the snapshots from the molecular dynamics calculations (AMBER) are also monitored by MIDAS. DISPLAY was used to show the "movie" of the trajectories from molecular dynamics calculations. We rely heavily on the Computer Graphics Laboratory facility during the structural refinment process, while creating graphics displays for upcoming scientific conferences and publications, and while finishing up my dissertation. I also used the Computer Graphics Laboratory facilities for class assignments and the final project for PC260: Computer Graphics.
NIH ExPorter
NIH ExPorter