Browsing by Subject "EPR spectroscopy"
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Item Metal dependent structure, dynamics, and function in RNA measured by site-directed spin labeling and EPR spectroscopy(Texas A&M University, 2007-04-25) Kim, Nak-KyoonThe structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).Item Probing Iron Accumulation in Sacchromyces cerevisiae Using Integrative Biophysical and Biochemical Techniques(2012-02-14) Miao, RenIron is an essential element for life. It is involved in a number of biological processes, including iron sulfur (Fe/S) cluster assembly and heme biosynthesis. However it is also potentially toxic due to its ability to induce formation of reactive oxygen species (ROS) via Fenton chemistry. Therefore its uptake, trafficking and utilization must be regulated to avoid its toxicological effect. It has been recently discovered that Fe/S cluster biosynthesis machinery plays a key role in the cellular iron regulation and its disruption leads to impaired iron regulation and iron accumulation within mitochondria. The iron accumulation resulted from impaired Fe/S cluster assembly in the eukaryotic model organism Saccharomyces cerevisiae (baker?s yeast) was studied. Various biophysical (e.g. M?ssbauer, EPR, UV-vis spectroscopy) and biochemical (e.g. Western blots, PCR, enzyme activity assay, etc.) techniques were used to characterize the iron content in yeast mitochondria isolated from several mutants strains. In these mutants one of the proteins involved in Fe/S cluster biosynthesis (Yah1p and Atm1p) is mutated and iron regulation and metabolism are disrupted. By integrating the results obtained from these different methods, it was determined that excess iron accumulates in the mutant mitochondria as inorganic phosphate Fe(III) nano-particles exhibiting superparamagnetic behaviors. Oxygen is required for iron accumulation and nanoparticle formation. The Fe(III) nano-particles can be chemically reduced to Fe(II) then largely exported from the mitochondria. These biophysical and biochemical methods were also used to examine the iron distribution in whole yeast cells of the Aft1-1up strain in which iron regulon genes are constitutively activated and compared to that of Yah1p-depleted and wild type yeast. Constitutive activation of iron regulon genes does not alter the cellular iron distribution significantly. However disruption of Fe/S cluster assembly by Yah1p depletion causes dramatic cellular iron redistribution: the vacuolar iron is largely evacuated and most of the cellular iron probably precipitates in mitochondria as Fe(III) nanoparticles. The results provide novel insights into iron trafficking and possible signal communications between organelles within cells.