Abstract
Electron Paramagnetic Resonance (EPR) spectroscopy is used to study dynamics and conformational changes in the RNA glycine riboswitch. The dynamic role of the leader-linker interaction within glycine riboswitch conserved sequences is probed through site directed spin labeling and continuous wave EPR. Inter-aptamer and aptamer-expression platform interactions are elucidated through double electron-electron resonance spectroscopy. Incorporation of spin labels is achieved through optimized ligation methodologies allowing synthetically modified RNA to be joined to larger RNA sequences. Expected folding and burial of riboswitch elements will lead to restricted motion of the spin label and, additionally, pulsed EPR experiments yield distance distribution profiles indicating conformational exchange between states in the absence and presence of glycine.
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