Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name




First Advisor

David Rueda


We have used FRET, single molecule spectroscopy, and several other biophysical techniques to study how the folding of RNA allows it to perform its various functions by recognizing and binding a target ligand. We have shown that the c-di-GMP riboswitch undergoes a large, global conformational change upon binding of the ligand. The folding dynamics of the c-di-GMP riboswitch upon Mg2+ binding help to pre-organize the aptamer for efficient ligand binding and ultimately efficient gene expression. We have also investigated two instances, a fluorophore-binding aptamer and molecular beacon, where the folding of RNA can be used to detect an analyte. We have demonstrated that binding of the fluorophore, TAMRA, to an aptamer enhances the fluorescent properties of the fluorophore. Specifically, it increases both its quantum yield and fluorescent lifetime. This will provide an added advantage to the use of these aptamers in labeling an mRNA in vivo. We have shown that 2' modifications do not affect the folding and binding of a molecular beacon to its target. The common use of these 2' modifications does not hamper their use for in vivo studies. Whether natural or artificial, the folding of RNA to specifically recognize a target can be employed by both cells and scientists to perform a wide array of functions.