Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)



Committee Member

Hugo Sanabria, Committee Chair

Committee Member

Andrew Tennyson

Committee Member

Feng Ding

Committee Member

Leah Casabianca


Förster Resonance Energy Transfer (FRET) is a promising methodology which is used by researchers in determining structural information of biomolecules. Other methodologies such as X-ray diffraction, nuclear magnetic resonance (NMR) and electron microscopy (EM), and X-ray scattering (SAXS) and circular dichroism (CD) can only give snapshots of the functional conformers. In the applications of most cases, FRET can only be used to give a qualitative result such as “yes” or “no” pattern. In our lab, we are able to expand this ability by applying FRET to quantitatively determine the structure and dynamic information in the biological system with high accuracy. We first apply this methodology in measuring our standard double strand DNA in order to identify its ability to obtain the interdye distance with high accuracy. Then, we are able to identify the fast dynamic which happens in mRNA followed by a kinetic pathway of its folding pattern. Finally, we used FRET as well as discrete molecular dynamics (DMD) simulation in determining dynamic behavior of PDZ domains.



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