Publication Date

April 2009


Knee, Joseph




English (United States)


6-methyl isoxanthopterin (6-MI) is a fluorescent guanine analog whose excited state properties are perturbed upon incorporation into duplex DNA in a sequence-dependent manner. This thesis combines Molecular Dynamics (MD) simulations and Time-Dependent Density Functional Theory (TD-DFT) excited state calculations to model the structures and excited states of 6-MI DNA. Three computational methods, TD-PBE0, TD-B3LYP, and CIS, were evaluated for treatment of local 6-MI DNA structures with particular regard for charge transfer energies. To build a framework for understanding the effect of DNA incorporation on the excited states of 6-MI, calculations were run on canonical two- and four-base structures with adenine and thymine in stacked positions and cytosine in base-paired position. Compared to values obtained for the 6-MI monomer, S1 oscillator strengths increased slightly with cytosine pairing, decreased slightly with thymine stacking, and decreased substantially with adenine stacking.



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