Date of Degree


Document Type


Degree Name





Ruth E. Stark

Committee Members

Harry D. Gafney

Vinod M. Menon

Bonnie L. Gersten

Subject Categories



Biopolymers are essential components of numerous natural and synthetic macromolecular assemblies. In the present study, the structural properties of biopolymers ranging from fungal melanins to synthetic nucleic acids were investigated using spectroscopic methods and theoretical modeling. (1) Computational modeling and molecular dynamics simulations were used to study the structural properties of a short single-stranded (ss) DNA. The dependence of the conformational stability and flexibility of the ssDNA on the thermodynamic conditions of the system was demonstrated. (2) Time-resolved fluorescence spectroscopy involving an organic donor-quencher pair was utilized to study the conformational properties of Y-shaped DNA. Results highlighted the different distances between the arms of the Y-DNA and indicated the overall structural stability of the Y-DNA system. Time-resolved fluorescence techniques were applied to investigate the distance dependence of the non-radiative energy transfer process between an organic donor (fluorescein) and a gold nanoparticle quencher connected by double stranded (ds) DNA. (3) Synthesis of phospholipid-conjugated gold nanoparticles and their self-assembly onto an aqueous subphase were tested. The resulting lipid-capped nanoparticles were characterized by optical methods such as UV-Vis absorption spectroscopy and dynamic light scattering. The effects of bio-functionalization on the size of biotin-capped gold nanoparticles were investigated using optical techniques. (4) Solid-state nuclear magnetic resonance (NMR) spectroscopy was utilized to elucidate the structural characteristics of fungal melanins. Various spinning speeds, temperatures, magnetic field strengths, and isotopic labels were utilized with 1D and 2D 13C MAS NMR, revealing distinctive structural fingerprints of the fungal melanins generated biosynthetically with L-dopa, methyldopa, epinephrine, and norepinephrine. These pigments exhibited differences in their aromatic and aliphatic structures and probable biosynthetic pathways, and it was possible to delineate proximities between particular melanin and membrane-related molecular groups.


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