Document Type



Doctor of Philosophy (PhD)



First Advisor's Name

Yesim Darici

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Jin He

Second Advisor's Committee Title

Committee Member

Third Advisor's Name

Xuewen Wang

Third Advisor's Committee Title

Committee Member

Fourth Advisor's Name

Yuk-Ching Tse-Dinh

Fourth Advisor's Committee Title

Committee Member

Fifth Advisor's Name

Jaroslava Miksovska

Fifth Advisor's Committee Title

Committee Member


Biomolecular interactions, Heme proteins, DNA topoisomerases, DNA supercoiling, Surface plasmon resonance (SPR), SPR data fitting, Quartz nanopipettes, label-free methods, Finite element simulations, Carbon nanotube based nanoporous membrane devices

Date of Defense



Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions.

Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations.

In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism.

Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.




Chapters 1 and 2 are the Introduction and Methods, respectively. Chapter 3 has been adapted from the research results for which manuscripts are being prepared for publication. The majority of the contents in chapters 4 through 8 have been adapted from published papers. Chapter 9 is the summary and future work.



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