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Date of Award


Access Type

Campus Access

Document type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Chemical Engineering

First Advisor

Harry Bermudez

Second Advisor

T.J. (Lakis) Mountziaris

Third Advisor

Neil S. Forbes

Subject Categories

Biomedical Engineering and Bioengineering | Chemical Engineering | Pharmacy and Pharmaceutical Sciences


Beyond the biological applications, the unique molecular recognition properties of DNA are of interest as ideal building blocks. Rationally designed DNA nanostructures serve as excellent delivery vehicles due to their well-defined three dimensional nanostructures and versatile conjugations with biomolecules. Additionally, nucleic acid motifs can have numerous functions through the mechanisms of riboswitches, DNAzymes, I-motif, aptamers, and antisense or RNA interference. The combination of both structural and functional aspects of DNA properties enables generation of versatile nano-materials that can interact with biological molecules and trigger specific responses to its environment. We previously reported the enhanced stability of a DNA tetrahedron to both specific and non-specific enzymatic digestion. The enhanced stability of DNA nanostructures motivated us to construct DNA pyramids with antisense capabilities. We have demonstrated the construction of DNA pyramids that are capable of delivering antisense DNA, thereby degrading mRNA and subsequently inhibiting target protein expression in vitro. We were able to confirm antisense activity of the DNA pyramids by the down-regulation of both EGFP and a tumor related protein MDM2 in mammalian cells. To explore additional responsive character of DNA nanostructures, we introduced an I-motif, which is formed under acidic condition, to the DNA nanostructures so that a DNA pyramid is able to exhibit pH responsive features. A pH change triggers a conformational change of the DNA pyramid, thereby enabling release of a cargo inside the DNA pyramid. Circular dichroism and FRET analysis were used to confirm the pH dependent formation of an I-motif and subsequent changes in DNA pyramid size. Dissociation of a cargo protein EGFP from the DNA pyramid was achieved using either pH, addition of EDTA or imidazole. We believe that by integrating multi-functional groups in DNA nanostructures and exploring responsive character of DNA nanostructures, powerful and versatile nano-biomaterials will be generated.