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Wed, 15 Jun 2022 16:29:21 +0000
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Notice and Invitation
Oral Defense of Doctoral Proposal
Department of Bioengineering
College of Engineering and Computing, George Mason University

Matthew Chiriboga
Bachelor of Science, Biochemistry, Ithaca College, NY 2017

Understanding New Energy Transfer Modalities Using DNA Scaffolds for Precise Sub-Nanoscale Positioning


Thursday, June 16, 2022, 10:00 am
Update: Proposal will now be virtual
Link here<https://gmu.zoom.us/j/96870618695?pwd=TmoxTFpoa1dXZHc5MDNaMnh6VlVXUT09>
Meeting ID: 968 7061 8695
Passcode: 527313

Committee
Dr. Igor Medintz, Director
Dr. Parag Chitnis, Co-Director
Dr. Remi Veneziano, Chair
Dr. Patrick Vora
Dr. Sebastián Díaz


Abstract
Crucial to the design and fabrication of nanophotonic devices is a thorough understanding of the near-field behavior of fluorophores. In general, the nearfield can be defined as the region of space where the radial distance from an antenna is less than the wavelength of light the antenna interacts with. For our particular interests we limit our scope even further to the range at which resonance energy transfer (RET) mechanisms can occur. The most common RET mechanism is Förster resonance energy transfer (FRET), which is typically known to occur from 2 to 10 nanometers. FRET is a non-radiative energy transfer (ET) due to the dipole-dipole coupling between two fluorophores. The energy transfer efficiency (EET) of FRET decays by the 6th power of the separation distance between the two fluorophores. As a result, small errors or fluctuations in fluorophore positioning can dramatically affect and ultimately nullify the expected behavior of the system. These constraints emphasize the need for robust and predictable scaffolds, upon which we can arrange fluorophores with, ideally, sub-nanometer precision and accuracy. Although there are many functional nanomaterials available, none are as versatile or convenient for fluorophore scaffolding as DNA. The field of structural DNA nanotechnology views DNA from the perspective of a biopolymer taking advantage of the intrinsic chemical and physical properties. Exploiting these properties, DNA can be designed to self-assemble into near arbitrary 2- and 3-dimensional geometries. Fortunately, the chemical nature of DNA is also amenable to the attachment of most nanophotonic materials such as organic dyes, semiconductor quantum dots (QDs), gold nanoparticles, and lanthanide metal chelates. This makes DNA an indispensable tool to prototype RET systems and outline the design principles crucial to engineering with emergent nanophotonic modalities with sub-nanometer precision. Herein, we propose using self-assembled DNA scaffolds to position fluorophores into novel ET arrays. By exciting the system with input light irradiation, we can observe the energy dissipation and outline the fundamental design principles which favor useful ET. Using DNA scaffolds, we can obtain extreme control over the positioning of pseudoisocyanine dye (PIC) aggregates and ultra-small fluorescent gold nanoclusters (AuNCs). Both PIC and AuNCs have generated significant interest for their proposed unique optical properties. For example, PIC aggregates have been shown to exhibit coherent, wavelike, exciton delocalization leading to increased exciton transport efficiency. However, PIC aggregates are notoriously unstable making exciton delocalization difficult to study and providing challenges when designing systems which aim to integrate exciton delocalization into traditional RET arrays. AuNCs on the other hand, are a new class of material with a tunable near infrared (NIR) emission that are suggested to engage in ET over longer distances than is traditionally understood. However, the underlying interaction mechanism and the subsequent limitations are unknown. The research surrounding both materials could benefit from the use of DNA scaffolds to prototype, characterize, and better understand their properties. An improved basic understanding of these materials would impact applications in bio-sensing, optoelectronics, and light harvesting. Moreover, the realization of these DNA based ET platforms would yet again demonstrate the versatility of DNA as a framework for nanoscale engineering and as an indispensable tool for basic research.





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