Understanding Novel Energy Transfer Modalities Using DNA Scaffolds for Precise Sub-Nanometer Positioning

A central theme in the field of nanophotonics is the characterization of new materials that display unique light-matter interactions. In practice, this knowledge is asserted through an iterative process of model design, assembly, and characterization. The end result of this process is a set of logical design principles that are utilized to manufacture novel nanomaterials. Of particular interest is controlling the transfer of excited state energy between fluorophores separated by distances of less than 20 nm. At this scale, energy transfer through non-radiative dipole-dipole coupling, categorically denoted as resonance energy transfer (RET), dominates the interaction. In RET mechanisms, the energy transfer efficiency between fluorophores is inversely proportional to their separation distance. For example, the most common RET mechanism, Förster resonance energy transfer (FRET), exhibits a 6th power decay as a function of separation distance. As such, small fluctuations in fluorophore positioning will dramatically affect and can ultimately nullify the expected behavior of the system. Therefore, to develop prototype nanosensors exploiting RET, there exists a demand for a robust yet programmable molecular scaffold. Although there are many functional nanomaterials available, none are as versatile or convenient for fluorophore scaffolding as DNA. By exploiting the inherent chemical properties of DNA, scaffolds can be designed to self-assemble into near-arbitrary 2- and 3-dimensional geometries. Furthermore, the chemical nature of DNA makes it amenable to labeling with various optically active materials such as organic fluorophores, colloidal semiconductor nanocrystals, and noble metal nanoparticles. Herein, we use self-assembled DNA nanostructures as a tool to control the positioning and density of fluorophores in resonance energy transfer cascades. Specifically, we use DNA nanostructures to further describe the limits of multidirectional energy transfer between pseudoisocyanine (PIC) dye aggregates. We then go on to identify a previously unreported method of forming PIC aggregates and demonstrate that the photophysical properties of said aggregates can be tuned by merely modifying the underlying DNA sequence. Next, we pivot to a new class of material, namely 2-dimensional colloidal semiconductor nanoplatelets. We utilize a labeled peptide-PNA-DNA hybrid platform to demonstrate energy transfer with the platelets acting as both resonance energy donors and acceptors. Finally, we address the matter of nanostructure formation quality assurance by reconfiguring a deep convolutional neural network (dCNN) to scour atomic force microscope (AFM) images of DNA nanostructures, identifying fully formed nanostructures, and classifying them by respective geometries.

Author

• Chiriboga, Matthew

• DNA Nanotechnology
• Dye Aggregates
• Förster resonance energy transfer
• Machine Learning
• Nanoparticles
• Nanophotonics

Identifier

hdl:1920/14044

OAI identifier oai:identifier

oai:MARS:1920/14044