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Christopher Green

October 22 @ 3:00 pm - 5:00 pm MDT

Dissertation Information

Title: Nanoscale Optical and Correlative Microscopies for Quantitative Characterization of DNA Nanostructures

Program: Doctor of Philosophy in Materials Science and Engineering

Advisor: Dr. Wan Kuang, Electrical and Computer Engineering, Co-Chair and Dr. William L. Hughes, Materials Science and Engineering, Co-Chair

Committee Members: Dr. Elton Graugnard, Materials Science and Engineering and Dr. Hao Chen, Electrical and Computer Engineering

Abstract:

Methods to engineer nanomaterials and devices with uniquely tailored properties are highly sought after in fields such as manufacturing, medicine, textiles, energy, and space. DNA enables programmable self-assembly of nanostructures with near arbitrary shape and size and with unprecedented precision and accuracy. Additionally, DNA can be chemically modified to attach molecules and nanoparticles, providing a means to organize active materials into devices with unique or enhanced properties. One particularly powerful form of DNA-based self-assembly, DNA origami, provides robust structures with the potential for nanometer-scale resolution of addressable sites. The utility of DNA origami has been demonstrated through multiple applications, such as plasmonic and photonic devices, electronic device patterning, information storage, drug delivery, and biosensors. Despite these demonstrations, and the potential of DNA nanotechnology, few products have successfully transitioned from the laboratory to industry.

One of the biggest challenges to commercialization is the difficulty in achieving high-precision self-assembly at high yields. In a high-volume manufacturing environment, methods to measure and quantify assembled structures (i.e., metrology) are essential. Common high-resolution imaging techniques used to characterize DNA nanostructures, such as atomic force microscopy and transmission electron microscopy, cannot facilitate high-throughput characterization, and few studies have been directed towards the development of improved methods for nanoscale metrology. DNA-PAINT super-resolution microscopy enables high-resolution, multiplexed optical imaging of DNA nanostructures and offers the potential for inline optical metrology. In this work, nanoscale metrologies utilizing DNA-PAINT were developed for DNA nanostructures and applied to characterize DNA origami arrays and defects in DNA origami.

For metrology of DNA origami arrays, an embedded, multiplexed optical super-resolution methodology was developed to characterize the periodic structure and defects of two-dimensional arrays. Images revealed the spatial arrangement of structures within arrays, internal array defects, and grain boundaries between arrays, enabling the reconstruction of arrays from the images. The nature of the imaging technique is also highly compatible with statistical methods, enabling rapid statistical analysis of processing conditions. To obtain a greater understanding of DNA origami defects at the scale of individual strands, correlative super-resolution and atomic force microscopies were enabled through the development of a simple and flexible method to bind DNA origami directly to cover glass, while simultaneously passivating the surface to single-stranded DNA. High-resolution, correlative microscopy was performed to characterize DNA origami, and spatial correlation in super-resolution optical and topographic images of 5 nm was achieved, validating correlative microscopy for single strand defect metrology. Investigations of single strand defects showed little correlation to structural defects on DNA origami, revealing that most site defects occur on strands that are present in the structure, contrary to prior reports. In addition, structural defects were observed more often at sites resolved in SRM images, suggesting that the stability of DNA origami was decreased by DNA-PAINT imaging.

The presented work demonstrated the development and application of advanced quantitative characterization techniques for structure-property-processing studies of DNA nanostructures, the results of which will accelerate fundamental research and applications of DNA nanotechnology.