Nanoscale Optical and Correlative Microscopies for Quantitative Characterization of DNA Nanostructures

Methods to engineer nanomaterials and devices with uniquely tailored properties are highly sought after in fields such as manufacturing, medicine, energy, and the environment. The macromolecule deoxyribonucleic acid (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. DNA origami are assembled from one large DNA scaffold strand and many unique, short staple strands; each staple programmatically binds the scaffold at several distant domains, and the coordinated interactions of many staples with the scaffold act to fold the scaffold into a desired shape. 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 the promise of DNA nanotechnology, few products have successfully translated from the laboratory to industry. Achieving high yield and high-precision synthesis of stable DNA nanostructures is one of the biggest challenges to applications of DNA nanostructures. For adoption in manufacturing, methods to measure and inspect 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 imaging of reactive sites on 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 single site defects on 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 the 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 synthesis 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, 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, the results suggest that the structural stability of DNA origami was decreased by DNA-PAINT imaging. The presented work demonstrated the development and application of advanced characterization techniques for DNA nanostructures, which will accelerate fundamental research and applications of DNA nanotechnology