UC Berkeley

Plasmon rulers consisting of optically coupled metal nanoparticles linked by biological macromolecules have provided a tool for bio-imaging and enzymology that is non-bleaching, non-blinking, and biocompatible. A pair of plasmonic nanoparticles couple when they are in spatial proximity, resulting in spectral shifts and increased scattering intensity. Previ- ous research has developed synthetic techniques for precisely assembling gold nanoparticles using DNA. Two self-assembled plasmonic nanoparticles have been shown to be an enzyme- responsive material in one-dimension. In order to visualize the subtle conformational changes ubiquitous in biological systems, three-dimensional, anisotropic nanoparticle assemblies are required.

This dissertation reports two examples of next-generation plasmon rulers. DNA-assembled dimers of gold nanorods can act as a three-dimensional plasmon ruler only if the relative orientation of the particles can be controlled. By tuning the conditions of electrophoretic separation and the DNA structure, a sample of gold nanorod dimers that are attached side-by-side can be isolated from those attached end-to-end. TEM characterization of these oriented dimers shows a statistically significant deviation from randomly oriented nanorod pairs. Because of the high yield of oriented nanorod pairs, this colloidal sample can serve as an ensemble biosensor.

A three-dimensional plasmon ruler can also be synthesized by increasing the complexity of the underlying DNA structure. Four DNA strands, each attached to a gold nanoparticle, hybridize such that each strand folds into one face of a chiral pyramid. The sequence of the four strands was designed to maximize the yield of one enantiomer based on tertiary structure of the double helices. This structure is a circular dichroism-based nanoparticle ruler for subtle biological events, such as the extension of DNA by a DNA-binding protein.

Additionally, the DNA-assembled gold nanoparticle system was characterized by state- of-the-art electron microscopy. A method called individual particle electron tomography can be used to image single macromolecules. By tuning the parameters of the negative stain, the transmission electron microscope (TEM), and the buffer conditions, this method has been extended for the reconstruction of a 3D density map of an individual DNA double helix labeled by two nanoparticles. Previous work on cryo-EM imaging of DNA nanostructures without gold nanoparticles has relied on averaging many images together to create a com- posite density map. This work represents an electron microscopy constructed density map of a DNA double helix.

Liquid-phase TEM can probe and visualize dynamic events with structural or functional details at the nanoscale in a liquid medium. The grapheme liquid cell was adopted to seal an aqueous sample solution containing DNA-assembled gold nanoparticle dimers against the high vacuum in TEM. Quantitative analysis of collected real time nanocrystal trajec- tories reveals the fidelity of the DNA in the presence of the electron beam as well as the reconstruction of the 3D configuration and motion of the nanostructure.