UC Berkeley

Many diseases, such as neurodegenerative disorders, cancer, and autoimmune diseases are caused by or exhibit symptoms of abnormal regulation of signaling proteins. In order to obtain a molecular understanding of diseases, we require tools capable of probing the intricate signaling pathways that govern biological function. Understanding the role these proteins play as they circulate between cells will allow us to examine disease progression from an intercellular point of view. Currently, it is difficult to study these proteins in their natural environment, in vivo, because they are created and function on very broad time and length scales. Existing protein detection methods have several limitations as they are optimized for intracellular imaging, performed in vitro, require lengthy sample handling, function over short time scales, or have molecular recognition elements that are unstable in biological media.

This dissertation presents a modular platform to create optical nanosensors that are able to address current limitations in signaling protein detection. Nanosensor elements require optimization of both signal transduction and molecular recognition elements. Single-walled carbon nanotubes (SWCNTs) are nanoparticles that are ideal signal transducers for biological imaging. SWCNTs have optical properties well-suited for biological sensing such as infinite fluorescence lifetime, no blinking, small size, and fluorescence in the near-infrared region of the electromagnetic spectrum that is least attenuated by biological systems. Several SWCNT nanosensors have already been developed for signaling small molecule targets and peptides, but, to date, none have been created for signaling proteins.

In order to create a robust imaging platform based on SWCNTs for sensing signaling proteins, it is possible to couple molecular recognition elements to SWCNT signal transducers using dual noncovalent and covalent functionalization strategies. The development of noncovalent molecular recognition elements is explored using peptide mimetic polymers called peptoids. The discovery of a synthetic peptoid binding loop for wheat germ agglutinin protein as a proof-of-principle case study shows the ability to utilize diverse chemical materials to create a fully synthetic binding element for desired protein targets. Additionally, the development of covalently functionalized SWCNTs is explored for the creation of multifunctional optical SWCNT nanosensors. Here covalently functional groups provide functional handles that work synergistically with noncovalent passivation to enable the development of a diverse nanosensor toolbox.

The findings presented in this dissertation lay the foundation of valuable techniques and materials to optimize the binding to and study of signaling proteins. Future work to streamline the development of novel nanosensors is discussed, and the framework for the creation of other biological nanomaterial tools through these noncovalent and covalent techniques is also explored.