DNA and RNA are virtually unique among polymers in organic chemistry to display role-base self-assembly over a broad range of molecular structure. This self-assembly is the basis of biotechnology and genetics, and is the focus of this proposal. Work in the Benner laboratories has shown that the Watson-Crick base pair can support 12 nucleobases joined in six distinct base pairs, each joined by different patterns of hydrogen bonding, to give An Expanded Genetic Information System (AEGIS) following an expanded set of Watson- Crick pairing rules. AEGIS can be copied via template-directed polymerization catalyzed by DNA and RNA polymerases. Work in the Tan laboratories has developed and exploited near-field scanning optical microscopy (NSOM) tools to image single molecules with 10- 20 nm resolution on two-dimensional surfaces, in particular, nanostructure functional probes having the dimensions of single molecules. Using these technologies, Tan has imaged a variety of molecules and nanostructures (buckminsterfulleranes, DNA chains, and cell membranes), photonanofabricated a variety of biochemically functionalized nanostructures, analyzed the kinetics of single enzyme molecules, and probed the release of metabolites inside single cells. The two research groups, housed in adjacent buildings, therefore have technologies ideally matched to undertake a collaborative project focusing on the practical aspects of synthesis/fabrication through bio-self assembly of nanostructures. Procedures for synthesizing the components of the nanostructures using biocatalysts (in particular, thermostable DNA polymerases) will be explored, with an eye towards in situ generation of the components of nanostructures. The cells of the largest nano-nets will be loaded with photoreactive groups that can be written/read by NSOM. We hope that this will create a small readable/writable memory element with obvious relevance to practical applications.
