This Nanoscale Interdisciplinary Research Team (NIRT) award supports a group of five faculty, including four at the University of Florida and one at Cornell University, to develop tools capable of measuring the distribution and concentration of specific messenger RNA molecules (mRNAs) in defined subcellular regions of single nerve cells. Initial effort will use neurons from the model organism, Aplysia. Use of the tools will then be extended to neurons from higher organisms with the goal of understanding how neurons establish new connections or synapses. Using electron beam technology, the team will fabricate one dimensional (1-D) DNA nanoarrays for the capture and direct assay of the mRNAs. Detection will employ molecular beacons to generate a fluorescent signal in the presence of specific target mRNAs; the beacons are fluorescent nanoparticles consisting of self-assembling branched DNA nanostructures designed using an artificially expanded genetic alphabet (AEGIS). Nanofluidics and dip-pen nanolithography will be tasked with delivery of the nanoparticles to specific sites in the DNA array. Fluorescence will be detected by optical imaging. Software specialized for analyzing biological molecules will archive and interpret recovered mRNA sequences using interpretive proteomics tools developed from evolutionary models. The project will benefit from a collaborative setting where students at all levels engage multiple disciplines. If successful, this will provide an educational paradigm for the training of the scientists of the future, as well as demonstrating the utility of nanoscience and engineering in the study of classical problems in biology.
