NSF 0944125 Period of Performance: September 15, 2009 to August 21, 2011 Principal Investigator: Steven R.J. Brueck, Ph.D. 505-272-7800 / brueck@chtm.unm.edu Co-Principal Investigator: Gabriel P. Lopez, Ph.D. 505-277-4939 / gabriel.lopez@duke.edu The broad goal of this work is to establish the understanding and methods necessary to implement high-density arrays of nanoscale channels as versatile, sensitive and selective components for chip-scale biodetection systems. For this purpose we study the manipulation and extension of DNA in 1D channels as a function of an applied electric field. This project is enabled by, and an extension of, NSF- and ARO-funded collaborative work by the PIs that has demonstrated that nanochannel arrays can be used for chip-based molecular separations in porous barriers embedded in nanochannel arrays. We have also investigated and developed simple quantitative methods for detection of the model proteases (including toxins such as botulinum neurotoxin and viral proteases from lethal pathogens such as West Nile virus and Dengue virus) in chip based microfluidic systems via fluorescent-based techniques. Proteases are very important targets due to their crucial role in a number of biological pathways. Our goal was to develop simple and sensitive microassay methods that require no wash steps or secondary labeling reactions. We have continued the development of nanoscale channels fabricated by a combined top-down/bottom-up process using interferometric lithography as an inexpensive, high resolution technology to scales as small as 50 nm and then using directed self-assembly of colloidal nanoparticles to extend the length scales to sub ~ 10 nm features. Innovations demonstrated in this program include use of porous barriers, composed of interruptions in channels filled with nanoparticles that present a tortuous pathway for the stretched DNA to infiltrate from one nanochannel to another, and use of multiple level structures where the space between the levels is again a porous nanoparticle region. This has the advantage that transport in the free space above the porous regions is eliminated. Specific studies included investigations of the stretching/compression of long DNA with an applied bias. In collaboration with Professor Elliott Brown at Wright State University and Dr. Edgar Mendoza at Redondo Optics, we have demonstrated high resolution THz spectroscopy of RNA and DNA molecules in nanochannels. The nanochanels serve two important functions: 1) increasing the relative concentration of the RNA/DNA molecules to reduce the water absorption features that often obscure the weak polymer signatures, and 2) stretching the DNA to allow a simple spectroscopic signature and reduce self-collisional effects that result in rapid redistribution of energy out of specific modes and hence broadening of the features. The chip-based microfluidic systems work has concentrated on developing biomimetic systems for sensing biological toxins. The basic idea is to coat silica beads with lipid bilayers that are attacked by adsorption of the toxins just as biological cells are attacked. Once the lipid layers have been exposed to a volume of suspected toxins, the lipid bilayers are separated from the silica beads and the transport of the resulting species is studied by fluorescence techniques in microchannels downstream from the beads. This method does not require prior knowledge of the toxin, but works by sensing the attachment of foreign moieties to the lipid bilayers. Future plans include the development of multi-channel microfluidic systems for the analysis of multiple protease toxins and controls.
