NSTI Nanotech 2009

Genomic Analysis via Nanoconfinement: Nanocoding

K.L. Kounovsky, K.D. Potamousis, T.M. Schramm, J. de Pablo, D.C. Schwartz
University of Wisconsin - Madison, US

Keywords: nanoslits, DNA


The high-throughput analysis of individual DNA molecules is altering the pace and scope of biological investigation. In this regard, the Optical Mapping System was developed as a single molecule platform for construction of physical maps that span entire genomes (1-3). This platform effectively discovers genomic structural alterations including insertions, deletions, etc.; however, a system with greater throughput enables not only the characterization of individuals but entire human populations. For this purpose, we developed new ways to present very high densities of arrayed DNA molecules using nanoconfinement through the development of new fluidic devices with nanoslit features. Genomic DNA molecules are “barcoded” by the sequence-specific incorporation of fluorochrome labels prior to loading within nanoslits for presentation and optical detection. As such, a major goal was to design and fabricate nanoslit devices for the efficient loading of barcoded molecules. Part of this effort was centered on the characterization and leveraging of novel molecular confinement phenomena that enhanced the resolution of detectable barcode features.
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