NIRT: Manipulation of DNA-Protein Interactions at the Nano-Scale

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0304316LarsonThis proposal was received in response to Nanoscale Science and Engineering initiative, NSF 02-148, category NIRT. The objective of this proposal is to design and build a microfabricated platform for study of DNA/protein interactions at the nano-scale. These interactions are at the heart of the cellular machinery for maintaining and transcribing DNA, and include transcription factors, as well as histones and other chromatin proteins. These DNA/protein interactions are under active study at the cellular level, but the next steps towards a detailed understanding of them require their study at smaller length scales, including the nanoscale. Therefore, a microfabricated devise will be built, which contains a main channel of length 20 to 30 microns and of width ranging from 20 nm to 2 microns. Individual DNA molecules will be stretched in the channel and positioned using high frequency electric fields, and anchored at gold electrodes using thiol groups chemically attached to the ends of the DNA molecules. This long, very thin, channel will be joined to thin side channels for addition of DNA-interacting proteins locally to specific regions of the DNA molecule. The proteins will be further localized by use of capture electrodes as well as hydrodynamic focusing using flow through other side streams, and other confinement methods. The channels will be etched in silicon, and bonded to a thin glass substrate, to permit examination by optical microscopy. The broader impacts of the proposal include the integration of the proposed research with the introduction of a new Nanoscale Science and Engineering (NSE) curriculum for graduate students. The new course will focus on nano- fabrication issues related to integration of electronic function with microfluidics and transport issues related to the processing of biological samples.