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Nanofluidic Separation of Long DNA Molecules


OBJECTIVE: Design, fabrication, and demonstration of an electrophoretic capillary nanofluidic integrated sensor platform effective for the separation of biological molecules into different sizes for use in detection, identification, and classification applications. DESCRIPTION: Recently methods have been developed to rapidly separate long-strand polymers according to length. The separation mechanism utilizes confinement-induced forces to separate the polymers into different size fractions. Researchers have examined interfaces between regions of vastly different configuration entropy, where small fragments can become trapped in favorable regions, but the larger fragments cannot completely enter due to the large size. Researchers have also examined mechanical and/or field-induced dielectrophoretic DNA trapping due to the surface roughness within nanopores and selective binding of nucleic acids to silica particles. Nanofluidic separators hold the promise for rapid, inexpensive separation of DNA strands and other polymers into fractions that are characterized by different polymer strand lengths. However, the work has been hampered by a complete understanding of the transport behavior of long and short DNA strands in nanochannels. This topic seeks to address transport phenomena in micro and nano channels with the goal of building better separation devices. PHASE I: Examine the transport behavior of long and short DNA strands in fused silica nanochannels with the application of electrical fields of different strengths. Examine mechanical and/or field-induced dielectrophoretic DNA trapping due to the surface roughness within the nanochannels. Examine areas within the nanofluidic channels with induced interfaces between regions of vastly different configuration entropy. Examine methods for utilizing DNA transport in nanochannels as a method for separating the DNA into fractions of differing length. PHASE II: The Phase II effort of the program should build and test a functioning nanofluidic separation platform. The research and development work should include an assessment of the prototype"s ability to separate relevant bio-materials and/or bio-agent targets into fractions according to length. The prototype nanofluidic sensor platform should be packaged in a form factor that readily interfaces with spectroscopy systems. The separation system should allow for stand-alone operation with fluidic and electrophoretic control that is self-sustained to facilitate a transparent operation by the user. PHASE III DUAL USE APPLICATIONS: Further research and development during Phase III efforts will be directed towards refining a final deployable design, incorporating design modifications based on results from tests conducted during Phase II, and improving engineering/form-factors, equipment hardening, and manufacturability designs to meet U.S. Army CONOPS and end-user requirements. Specifically improved nanofluidic separation will have relevance to scientific studies on biological materials and structures, to the detection and identification of biological threats, to medical diagnostics of biological induced diseases, to the monitoring of commercial consumables for biological contamination, just to name a few possibilities. REFERENCES: 1. Mario Cabodi, Stephen W. P. Turner, and Harold G. Craighead,"Entropic Recoil Separation of Long DNA Molecules", Analytical Chemistry, volume 74, number 20, pages 51695174, 2002. 2. Stephen L. Levy, John T. Mannion, Ji Cheng, Christian H. Reccius, and Harold G. Craighead,"Entropic Unfolding of DNA Molecules in Nanofluidic Channels", Nano Letters, volume 8, number 11, pages 3839-3844, 2008. 3. Georgette B. Salieb-Beugelaar, Juliane Teapal, Jan van Nieuwkasteele, Danil Wijnperl, Jonas O. Tegenfeldt, Fred Lisdat, Albert van den Berg, and Jan C. T. Eijkel,"Field-Dependent DNA Mobility in 20 nm High Nanoslits", Nano Letters, volume 8, number 7, pages 1785-1790, 2008. 4. Jian Wen, Lindsay A. Legendre, Joan M. Bienvenue and James P. Landers,"Purification of Nucleic Acids in Microfluidic Devices", Analytical Chemistry, volume 80, issue 17, page 64726479, 2008. 5. Qirong Wu, Joan M. Bienvenue, Benjamin J. Hassan, Yien C. Kwok, Braden C. Giordano, Pamela M. Norris, James P. Landers, and Jerome P. Ferrance,"Microchip-Based Macroporous Silica Sol & #8722;Gel Monolith for Efficient Isolation of DNA from Clinical Samples", Analytical Chemistry, volume 78, number 16, pages 5704-5710, 2006. 6. A Bhattacharyya and C.M. Klapperich,"Thermoplastic microfluidic device for on-chip purification of nucleic acids for disposable diagnostics", Analytical Chemistry, volume 78, number 3, pages 788-792, 2006. 7. M. J. O'Brien, P. Bisong, L. K. Ista, E. M. Rabinovitch, A. L. Garcia, S. S. Sibbett, G. P. Lopez and S. R. J. Brueck,"Fabrication of an Integrated Nanofluidic Chip using Interferometric Lithography", Journal of Vacuum Science and Technology B, volume 21, pages 2941-2945, 2003.
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