Diffusion of Confined DNA

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ID: MPS/DMR/BMAT(7623) 1206045 PI: Dorfman, Kevin ORG: University of MinnesotaTitle: Diffusion of Confined DNAINTELLECTUAL MERIT: Nanochannel confined DNA is an emerging technology for obtaining sequence specific information directly from genomic DNA. The development of this new technology has been accompanied by a renewed interest in the physics of confined, semi-flexible chains. While the classical theories developed more than 30 years ago by de Gennes and Odijk provide a complete description for the extension and diffusivity of a flexible chain, experimental data indicate that these theories do not describe semi-flexible chains such as DNA over most of the range of confinement. Simulations have provided concrete evidence for the existence of two regimes between the limits described by Odijk and de Gennes: an "extended de Gennes" regime and a "transition regime," but these state-of-the-art theories remain untested. The specific aims of this experimental proposal are: (1) test the predictions for the extension of DNA in the transition and extended de Gennes regime, (2) develop a proper definition for the effective width of confined DNA that accounts for surface properties, and (3) test the predictions for the diffusion coefficients of DNA in the transition and extended de Gennes regimes. The proposed experiments take advantage of a new approach to fabricate relatively inexpensive prototype nanochannels with the precision required for physical studies. This project should lead to a comprehensive, quantitative understanding of the extension and diffusion of DNA in confinement.BROADER IMPACTS: Nanochannel confinement is an emerging method for DNA barcoding, where the DNA is stretched and fluorescent genomic information is optically "read" from the linearized DNA. DNA barcoding rapidly provides genome-scale information with kilobase pair resolution, serving as an important complement to second-generation genome sequencing and hybridization microarrays. The nanochannel sizes used for DNA barcoding normally lie in the transition regime or the extended de Gennes regime. The fundamental results gained from this project will provide the foundation for the further engineering of these devices. The research in this project will train graduate and undergraduate students in nanofabrication, polymer physics, and transport phenomena. The participation of underrepresented minorities will be increased further through a summer research program with the Chemistry Department at Grambling State University, an HBCU. Participation in the "Energy and U" program will promote interest in science and engineering in students in grades 3-12. "Energy and U" is an interactive program that teaches the first law of thermodynamics in an age-appropriate manner through dramatic demonstrations of energy conversion. Thousands of students attend the program each year, including many students from inner city and underprivileged schools.