CAREER: Dynamics of DNA during Electrophoresis in Artificial Sieving Matrices

University Of Minnesota-Twin Cities, Minneapolis MN

Investigators

Abstract

Proposal Number CTS-0642794 Principal Investigator: Kevin D. Dorfman University/Institution: University of Minnesota-Twin Cities CAREER: Dynamics of DNA during Electrophoresis in Artificial Sieving Matrices This project involves theoretical modeling and experimental investigation of microfluidic electrophoresis of DNA. DNA electrophoresis remains not only one of the most important tools in molecular biology and genetics, but also an ideal platform for testing fundamental theories of polymer dynamics and coarse-grained averaging of separation processes. The proposed research will address topics relevant to polymer physics, stochastic processes, and chemical engineering, working across multiple length scales to connect microscopic motion to macroscopic observables. The research component is an integrated theoretical and experimental program that addresses a range of fundamental issues arising during DNA separations in microfabricated post arrays, including the hindered relaxation phenomena in an external field and the role of the order of the post lattice. The research focuses on effects that arise from the proximity of posts in real separation devices, which are not addressed by the existing body of knowledge on DNA collisions with a single, isolated post. The experimental work spans multiple scales, combining ensemble-averaged measurements of the transport over several millimeters with detailed single-molecule observations of the local transport at the macromolecular scale. The microscopic insights will be used to construct new theoretical models, based upon continuous-time random walk theory, that rationalize the ensemble-averaged experimental results and predict new behavior that can be tested experimentally. In addition to training graduate students, the education component of this proposal consists of three parts: (i) developing a new course on the theory of electrophoresis and lab-on-a-chip technology; (ii) summer research opportunities for underrepresented minorities through a collaborative outreach program with the University of Puerto Rico at Mayaguez; and (iii) a K-12 outreach program with Edison High School in Minneapolis. Most importantly, the research will link theory to experiment in a well-defined microstructured environment. The proposed work will lead to improved DNA separation devices, suitable for applied and fundamental research. Artificial matrices are poised to replace pulsed-field gel electrophoresis for important applications in genome mapping and DNA fingerprinting, but the incomplete understanding of the dynamics of DNA in artificial matrices has prevented this technique from moving beyond the proof-of-principle stage and into routine use. The fundamental results could also impact related separation techniques, such as electrochromatography and microfluidic HPLC. The summer research program with the University of Puerto Rico at Mayaguez will provide advanced training in computational and experimental techniques that are unavailable to these students at their home university. The outreach program with Edison High School in Minneapolis will integrate the research activities with education at the K-12 level.