Looping Dynamics of Semiflexible Polymers

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ID: MPS/DMR/BMAT(7623) 1006485 PI: Todd, Brian ORG: Purdue UniversityTitle: Looping Dynamics of Semiflexible PolymersINTELLECTUAL MERIT: Intramolecular loops can form whenever a polymer chain contains more than one reactive site. The physics underlying this process is the diffusive transport of two distal polymer segments to a common location ("looping"). Most polymer theories predict that polymer looping reactions do not follow traditional kinetic models, but these predictions have not been fully tested experimentally. The goal of the proposed research is to characterize semiflexible polymer looping dynamics, using DNA as a model experimental system. In particular, the PI will test a recent theoretical prediction that semiflexible polymer looping is amenable to a simple description based on Kramers rate theory. This simple description would greatly facilitate predictions of looping kinetics in practical biopolymer design applications, such as the kinetically-determined processing of DNA nanoparticles for non-viral gene therapy. Two independent methods of measuring polymer looping rates are proposed. In the first, a fluorophore will be attached to one end of the polymer and a quencher to the other. Looping kinetics can then be determined from loop-mediated fluorophore quenching, measured via fluorescence correlation spectroscopy (FCS). The second method uses kinetic competition between looping and a second-order capping reaction. The proposed research will characterize semiflexible polymer looping, culminating in a model that details the influence of polymer structure on the looping rate. This deepens our understanding of segmental motion in semiflexible polymers and extends a widely used biopolymer model into applications involving looping.BROADER IMPACTS: A major goal of this project is to train students to think about how polymer physics can be used in interdisciplinary applications such as biomaterials design and molecular biology. The PI has recruited two talented graduate students into the laboratory, and it is expected that the laboratory will soon contain a mix of students at different levels. The PI is a mentor in the "Horizons Program" for at-risk students at Purdue and hopes to attract some of his mentees into his lab. He will also continue to recruit and retain underrepresented minorities through mentoring, lab tours, and programs supported by the College of Sciences at Purdue University. In the past, the PI was a director of a mentoring program in a 100% minority public middle school in East Cleveland, Ohio. He plans to continue outreach with middle school-aged students in West Lafayette, Indiana. The PI is currently developing an outreach laboratory designed to introduce concepts of "bottom-up" materials design to middle school-aged students. The idea is to challenge the students to design "co-polymer sequences" out of macroscopic magnetic and non-magnetic "monomers" that are capable of self-assembling into structures, such as loops, knots, and cubes. Modest funding is included in the budget to purchase the materials to make these demonstration kits. When not in use, the demonstration materials will be made available to K-12 teachers through the department's Physics Outreach Resource Room.