(209c) Unraveling the Behavior of DNA through Multiscale Modeling

Knotts, IV, T. A. - Presenter, University of Wisconsin-Madison
Deublein, S. - Presenter, University of Wisconsin-Madison
De Pablo, J.J - Presenter, University of Wisconsin-Madison

Over the past few decades, the power to control and manipulate DNA has benefited a variety of fields including biology, biotechnology, genetics, and genomics. Moreover, the inherent self-assembly capacity of DNA, its mechanical properties, and its polymeric behavior are so desirable, that DNA is increasingly being used to solve problems of interest in almost all fields of science and technology. Despite this ubiquity, very little is understood at the molecular level about the underlying biophysics?even in processes as common as hybridization and replication. Understanding this behavior is beneficial from both a fundamental and an applied perspective. Increased insight improves our ability of manipulation and provides models for design optimization of next-generation technologies. To this end, we previously created and validated a new, coarse grain model of DNA, which showed remarkable predictive capabilities of both the thermal and mechanical properties of the molecule. We have since applied this model to understand a variety of important systems involving DNA. Following a brief introduction to the model, I will present findings for several systems of interest. These include viral packaging of DNA, the wrapping of DNA around histones, the dynamics of nicked DNA, and the behavior of DNA in micro/nano-fluidic devices. I will also describe efforts to improve hybridization efficiency in DNA microarrays. The results, taken as a whole, attest to the power of multiscale modeling to compliment and expand upon current experimental capacity.