DNA is an extraordinarily long biopolymer whose structure greatly influences its function. Here, the term structure refers to the geometry and stress of the molecule while the term function refers to the biological processes the molecule supports including replication, transcription, and gene repair. For example, the protein-induced “looping” of DNA is a well-known mechanism for gene regulation.
In cases such as that illustrated below, the structural loop serves as a biological “switch” that regulates transcription. In this talk, we will consider DNA structures that form on length scales ranging from tens of nanometers through several microns or longer (hundreds to many thousands of base pairs). Such “long-length scale” structures include DNA loops and supercoils which are simply too large to resolve using the all-atom descriptions of molecular dynamics. Instead, we describe these structures using a continuum model for DNA in the form of a nonlinear computational rod model. The rod formulation accounts for the elasticity of the DNA double-helix and its intrinsic curvature which is also sequence-dependent. Example results will illustrate the formation of supercoils (plectonemes) and the expected DNA loops for wild-type and mutated forms of the
Lac-repressor DNA/protein complex as also observed in the experimental literature.

Protein-mediated DNA looping in the bacterium E. coli. Computational rod model used to compute the intermediate loop of DNA bound at two operator sites to the Lac repressor protein.

Bio: Noel Perkins received his education at U. C. Berkeley where he was awarded his B.S. (1982), M.S. (1984), and Ph.D. (1986) degrees in Mechanical Engineering. Following a postdoctoral appointment at the Institute for Sound and Vibration Research (Southampton, England), he joined The University of Michigan in 1987 where he is presently an Arthur F. Thurnau Professor in Mechanical Engineering. His research interests include computational and nonlinear dynamics, MEMS inertial sensor applications for human motion, and the mechanics of single molecule DNA. He has served as an Associate Editor for the ASME Journal of Applied Mechanics, Guest Editor for the International Journal of Non-linear Mechanics and presently serves on the editorial boards for the Journal of Sound and Vibration, Journal of Vibration and Control and Vibroengineering. He is a Fellow of the American Society of Mechanical Engineers and a recipient of The GM Outstanding Distance Learning Faculty Award, the Academic Challenge Award from the Technical University of Munich, and the University of Michigan Amoco Undergraduate Teaching Award. He is founding partner of Cast Analysis, LLC that manufactures a fly casting training system for the fly fishing industry.

Host: Professor Jeff Moehlis