ME 100/200 Seminar on "Exploring the Principles of Biological Self-Assembly By Design"


Tuesday, October 7, 2014 - 3:30pm


ESB 2001


Dr. Rebecca Schulman, UC Berkeley

Abstract:  DNA self-assembly processes are a new opportunity to synthetically investigate how the complex, multiscale spatial organization seen in biology can arise.  Because DNA sequences have simple, well-characterized chemistry and structure and a combinatorial number of molecular interfaces, we can emulate the sophistication of biological self-assembly processes.  Perhaps the most fundamental biological mechanism is sequence replication and Darwinian evolution. I'll describe the design and realization of an autonomous, enzyme-free system to replicate sequences within ribbon crystals using a chemical alphabet consisting of DNA "tile" monomers.  We control the mutation rate by designing the crystal monomers so that information copying
during growth is "proofread" by a process inspired by kinetic proofreading in biology.

The cytoskeleton creates dynamic, adaptive structure in eukaryotic cells based on local rules.  I'll describe how we can synthethically mimic one cytoskeletal construction primitive, the assembly of filaments such that they bridge fixed start and destination landmarks. The "start" landmark is a nucleation site for a DNA nanotube, a stiff
polymer.  A nucleated nanotube grows until its end attaches to a "destination" landmark, forming a stable link.  The dynamics of tube nucleation, growth and diffusion together control assembly, which we track with time-lapse fluorescence microscopy.

Bio:  Rebecca Schulman is currently the Miller Postdoctoral Fellow with the Department of Physics at UC Berkeley. She received her B.S. from MIT, and her Ph.D. in the group of Eric Winfree at California Institute of Technology, in the field of computation and neural systems. Schulman’s research focuses on the principles of biological assembly, design and use of synthetic biological materials, mechanically active materials and sensors, and self replicating and self-repairing materials.  Particularly she looks to create new materials that are models of features unique to living systems, focusing on structure and information flow rather than on the synthesis of particular molecules.

Host: Prof. Megan Valentine

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