Schulman MPP 2011

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A Mechanism for Chemical Sequence Replication Built from Designed, Modular Components

  • Rebecca Schulman, UC Berkeley

Abstract

It is a grand challenge to construct systems which have the self-assembled, dynamic structure and the directed information flow of even the simplest biological cells. DNA self-assembly processes offer a new opportunity to address this challenge. The hybridization rate and bound structure of two DNA molecules can often be predicted, and we can build 2- and 3-dimensional structures by creating branched DNA junctions. These attributes allow us to design DNA assembly reactions with hundreds of distinct species which together perform complex self-assembly and information processing tasks. 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," and can similarly alter the nucleation rate by designing the components to have a specific critical nucleus. In principle, this process is accurate enough to permit high-yield, 1000-fold increases in 4-bit sequences, replication of longer sequences, and Darwinian evolution. Further, we can imagine evolving complex functional patterns using this system.

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