Simulation and analysis of in vitro DNA evolution

Details Simulation and analysis of in vitro DNA evolution Simulation and analysis of in vitro DNA evolution

2003-01-21

arxiv.org/abs/cond-mat/0301372v1

Physics

Condensed Matter

11 pages, 11 figures. Submitted to PNAS

Scientific paper

10.1103/PhysRevLett.92.038101

We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic simulations of evolution starting from a single DNA sequence. We identify different parameter regimes characterized by distinct evolutionary behaviors. For each regime we find analytical estimates which agree well with simulation results. For small population sizes, the DNA evolutional path is a random walk on a smooth landscape. While for large population sizes, the evolution dynamics can be well described by a mean-field theory. We also study how the details of the DNA-protein interaction affect the evolution.

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