Simulation and analysis of in vitro DNA evolution.

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. Varying the evolution parameters reveals three different regimes characterized by distinct evolutionary behaviors, and for each regime we find analytical estimates which agree well with simulation results. We also study how the details of the DNA-protein interaction affect the evolution.