Dynamics of DNA-Protein Interaction Deduced from in vitro DNA Evolution

We report the first experimental study of the dynamics of in vitro evolution of DNA. Starting from a random pool of DNA sequences, we used cycles of selection (binding to the lac repressor protein), amplification, and mutations to evolve to a unique DNA sequence, the lac operator. Statistical analysis of the DNA sequences obtained during the cycles of evolution shows that the DNA bases are selected at different rates. The rates of selection provide a quantitative measure of the interaction of the DNA bases with the protein during the complex formation. A model reproduces the evolution dynamics of the DNA population but cannot give the fine structure of the DNA-protein interaction.