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 $\mathrm{lac}$ repressor protein), amplification, and mutations to evolve to a unique DNA sequence, the $\mathrm{lac}$ 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.