  Homologous recombination facilitates the exchange of genetic material between
homologous DNA molecules. This crucial process requires detecting a specific
homologous DNA sequence within a huge variety of heterologous sequences. The
detection is mediated by RecA in E. coli, or members of its superfamily in
other organisms. Here we examine how well is the RecA-DNA interaction adjusted
to its task. By formulating the DNA recognition process as a signal detection
problem, we find the optimal value of binding energy that maximizes the ability
to detect homologous sequences. We show that the experimentally observed
binding energy is nearly optimal. This implies that the RecA-induced
deformation and the binding energetics are fine-tuned to ensure optimal
sequence detection. Our analysis suggests a possible role for DNA extension by
RecA, in which deformation enhances detection. The present signal detection
approach provides a general recipe for testing the optimality of other
molecular recognition systems.
