RecA-mediated homology search as a nearly optimal signal detection system.
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 the RecA-DNA interaction is 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.
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
Yonatan
Y
Savir
Tsvi
T
Tlusty
D001483:Base Sequence; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011938:Rec A Recombinases / Q000378:metabolism*; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid; D015398:Signal Transduction; D013816:Thermodynamics
D029968:Escherichia coli Proteins; D011938:Rec A Recombinases