Modularity optimizes target recognition in the CRISPR-Cas immune system

CRISPR-Cas has become a ubiquitous genetic editing tool for developing cell lines, disease models, and gene therapies, yet there is still more to be understood about the specificity and potential off-target activity of this tool. Here, a stochastic model is developed to study the targeting activity of the endogenous CRISPR-Cas immune system in bacteria against viruses. Based on the energy landscape of the recognition reaction, the significance of two biological modules is explored: (1) a short DNA motif called the PAM and (2) an RNA guide that matches a roughly 30-bp DNA sequence in the target genome. The model results indicate the further division of the RNA guide into two modules based on differences in the sensitivity to DNA mismatches, which is in line with experimental observations of a "seed" region. The modularity of the CRISPR-Cas immune system appears to manage the tradeoff among having enough specificity to avoid self-targeting, having enough cross-reactivity to recognize mutated virus DNA, and launching a fast enough immune response to protect against an unfolding infection.