Skip to main content
. 2017 Oct 3;113(7):1416–1424. doi: 10.1016/j.bpj.2017.08.013

Figure 2.

Figure 2

A discrete-state stochastic model to describe the DNA interrogation processes by CRISPR-Cas9 protein-RNA complexes. For convenience, a single Cas9-RNA molecule searching for the specific target on a single DNA molecule is considered. The DNA molecule of length L has l PAM sites, and one of them leads to the target sequence on DNA. The state 0 corresponds to the RNA-Cas9 complex in the solution. States of the type 1 (labeled also as “PAM”) correspond to the RNA-protein complex bound to the PAM site only, whereas the states of the type 2 (labeled also as “DNA+PAM”) describe the situation when the DNA interrogation is taking place. The association/dissociation rates from the solution to the PAM states are given by rates kon and koff, respectively. The forward/backward transition rates between states of type 1 and 2 are given by k1 and k2, respectively. The rate for off-target cutting from the DNA+PAM states (not connected to the target) is equal to r. To see this figure in color, go online.