Fig. 1
From: CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Players of the energy model that determines the approximate free energy (ΔGB) of any Cas9–gRNA–DNA binding. In this model, that is posterior to the Cas9–gRNA binding, there are four main contributions to the overall free energy. The first contribution is ΔGH for the gRNA–DNA hybridization, computed with RNA–DNA duplex energy parameters and weighted by a position-wise estimate of the Cas9 influence in the binding. The second contribution is the ΔGO penalty to open the DNA–DNA duplex in the target region and it is computed with DNA–DNA duplex energy parameters. The third contribution is the ΔGU penalty that is the free energy of the gRNA (first 20 nt) folding. This is computed with RNAfold program which incorporates RNA–RNA duplex energy parameters [32]. The fourth contribution is the correction factor δPAM that is determined by the PAM sequence of the target