Modeling introduction

We've constructed two models.

The first one aims at predicting the expression level of a tandem promoter system. This model takes into consideration of the type of sub-promoters, the order of sub-promoters and the number of sub-promoters. With the help of this model, one can employ limited expression element to reach a desired expression level in any species, especially in non-model organisms that have few known expression element.

The second model aims at bringing in some more insight about the off-target behavior of Cas9 by taking a new approach and analyzing all off-target studies published. In the analysis of Cas9 binding, it revealed the potentiality of nucleic acid thermodynamic model in Cas9 off-target predicting, as well as its limits. It suggested that the gRNA-Cas9 will tolerate mismatches more generously when the gRNA-DNA binding energy is too high or too low. After the dCas9 off-target rate analyzed, kinetic of Cas9 cleaving is derived. And the following concentration-time function of the cleaved product suggested that expression time of Cas9 is as important as the concentration of Cas9.