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Introduction

One of the goal of our project is to visualize the system “bring DNA closer” with the tri-partite GFP. In a first place, we decide to focus the modeling part on the question “what is the optimal distance between the two dCas9 for fluorescence?” Our system is divide in 4 parts:

• Two dCas9
• Two linker
• Tri-partite GFP

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This question is essential because the distance between the dCas9 may cause major problem: if this system doesn’t work we may not see the effect of the other system. In fact, the 3D structure of our linker may interact with the dCas9 or the GFP because of steric hindrance.

3D Model

The first step of this is the 3D model. We use the PDB website to find all proteins of our system and use Pymol to assemble all the system. For this model we have:

• Two identical dCas9 from Streptococcus pyogenese instead of Streptococcus thermophiles and Neisseria meningitidus
• The wild type GFP with the 10th and 11th beta sheet remove

The first limit was the linker. We don’t have any information but is sequence. So we decide to use the software PEP-FOLD for having a 3D simulation. The prediction was not usable for our model because the results were very improbable. We decide to build 3 different models: one with a small end to end distance, one with a long distance and one last with the mean between this two values. We had a first answer: the optimal distance lays between 73 and 110 base pairs.