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The project aim to study how bacterial (e.coli) DNA organization can influence gene expression. In order to answer our question, the team decide to create a new tool based on CRISPR-Cas9 to bring together two distant DNA regions. This new tool is expected to assess the effect of DNA spatial conformation on gene expression. As a results, we have designed a bring DNA closer tool (BDC tool) and a visualization tool.

Here, we will expose you our experimental strategy.

Characterization strategy

Tripartit Split-GFP and FRB/FKBP12 dimerization systems

Preliminary we have designed two biobricks to test the FRB*/FKBP12 interaction and the tripartite GFP. FRB* has been fused with one subunit of GFP (GFP 11) and FKBP12 has been fused with another one (GFP10).

In order to test the system we built a plasmid containing three biobricks to express the full system. Then we transform it in E.coli to asess the system.The system will be test measuring GFP fluorescence in absence or not of rapalog (rapamycin analog). We also plan to test it in bacterial containing just two parts (FRB-GFP11 and FKBP12-GFP10) instead of the three (without GFP1-9).

This construction will give us our first results and validate the functionality of tripartite GFP and dimerization of FRB* and FKBP12.

Assessment of the minimal distance to have fluorescence

One of the goal of our project is to assess the system bring DNA closer tool with the tri-partite GFP. To assess the effect of the bring DNA closer tool, we have to know the minimal distance needed to such fluorescence emission.

This question was also the core of our modeling part which answer the question: “What is the optimal distance between the two dCas9 for fluorescence?”

This question is essential because the distance between the dCas9 may cause major problem. First, the steric hindrance and the dCas9 footprint may avoid the GFP assembling for target sequence too close. Second, the proteins size we have chosen avoid GFP assembling if there are too far away. As a result, fluorescence emission would be detect only if the proteins, as well as, the DNA regions are distant between a precise range of distance.

To assess experimentally such distant, the team has decided to design different plasmids containing the visualization target sequences separate from each other with different distances. To do so, the team has designed specific primers to carry out RT-PCR and obtain from a plasmid in which the target sequences are distant with 1kB, different plasmids. This plasmid would have been express with the composite biobrick composed of the biobricks 3, 4 and 5. The target sequence would have been separate from :

• 1kB
• 500pB
• 150pB
• 75pB
• 50pB

Assessment of the DNA regions brought closer

In order to test our BDC tool, all the biobricks should been express in E. coli, as well as all the sgRNAs corresponding to each dCas9s. After, the team would have measure the GFP fluorescence variations in absence or not of rapalog.

Gene expression tests

In order to test a possible influence of the spatial proximity in gene expression. The team would have test the expression of two different reporter genes. In the aim to have more accurate variation measurements, we should have used enzymes as luciferase and Beta-Galactosidase.