Model

In our design, integrases compute the output of the logic gates. Integrases allow to flip one fragment of DNA. The model we developped is described here.

Chemical Species

• Bxb1: integrase that can fold into two conformations called Bxb1a and Bxb1b. Even if those conformations have the same sequence of amino acids, their tertiary structure are different. As it is experimentally difficult to differentiate these two conformations, we chose to regroup them under the specie Bxb1.

• ΦC31: integrase that can fold into two conformations called ΦC31a and ΦC31b. Similarly to Bxb1, we chose to factorize these two conformations under the specie ΦC31.

• DBxb1: dimer of Bxb1. Bxb1a (respectively Bxb1b) forms a dimer DBxb1a (respectively DBxb1b). To be coherent, dimers re not differentiated depending on their spatial configuration.

• DΦC31: dimer of ΦC31. ΦC31a (respectively ΦC31b) forms a dimer DΦC31a (respectively DΦC31b). The different spatial configuration are not taken into account.

Modelization of DNA-binding sites and flipping

Each dimer of integrases can bind to a DNA binding site. As the flipping is irreversible, hese DNA binding sites can be three possible states:

• SI_{IntegraseName}: inactive DNA binding site. No dimer is bound to this site, which has never been flipped.

• SA_{IntegraseName}: active DNA binding site. A dimer is to this site.

• SF_{IntegraseName}: flipped DNA binding site. This DNA binding site has been used by a flipping.

Add Illustration of the three states

Each fragment that can be flipped by integrases is surrounded by two DNA-binding sites. These two DNA-binding sites

Characterization

Data

Assumptions

Parameter fitting

Range of validity of the assumptions

Characterization

Data

Assumptions

Parameter fitting

Range of validity of the assumptions