Model

Each fragment that can be flipped by integrases is surrounded by two DNA-binding sites. Those sites correspond to the binding sites of a particular integrase. In our model, the flipping fragment is made of a terminator. Therefore, this fragment is modeled via two states:

• T_on: terminator is on, transcription is blocked. It corresponds to our initial state.

• T_off: terminator is off, transcription is active. It corresponds to one flipping of the terminator.

In our design, we are interested in a double flipping.