Homework: The Inverter¶

In the lecture we constructed the "Hello world" plasmid. Upon induction with IPTG, it expresses a protein that colors it pink. This can be seen as a Buffer gate Y = BUF(A) with digital input A, digital output Y, and steady-state relation Y = A.

In the homework, you will adapt this design to an Inverter Z = INV(A) with digital input A, digital output Z, and steady-state relation Y = not(A). All of this should be done with Python code like in the lecture.

Problem 1: Genetic Design¶

Identify genetic components that you need to create the inverting logic. You should keep the lac promoter for the IPTG input, but add a second promoter and other required parts. Draw this design.

Problem 2: Construct the linear fragment¶

Put them all together on a single linear fragment. You may assume that you can order this from a company - in particular, there is no need to split this up into smaller fragments that need to be glued together with Gibson Assembly. Draw the fragment and describe your design decisions.

Problem 3: Simulate Gibson Assembly¶

Simulate Gibson Assembly of the linearized backbone (you can choose between restriction enzymes and PCR as you like). Draw the final construct and describe your design decisions.