2023 ACS Synthetic Biology Paper

Note:

The scripts to simulate the results from the 2023 ACS Synthetic Biology paper (Schaffter et. al.), Design approaches to expand the toolkit for building cotranscriptionally encoded RNA strand displacement circuits can be found here . See the paper for a detailed description of each experiment and/or simulation.

In the paper a relatively weak output toehold (w) was used in some contexts. Gates with w output toeholds had their reverse strand displacement rate constant decreased compared to the default in molecular_species().