Designing Dynamical Molecular Systems with the PEN Toolbox

Abstract

This tutorial paper focuses on the design, simulation, and optimization of polymerase–exonuclease–nickase (PEN) toolbox systems. The PEN toolbox is a molecular programming framework that relies on the interaction between DNA molecules and enzymes to produce highly non-linear dynamic systems. The flip side of that expressivity is that the design of systems relies heavily on trial-and-error, thus calling for computer assistance. The paper includes a description of the high-level application programming interface of DACCAD, the main simulation library for PEN toolbox systems, and introduces methods to extend the existing software to match the designer’s needs. Several examples are provided to illustrate that approach.