Integrating computer-aided engineering and computer-aided design for DNA assemblies

Abstract

Functional properties of modern engineering products result from merging the geometry and material properties of underlying components into sophisticated overall assemblies. The foundation of this design process is an integration of computer aided design (CAD) tools that allow rapid geometric modifications with robust simulation tools to guide design iterations (i.e. computer-aided engineering, CAE). Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing, and biophysics. However, currently these self-assembled DNA nanodevices rely primarily on geometric design, and hence, they have not demonstrated the same sophistication as real-life products. We present an iterative design pipeline for DNA assemblies that integrates CAE based on coarse-grained molecular dynamics with a versatile CAD approach that combines top-down automation with bottom-up control over geometry. This intuitive framework redefines the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.