Coding Agents as a Mechanism for Formalizing and Transferring Domain Knowledge in DNA Origami Design

Abstract

This work investigates the use of a coding agent to design and manipulate DNA origami structures through the caDNAno2 design interface. The design methodology produced by the agent is saved as transferable, repeatable text-file instructions interpretable by another coding agent, converting informal domain expertise into formalized, distributable protocols. We demonstrate this through a parametric pipeline for simple single and multi-layer designs, identifying several failure modes that each required explicit domain knowledge from the human designer. Once encoded, this knowledge enabled the agent to autonomously extend designs to arbitrary lattice dimensions, generate structures to physical specifications, execute targeted edits from natural language prompts, and run the full pipeline from design through molecular dynamics simulation.