Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures

Abstract

We introduce an automated procedure of coarse-grained molecular dynamic simulation for DNA nanostructure that has great potential for realizing molecular robotics. As DNA origami is now a standardized technology to fabricate DNA nanostructures with high precision, various computer-aided design software has been developed. For example, a design tool called caDNAno with a simple and intuitive interface is widely used for designing DNA origami structures. Further, a simulation tool called oxDNA is used to predict the behavior of such nanostructures based on coarse-grained molecular dynamics. These tools, however, are not linked directly; thus, repeating the cycle of design and simulation is cumbersome to the user. Moreover, the computer skills required to setup, launch, and run an oxDNA simulation are a potential barrier for non-experts. In our proposal, oxDNA simulation can be launched on a web server simply by providing a caDNAno file; the web server then analyzes the simulation results and provides a visual response. The validity of the proposal is demonstrated using an example. The advantages of our proposed method compared with other conventional methods are also described. This simple-to-use interface for user-friendly simulation of DNA origami eliminates stress to users and accelerates the design process of complicated DNA nanostructures such as wireframe architecture.