Computer-Aided Design Software and Simulation Tools for DNA Nanoparticles

DNA nanostructures, particularly DNA origami nanoparticles, have been increasingly employed as structural constituents for sophisticated applications in materials science, therapeutics, drug discovery and delivery, as well as oncology treatment. DNA origami must be meticulously designed, simulated, and synthesized for verification prior to any viable applications. To facilitate this procedure, computer-aided design software and simulation tools have been developed to mitigate the constraints of the manual design methodology. Consequently, this study offers a thorough examination of the evolution of computer-aided design software and simulation tools for DNA nanoparticles in a chronological framework. In this review, design methodologies are categorized into bottom-up and top-down strategies, and organized into related families such as tile-based or frame-based architectures. Simulation methodologies are categorized based on simulation models, encompassing finite element models and coarse-grained models for molecular dynamics simulations at varying resolutions. This investigation not only delivers an overview of over four decades of software advancement for DNA nanostructures but also presents the prospects for future requirements, including the automation of the design and simulation of DNA nanoparticles into a unified platform and the application of the progress in deep learning, which undoubtedly conserves substantial time and effort both in silico and in vitro.