SNUPI: A Computational Framework for Rapid Mechanical Analysis of Structured DNA Assemblies

Structural DNA nanotechnology enables the programmable construction of nano- to microscale assemblies with high resolution, yet predicting their mechanical behavior prior to synthesis remains challenging. In this paper, we introduce SNUPI, a computational framework that predicts the shape and mechanical responses of structured DNA assemblies using finite element-based analysis. SNUPI uses design files from caDNAno and performs static analysis, normal-mode analysis, and Langevin dynamics simulations to evaluate equilibrium configurations, dominant deformation modes, thermal fluctuations, and intercalator-induced effects. We demonstrate that SNUPI can offer an efficient and accessible platform for pre- and postsynthetic evaluation, facilitating rational design and analysis of complex DNA architectures.