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.