DSSNA: Automated Nucleic Acid Structure Analysis in Molecular Dynamics

Abstract

This work presents DSSNA (Define Spatial Structure of Nucleic Acids) v2026, a free and open-source standalone GROMACS module for the automated analysis of nucleic acid structures from atomic coordinates that reproduces the core functionality of X3DNA and DSSR while extending it to the analysis of molecular dynamics (MD) trajectories. The algorithm identifies and classifies canonical and non-canonical base pairs, hydrogen-bond networks, stacking interactions, helices, and other elements of nucleic acid secondary and tertiary structure, using neighbor-search algorithms for efficient analysis of large trajectory datasets and a modular output system that lets users select the structural metrics required for a particular analysis. Application to a 1 s MD trajectory of a GUAA tetraloop mutant of the sarcin--ricin domain of Escherichia coli 23S ribosomal RNA (PDB: 1MSY) showed that persistent canonical base pairs form the structural core that maintains the secondary-structure profile, whereas most non-canonical base pairs and stacking interactions are transient. These results demonstrate that DSSNA enables the characterization of both static nucleic acid structures and the temporal evolution of structural interactions in MD simulations.