Vibrational characteristics of DNA nanostructures obtained through a mass-weighted chemical elastic network model

Abstract

Using the programmable and self-assembly characteristics of DNA, various DNA nanostructures have been designed and synthesized for specific applications, such as nanomachinery and chemical/biological sensors. Although their physical features and feasibility in engineering applications can be conjectured using experimental techniques such as atomic force microscopy and Raman spectroscopy, their vibration characteristics at low frequency states, which are the most dominant factors that determine their structural functions, are difficult to observe experimentally because it is almost impossible to capture the real-time atomic motion of DNA nanostructures. Here, we propose a novel method to elucidate the vibration characteristics of DNA nanostructures in atomic detail using a normal mode analysis based on a mass-weighted chemical elastic network model (MWCENM). Because the MWCENM is a precise method for modeling molecular structures that considers both chemical bond information and inertia effects, it can calculate both vibration frequencies and the corresponding mode shapes in atomic detail. In terms of vibration frequencies, our simulation results show good agreement, within an error deviation of 4.0%, with experimental data measured by Raman spectroscopy. Therefore, the proposed theoretical approach is a feasible method for understanding DNA nanostructure's vibration characteristics, including both frequencies and mode shapes, in atomic detail, adding to the molecular fingerprint provided by the conventional Raman spectrum.