Nanopores have emerged as versatile tools for the modification and analysis of single molecules. The use of DNA origami nanostructures, combined with solid-state nanopores, significantly enhances the practical and operational capabilities of these systems. The process of physical and chemical identification of molecules in nanopores always relies on the passage of ionic currents. DNA origami nanopores can undergo changes under ionic current conditions, potentially affecting their final performance. Therefore, investigating the stability and structure of DNA origami nanopores in the presence of ionic currents is crucial for their application in biomolecule identification. In this article, the computational electrophysiology method has been employed to investigate and analyze the structure of single-layer and double-layer nanopores. Initially, the effects of the potential field governing the system, induced by charge differences, on the nanopore were examined. Subsequently, the impact of ion concentration was studied. The results demonstrate a direct relationship between the structural changes of the nanopores and the magnitude of the charge difference governing the system, whereas this relationship is inverse concerning the ion concentration in the system. Given the differences between the two structures, it can be concluded that the single-layer nanopore exhibits greater structural stability.
Keywords: DNA origami nanopore; charge imbalance; ion concentration; ionic conductivity; potential difference.