An analysis on the effect of layer number on the stability of thin DNA origami nanopores

Purpose - The present study aims to design and simulate various types of deoxyribonucleic acid (DNA) origami-based nanopores and explore their stability under different temperatures and constraints. To create DNA origami nanopores, both one-layer and two-layer structures can be utilized. Design/methodology/approach - One of the key applications of DNA origami structures involves the creation of nanopores, which have garnered significant interest for their diverse applications across multiple scientific disciplines. DNA origami nanopores can be studied individually and in combination with other structures. The structural stability of these nanopores across various temperature conditions is crucial for enabling the passage of diverse payloads. Findings - Comparing these DNA origami structures can provide valuable insights into the performance of these nanopores under different conditions. The results indicate that two-layer nanopores exhibit better structural stability under various temperatures compared to one-layer nanopores. Additionally, small structural changes in two-layer nanopores enable them to maintain stability even at high temperatures. Originality/value - In this paper, various DNA origami-based nanopores were designed and simulated, focusing specifically on one-layer and two-layer configurations. The two-layer nanopore consistently exhibited superior stability across both free and restrained scenarios, undergoing fewer structural changes compared to the one-layer nanopore. As temperatures increased, the two-layer nanopore remained less susceptible to deformation, maintaining closer to its original shape. Moreover, in the free scenario, the geometric shape of the two-layer nanopore demonstrated fewer variations than the one-layer nanopore.