Rational Design of DNA Nanocarriers via Sequence and Length Modulation of Linker and Lock Domains: Insights from Coarse-Grained Simulations

Abstract

DNA origami nanocarriers offer programmable architectures for targeted molecular delivery, yet the interplay between lock design, linker composition, and global conformation remains poorly understood. Here, we employ coarse-grained oxDNA and hybrid ANM–oxDNA simulations to elucidate how these structural parameters collectively govern the stability and release dynamics of a thrombin-loaded DNA nanocarrier. Systematic temperature-dependent simulations reveal that lock stability scales strongly with duplex length—short locks (3–4 bp) dissociate spontaneously under mild thermal conditions, whereas longer locks (≥ 6 bp) remain tightly closed, requiring external activation for release. The kinetics of cargo release follow a thermally activated profile, with release times decreasing exponentially with temperature and reflecting cooperative effects among multiple linkers. Sequence composition further modulates this behavior: A–T linkers destabilize readily through weak bonding and slip, C–G linkers are stronger but prone to misalignment, and mixed linkers suppress slip to achieve maximal stability. Together, these findings provide a coarse-grained framework for the rational design of DNA-based nanocarriers, highlighting how lock length, sequence composition, and collective linker mechanics can be tuned to achieve thermally responsive yet mechanically robust DNA–protein assemblies.