Ordered self-assembly of DNA-modified nanoparticles in salt solutions

DNA-modified nanoparticles (DNA-NPs) have been widely applied in medical diagnosis and biosensors. Molecular dynamics (MD) simulation, a common method to track the dynamic changes of ions, nanoparticles and DNA, is able to predict the assembly behavior of DNA-NP, thus providing a fast and efficient method for precise regulation of experiments. At present, the simulation research of the DNA-NP self-assembly mainly focuses on DNA bonding, while the effects of electrostatic interactions between DNA and DNA, ions and ions, ions and DNA on the self-assembly structure and mechanism have not been systematically studied. We have constructed a coarse-grained model of DNA-NP self-assembly in salt solutions to appropriately simulate the experimental conditions. It can well match the directionality and saturation of DNA base pairing, as well as the electrostatic repulsive interactions between DNA, and ion-related effects. How the distribution of ions, electrostatic shielding and DNA hybridization regulate the assembled structure and kinetic properties of DNA-NP in monovalent or divalent salt solutions with different ionic concentrations are deeply investigated. Our simulated results reveal the thermodynamic stability and reversibility of the ordered self-assembly of DNA-NPs, in accordance with experimental results. They also provide a reasonable explanation for the susceptibility of nanoparticles to aggregation at high salt concentration for multivalent salt environments. Our research gives a preliminary attempt for the simulation of DNA-NP self-assembly in salt solution, provides theoretical guidance for designing DNA nanomaterials with controllable structures and properties, and promotes its research progress in the fields of medical diagnosis and biosensors.