Electrostatic action promotes bonding efficacy of DNA-modified nanoparticle self-assembly in solution

Abstract

Our study aims to develop a foundational framework for simulating DNA-modified nanoparticle (DNA-NP) self-assembly in salt solutions, focusing on electrostatic and bonding interactions. We employ a sophisticated coarse-grained model to explore bonding efficacy and thermodynamic analysis across various density systems by molecular dynamics method. Notably, in low-density systems, bonding percentage p_h is minimal at T = 1.2. By increasing cation concentration c⁺, controlling temperature, optimizing grafting number n and linker length, p_h can be significantly improved. For instance, at c⁺ = 0.5, the maximum p_h reaches 0.4 for n = 60, surpassing that for n = 100. Although higher DNA loadings can significantly influence nanotherapeutics and biological detection, an optimal grafting number (n = 60) is crucial for peak bonding efficacy at temperatures T = 1.08 ∼ 1.23. The peak value p_{h, max} is observed near t = 3 × 10⁶. The required bonding strength varies depending on the application field. For crystalline lattice formation, optimal linker length n_l is equal to 3. For probes or medical diagnostics, longer linker chains is recommended to enhance bonding strength and probe sensitivity. In higher density systems, there exist different optimization conditions. These insights are valuable for rational design of DNA-NP for targeted drug delivery and diagnostics among other biomedical applications.