Effect of Gold Nanoparticle Size and DNA Concentration on DNA-Nanoparticles Complexation: A Molecular Dynamics Study

Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Although different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, their role in the stability and packaging of AuNP-DNA complex remains unclear. In this study, we employ all-atom molecular dynamics simulations to investigate the influence of cationic ligand-functionalized AuNP (CAuNP) size and CAuNP-to-DNA ratio on DNA wrapping and binding affinity. The obtained results show that a single DNA interacting with smaller CAuNPs exhibits greater bending and wrapping due to their higher curvature. However, when two DNAs bind to smaller CAuNPs, electrostatic repulsion prevents the effective wrapping, which leads the DNAs to twist from their original orientation. Such behavior is not observed with larger CAuNPs since their increased size may mitigate repulsive forces. Further, the analysis on axial bending angle reveals that smaller AuNPs induce sharper DNA bending and larger AuNPs promote smoother bending. In addition, the potential of mean force (PMF) analysis confirms a stronger DNA binding affinity for larger AuNPs, with affinity decreasing when two DNAs attach to a single CAuNP. Our results from the DNA loading capacity calculations provide insights into the maximum number of DNA molecules that can be loaded onto CAuNPs of a given size. These findings offer key insights into optimizing the size of AuNP and DNA-to-AuNP ratios for the development of efficient gene delivery systems.