Atomistic insights into the mechanisms of DNA binding by atomically precise gold nanoclusters †

Monolayer-protected atomically precise gold nanoclusters (MPCs) have emerged as versatile soft nanomaterials for biointerfacing applications; however, the physicochemical principles governing their interactions with nucleic acids remain poorly understood due to the inherent complexity of the MPC-DNA interactions mediated by MPC's size and ligand functionalization. Here, we combine atomistic molecular dynamics with deep collective variable-based on-the-fly probability-based enhanced sampling (OPES) simulations to elucidate the binding mechanism of positively-charged guanidinium-based ligand functionalized gold nanocluster, Au 25 (S(CH 2) 2 (Gdm)) + 18 , to DNA and calculate the underlying free energy surfaces. MPC's attachment to the DNA is primarily governed by electrostatic interactions between guanidinium-functionalized ligands and DNA phosphate groups. Additionally, we found that the removal of interfacial water molecules facilitates the MPC binding process. Free-energy landscapes uncover the binding pathways with a pronounced preference for the MPC's binding to the major groove arising from favorable steric accommodation, ligand reorganization, and facile 1 water removal. Our results provide molecular-level insight into MPC-DNA recognition and establish enhanced sampling as a powerful framework for understanding nanocluster-nucleic acid interactions.