Tunable DNA Binding on Graphene Oxide via Polyethyleneimine Topology and Density: Mechanistic Insights for Nonviral Gene Delivery

Abstract

Graphene oxide (GO) functionalized with polyethyleneimine (PEI) is a promising platform for nonviral gene delivery, yet the effects of polymer architecture and surface density on DNA binding remain poorly understood. Here, we use extensive all-atom molecular dynamics (MD) simulations, including free energy calculations, to elucidate how the topology (linear vs. branched) and grafting density of PEI govern DNA adsorption on GO surfaces. By systematically varying the nitrogen-to-phosphate (N/P) ratio through adjustments in surface amine density, we study the direct impact of this parameter on DNA and GO-PEI interactions. In contrast to common understanding, our potential of mean force (PMF) analysis reveals a non-monotonic relationship between PEI coverage and DNA binding affinity, with intermediate densities yielding the strongest yet reversible interactions. This behavior results from a balance between favorable electrostatic and hydrogen bonding interactions and opposing steric and electrostatic repulsion, amplified by ionic screening at higher densities. Radial distribution function (RDF) analysis confirms the formation of dense chloride ion shells at high PEI densities, which inhibit DNA approach by neutralizing surface charge. We also show that topology plays a key role: branched PEI engages DNA more effectively through multivalent interactions within the grooves, while linear PEI binds more diffusely along the phosphate backbone. These mechanistic insights highlight the critical role of polymer structure and coverage in modulating DNA binding, offering design principles for optimizing GO-based gene delivery systems.