Molecular dynamics simulations of DNA/PEI complexes: effect of PEI branching and protonation state

Complexes formed by DNA and polyethylenimine (PEI) are of great research interest because of their application in gene therapy. In this work, we carried out all-atom molecular dynamics simulations to study eight types of DNA/PEI complexes, each of which was formed by one DNA duplex d(CGCGAATTCGCG)(2) and one PEI. We used eight different PEIs with four different degrees of branching and two protonation ratios of amine groups (23% and 46%) in the simulations to investigate how the branching degree and protonation state can affect the binding. We found that 46% protonated PEIs form more stable complexes with DNA, and the binding is achieved mainly through direct interaction between the protonated amine groups on PEI and the electronegative oxygens on the DNA backbone, with some degree of interaction with electronegative groove nitrogens/oxygens. For the 23% protonated PEIs, indirect interaction mediated by one or more water molecules plays an important role in binding. Compared with the protonation state, the degree of branching has a smaller effect on binding, which essentially diminishes at the protonation ratio of 46%. These simulations shed light on the detailed mechanism(s) of PEI binding to DNA, and may facilitate the design of PEI-based gene delivery carriers.