Molecular Dynamics Simulations of Polyethylenimine Mediated Nucleic Acid Complexation with Implications for Non-viral Gene Delivery

Gene therapy is a promising therapeutic technique that involves delivering nucleic acids into cells. Polycations have evolved into a major category of gene carriers. Polyethylenimine (PEI) is one of the most effective polycationic carriers. Furthermore, modifying PEI with certain lipophilic moieties was found to greatly improve its performance. Despite the great potential of PEI-based carriers, the understanding of complexation of nucleic acids with PEIs is still lacking at the atomistic level. In addition, the mechanisms for the beneficial effects of lipid modification remain unclear and to be probed.;In this dissertation, a series of molecular dynamics simulations were performed to investigate the PEI/nucleic acids complexation. We started our simulations from single DNA interacting with single PEI and investigated eight 600 Da PEIs with four different architectures and at two protonation ratios. We found that for these low molecular weight PEIs, compared with the protonation state, the degree of branching has a smaller effect on binding. We then increased the size of the system to incorporate one DNA with multiple PEIs and increased the molecular weight of the PEIs to 2 kDa. Unlike in the case of 600 Da PEIs, the simulations revealed distinct binding modes of branched and linear PEIs to DNA, demonstrating that the molecular weight of PEI is an important factor in PEI/DNA complexation. Following this simulation, complexation/aggregation of DNA molecules medicated by PEIs was studied by simulating multiple DNA molecules with excessive PEIs. We found that native PEIs condense DNA through two mechanisms - polyion bridging and electrostatic screening of the DNA charges. The effects of lipid substitution on polycation mediated nucleic acids aggregation was then explored by adopting lipid-modified PEIs in the simulations of multiple DNAs and siRNAs complexation. The lipid moieties were found to associate significantly with one another, which provides another mechanism of aggregating nucleic acids and stabilizing the formed polyplexes. The effects of lipid length and substitution level on the formed polyplexes were also investigated. This dissertation will advance the understanding of PEI/nucleic acids polyplexes at atomistic level. Moreover, the methodology adopted suggests a framework for systematically evaluating polycationic carriers using molecular simulations.