Chongbo Sun

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.

A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation

Polycations have been explored as non-viral carriers for effective delivery of small interfering RNA (siRNA). Modifying polycations such as polyethylenimine (PEI) with lipid substitution was found to improve the siRNA delivery efficiency of polycationic carriers. However, the role of such lipid modification is not clear and remains to be probed at the atomistic level. In this work, we elucidate the role of lipid modification through a series of all-atom molecular dynamics simulations on siRNA complexation mediated by a native PEI and four analogous obtained by different lipid modifications. The lipid modification does not affect PEIs capability of neutralizing the siRNA charge, neither does it affect the polyion bridging which plays an important role in siRNA complexation. Significant linkages among the lipid modified PEIs via association of lipid side-groups are observed and this results in more stable and compact PEI/siRNA polyplexes. The lipid associations between short lipids form and break frequently while the lipid associations between long lipids are more stable. For PEIs modified with short lipids, increasing the lipid substitution level results in more compact and stable siRNA structure. For PEIs modified with long lipids, increasing the lipid substitution does not change the amount of PEI linkage via lipid association, and has a reverse effect on compacting siRNA structure due to increased steric hindrance brought by the lipid association on individual PEIs. The simulation results generally correlate well with experimental data and suggest a framework of designing and systematic evaluation of polycation-based siRNA carriers using molecular dynamics simulations.

Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation

A series of all-atom molecular dynamics (MD) simulations of the complexation between DNA and 2 kDa branched and linear polyethylenimines (PEIs) are reported in this study. The simulations revealed distinct binding modes of branched and linear PEIs to DNA, with branched PEIs adhering to the DNA surface like beads and linear PEIs adhering to the DNA surface like cords. The dynamics of each PEIs binding state to the DNA during the simulations and how the PEIs neutralize the DNA were quantified. For both branched and linear PEIs, the addition of salt ions similar to physiological conditions were found to have only a small effect on DNA/PEI complexation compared to salt-free conditions. The simulation results reported here will be helpful to understand the mechanism of action for the PEI-based gene carriers.

Potential of mean force of polyethylenimine-mediated DNA attraction.

The aggregation of DNA molecules induced by cationic polymers is of importance to applications in gene delivery. In this work, we performed a series of umbrella sampling molecular dynamics simulations to calculate the potential of mean force (PMF) between two DNA molecules in the presence of polyethylenimine (PEI) molecules using the weighted histogram analysis method. The distance between the centers of mass of the two DNAs was chosen as the reaction coordinate, and the location and depth of the global minimum in the PMF curve were used to gauge the compactness and stability of the formed aggregate. The effects of PEI to DNA charge ratio (N/P charge ratio) and protonation state of the PEI were investigated. The DNA aggregation was found to be more favorable at higher PEI/DNA charge ratios and higher PEI protonation ratios. As compared with small multivalent ions, PEIs give rise to stronger DNA attraction even with an N/P charge ratio at which the DNAs are overneutralized. The effect of changing the protonation ratio on the compactness of the aggregate is more prominent than changing the N/P charge ratio, while the depth of the PMF well is more strongly influenced by the N/P charge ratio.

Probing the effects of lipid substitution on polycation mediated DNA aggregation: a molecular dynamics simulations study.

Understanding the molecular mechanism of DNA aggregation and condensation is of importance to DNA packaging in cells, and applications of gene delivery therapy. Modifying polycations such as polyethylenimine with lipid substitution was found to improve the performance of polycationic gene carriers. However, the role of the lipid substitution in DNA binding and aggregation is not clear and remains to be probed at the molecular level. In this work, we elucidated the role of lipid substitution through a series of all-atom molecular dynamics simulations on DNA aggregation mediated by lipid modified polyethylenimine (lmPEI). We found that the lipids associate significantly with one another, which links the lmPEIs and serves as a mechanism of aggregating the DNAs and stabilizing the formed polyplex. In addition, some lipid tails on the lmPEIs stay at the periphery of the lmPEI/DNA polyplex and may provide a mechanism for hydrophobic interactions. The enhanced stability and hydrophobicity might contribute to better cellular uptake of the polyplexes.

Structure of a polyelectrolyte around an electronically responsive cylinder.

The structure of a polyelectrolyte (PE) around a rigid cylinder is studied by considering the electrostatic and van der Waals interactions between them. The PE is represented by a helix of discrete charges. The cylinder core is allowed to be conducting or dielectric and responds to the external charges electronically. Approximating the cylinder surface locally as a half space, the electrostatic free energy of the PE-cylinder complex is obtained in closed form by solving the Debye-Hückel equation. We show that the competition between the van der Waals adhesion and the electrostatic repulsion between charges can result in an optimal wrapping geometry. The dependence of the optimal geometry on the salt concentration of the solution is demonstrated to be sensitive to the nature of the cylinder. In particular, it is shown that the salt concentration has a strong influence on the optimal geometry for a dielectric cylinder, while it hardly affects that for a conducting cylinder.

Lipid-Modified Polyethylenimine-Mediated DNA Attraction Evaluated by Molecular Dynamics Simulations

The effect of lipid modification on polyethylenimine (PEI)-mediated DNA attraction was studied by performing umbrella sampling molecular dynamics simulations that involved PEIs modified with three different types of lipids: oleic acid (OA), linoleic acid (LA), and caprylic acid (CA). The potential of mean force between two DNA molecules in the presence of these lipid-modified PEIs was calculated using the weighted histogram analysis method, and it predicted the stability and size of the DNA aggregate. When compared to native PEI, lipid modification was found to enhance the stability of DNA aggregation in the case of long lipids (LA and OA) but reduce the stability in the case of a short lipid (CA). In addition, LA-substituted PEI was shown to form stronger DNA aggregate than OA-substituted PEI, which correlates positively with previous experimental observations.

Molecular Dynamics Simulations of Polyplexes and Lipoplexes Employed in Gene Delivery

Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Delivery of genetic materials into patient cells is limited since nucleic acids are vulnerable to degradation in extra- and intra-cellular environments. Design of delivery vehicles can overcome these limitations. Polymers and lipids are effective non-viral nucleic acid carriers; they can form stable complexes with nucleic acids known as polyplexes and lipoplexes. Despite the great amount of experimental work pursued on polymer or lipid based gene delivery systems, detailed atomic level information is needed for a better understanding of the roles the polymers and lipids play during delivery. This chapter will review molecular dynamics simulations performed on polyplexes and lipoplexes at critical stages of gene delivery. Interactions between various carriers and nucleic acids during the formation of polyplexes/lipoplexes, condensation and aggregation of nucleic acids facilitated by the carriers, binding of the polyplexes/lipoplexes to cell membrane, as well as their intracellular pathway are reviewed; and the gaps in the theoretical field are highlighted.