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Potential of Mean Force of Polyethylenimine Mediated DNA Attraction Open Access


Other title
Potential of mean force
DNA aggregation
Type of item
Degree grantor
University of Alberta
Author or creator
Bagai, Sampada
Supervisor and department
Tang, Tian (Mechanical Engineering)
Examining committee member and department
Long, Rong (Mechanical Engineering)
Uludag, Hasan (Chemical and Materials engineering)
Department of Mechanical Engineering

Date accepted
Graduation date
Master of Science
Degree level
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 the PEI to DNA charge ratio (N/P charge ratio), protonation state of the PEI and lipid modification of PEI were investigated. Compared with small multivalent ions, PEIs give rise to stronger DNA attraction. The DNA aggregation was found to be more favorable at higher N/P charge ratios and higher PEI protonation ratios, with the depth of the PMF well more strongly influenced by the N/P charge ratio. The lipid substitution in the PEI molecules promotes the formation of more stable aggregates in case of long lipids but not in the case of short lipids.
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