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Potential of Mean Force of Polyethylenimine Mediated DNA Attraction

  • Author / Creator
    Bagai, Sampada
  • 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.

  • Subjects / Keywords
  • Graduation date
    2013-06
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/R3G320
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Master's
  • Department
    • Department of Mechanical Engineering
  • Supervisor / co-supervisor and their department(s)
    • Tang, Tian (Mechanical Engineering)
  • Examining committee members and their departments
    • Uludag, Hasan (Chemical and Materials engineering)
    • Long, Rong (Mechanical Engineering)