Paper Citing NAMD - Abstract
Sun, Chongbo; T'ang, Tian; Uludag, Hasan
Molecular Dynamics Simulations of PEI Mediated DNA Aggregation
BIOMACROMOLECULES, 12:3698-3707, OCT 2011
Understanding the molecular mechanism of polycation induced DNA aggregation and condensation is important for optimal design of gene delivery carriers. In this work, we performed a series of all-atom molecular dynamics (MD) simulations to investigate polyethylenimine (PEI) mediated DNA aggregation. We found that PEIs condense DNA through two mechanisms: polyion bridging and electrostatic screening of the DNA charges. At PEI/DNA charge ratio >1, PEIs can completely neutralize DNAs at a short distance (similar to 12 angstrom from the Cl' atoms), and this distance is found to be insensitive tc the exact value of the charge ratio. When excess PEIs are added to a formed DNA-PEI aggregate, they are found to bind to the aggregate and increase its cationic charge. The added PEIs can also replace the PEIs previously bound to the aggregate: The excess PEIs, however, do not change the spacing of the DNAs in the aggregates Our simulation results shed light on the mechanisms of PEI, and more generally polycation, mediated DNA aggregation and condensation.
