Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA

Bidisha Nandy, Prabal K. Maiti, Alexander Bunker

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    18 Citations (Scopus)

    Abstract

    We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

    Original languageEnglish
    Pages (from-to)722-729
    Number of pages8
    JournalJournal of Chemical Theory and Computation
    Volume9
    Issue number1
    DOIs
    Publication statusPublished - Jan 2013
    MoE publication typeA1 Journal article-refereed

    Keywords

    • POLYELECTROLYTE-MACROION COMPLEXATION
    • POLYAMIDOAMINE DENDRIMERS
    • GENE DELIVERY
    • PAMAM DENDRIMERS
    • TRANSFECTION
    • MECHANISM
    • CHARGE
    • CELLS
    • FIELD
    • SOLVENT

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