Nanomaterials with bio-recognition properties hold the promise of becoming the key driver for materials science, biomedical engineering, and drug delivery. Currently, very little is known about required surface modification of nanoparticles (NP) that can enhance biorecognition properties. Using all-atom molecular dynamics (MD) simulations, we performed a comprehensive investigation of the binding of ligand-functionalized gold NPs to various nucleic acids, where we systematically changed the net charge and surface chemistry of the nanoparticles. We explored parameters such as NP net charge, polarity, and salt concentration to find ideal conditions for the pairing with nucleic acids. Initially, our group performed extensive implicit solvent simulations, where the solvent is replaced by a dielectric continuum, to study the binding of gold NPs and DNA. Our results in implicit solvent show dramatic changes in DNA structure upon binding, even at a relatively low nanoparticle net charge. The use of GPU-accelerated MD in the AMBER software package has allowed us to simulate these same complexes in explicit solvent and to study the aggregation behavior of nanoparticles. The GPU-enabled results showed drastically different behaviors than observed in implicit solvent and a better agreement with the crystal structure of DNA on histone protein. Here, we present over 25 different NP-nucleic acid systems with varying salt concentration, nucleic acid type, or nanoparticle net charge. Nanoparticles with higher charge caused structural changes in both DNA and RNA. Salt concentration did not have an effect on systems with NPs of lower charge; however, lower salt concentration was associated with greater nucleic acid deformation for NPs with higher charge. The use of GPU-accelerated MD simulations allowed us to develop pseudo-phase diagrams mapping nucleic acid-nanoparticle interactions as a function of different variables.

Gold nanoparticle-nucleic acid modeling using GPU-accelerated molecular dynamics

249th National Meeting (2015)

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