(189r) Modeling Rosette Nanotubes Using the Martini Forcefield

Modeling Rosette Nanotubes Using the MARTINI Forcefield

Vyshnavi S. Karra, Hicham Fenniri, Francisco R. Hung

Department of Chemical Engineering, Northeastern University

Rosette nanotubes (RNTs) are biocompatible supramolecular nanostructures that are formed via self-assembly of building blocks of Watson-Crick DNA-inspired guanine-cytosine (G∧C) motifs. Similar to the double helix of DNA, hydrogen bonding between the individual motifs lead them to assemble into rings, called rosettes.1,2 A combination of π-π interactions between the rings and hydrophobic effects lead the rosettes to self-assemble into nanotubes. There are 2 types of RNTs, depending on how the nanotube is self-assembled: either the rings are stacked or they are assembled into helical coils. Because of its biocompatibility, RNTs have attracted attention for drug delivery and biological applications, such as encapsulating dexamethasone to enhance cell growth in bones.3 However, a fundamental understanding of the interactions of RNTs with cell membranes, proteins and other biomolecules could lead to the development of optimal RNTs for drug delivery and other applications. For example, nanotubes tend to “stick” to the blood vessel walls at higher probabilities than spherical nanoparticles, making them more difficult to implement as drug carriers.4 Using the MARTINI force-field,5 we are developing a coarse-grained model of these RNTs. Here, we present details of our model of the G∧C motifs, and report classical molecular dynamics simulations of individual motifs, rosettes and small RNTs in polarizable water. There are 2 main objectives of these MARTINI simulations: 1) to fine-tune the interactions between the different species in our systems, and 2) to assess the stability of the assembled structures. Results will be compared against existing atomistic simulations and experimental data.

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