(660f) Developing a Martini Coarse-Grained Model for Rosette Nanotubes

Rosette nanotubes (RNTs) are biocompatible supramolecular nanostructures formed via self-assembly of Watson-Crick DNA-inspired guanine-cytosine (G∧C) building block motifs. Similar to DNA’s double helix, hydrogen bonding between the individual motifs allow for self-assembly 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. Therefore, there are 2 configurations of RNTs: either the rings stack or they assemble into helical coils. Due to its biocompatibility, RNTs have been utilized for drug delivery and biological applications, such as encapsulating dexamethasone to enhance cell growth in bones.3 More recently, RNTs have showed potential in selective transport of ions through lipid bilayers and as single-molecule sensors.4 However, a fundamental understanding of the interactions of RNTs with various biomolecules could lead to the development of optimal RNTs for these applications. In this work we are developing a coarse-grained model of these RNTs based on the MARTINI force-field,5 reparameterized against all-atom potential of mean force (PMF) calculations and introducing a partial charge to some of the MARTINI beads. Here, we present the progress in developing our coarse-grained model of the G∧C motifs, by reporting classical molecular dynamics simulations of individual motifs, rosettes and small RNTs, with a goal of studying drug delivery,3 selective transport of ions and single-molecule sensing.4

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1. J. Uusitalo, H. Ingólfsson, P. Akhshi, D. Tieleman, and S. Marrink. J. Chem. Theory Comput., 2015, 11, 3932–3945.