High Performance Computing Studies of RNA Nanotubes

Based on the previous studies of RNA nanorings, in this contribu- tion we computationally analyze the structure and properties of RNA nanotubes, where we focus on nanotubes consisting of up to five nanorings of around 20nm in diameter. We have developed a molecular dynamics (MD) method and im- plemented it by using the NAMD and VMD packages in a high-performance computing environment to study the structural and thermal properties of the nan- otube in physiological solutions. In particular, we have analyzed such charac- teristics as the Root Mean Square Deviation (RMSD), the radius of gyration, the number of hydrogen bonds per base pairs, and the radial distribution func- tion for the different nanoclusters in nanotubes of various sizes. Due to flexibil- ity of RNA molecules, we can build various motifs which are essential in bio- nanotechnological applications such as scaffolding and drug delivery systems.

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