Coupled rings in rna nanotubes and properties of biological nanoclusters

Abstract

In this contribution, we study biological nanoclusters where the coupling between their parts is essential. The main focus is on the RNA-based nanostructures. RNA molecules are very flexible in nature. This feature allows us to build various motifs which are indispensable in bio- nanotechnological applications. Based on the previous studies on RNA nanoclusters, in this contribution we analyze the structure and properties of RNA nanotubes, where we focus on nanotubes consisting of a series of coupled nanorings of around 20nm in diameter. We did a molecular dynamics (MD) simulation using CHARMM force field implemented in the NAMD package to study the structural and thermal properties of the nanotube in physiological solutions. Specifically, we have studied the behavior of these nanoclusters in solutions of NaCl, MgCl2 and KCl. We have analyzed such characteristics as the Root Mean Square Deviation (RMSD), the radius of gyration, the number of hydrogen bonds per base pairs, and the ionic distribution around the surface of the RNA nanocluster under study in different solutions. The variation of energy and temperature with simulation time have also been studied for all sets of simulations. The change in these features with the nature of solution has also been studied.