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Modeling of RNA Nanotube using Molecular Dynamics Simulation



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PIRSA Number: 
14050058

Abstract

We construct the novel RNA nanpclusters- the RNAnanotubes made of several nanorings. We study the struc-tural properties (i.e. the Root Mean Square Deviation (RMSD)the radius of gyration and radial distribution function) ofRNA nanotube up to the size of about 20nm in physilogicalsolution that can be used for drug delivery into human body.We model RNA nanotube by utilizing molecular dynamicssimulation method implemented in NAMD and VMD. Thepatterns of energy and temperature variations of the systemsare also discussed. Furthermore we study the number of ionsaround the tube as a function of time at a particular temper-ature. We find that if the temperature increases the numberof ions increases within certain distance of the tube. We re-port that the number of ions within a certain distance aroundthe tubes decrease in quenched run. This indicates that someions evaporate with decrease in temperature a