3 April 2015 Studying properties of RNA nanotubes via molecular dynamics
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RNA molecules are very flexible in nature. This feature allows us to build various motifs which are essential in bionanotechnological applications. Based on our earlier developed models of RNA nanoclusters, in this contribution we analyze the structure and properties of RNA nanotubes in physiological solutions at different concentrations. Our major tool here is the molecular dynamics (MD) method that was implemented by using the NAMD and VMD packages, with which we study the structural and thermal properties of the nanotubes in physiological solutions. In particular, 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 radial distribution function (RDF) of a RNA nanotube at different concentrations of the physiological solution. Furthermore, the number of 23Na+ and 35Clions around the nanotubes within the distance of 5 Å at two different concentrations has also been analyzed in detail. It has been found that the number of ions accumulated around the nanotubes within the particular distance is growing by small amount while the concentrations of the 23Na+ and 35Clions are substantially increased.
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Shyam Badu, Shyam Badu, Roderick Melnik, Roderick Melnik, Sanjay Prabhakar, Sanjay Prabhakar, "Studying properties of RNA nanotubes via molecular dynamics", Proc. SPIE 9434, Nanosensors, Biosensors, and Info-Tech Sensors and Systems 2015, 94340E (3 April 2015); doi: 10.1117/12.2087444; https://doi.org/10.1117/12.2087444

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