Nano Archive

Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization

Paliy, Maxim and Melnik, Roderick and Shapiro, Bruce A (2009) Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization. Physical Biology, 6 (4). 046003.

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We study mechanical and thermodynamic properties of RNA nanostructures focusing on a hexagonal nanoring discussed in Yingling and Shapiro (2007 Nano Lett. 7 2328). We are concerned with the following main issues: (i) the stability of the nanoring versus temperature; (ii) the effect of the environment (solvent, counterions) on its stability; (iii) conformations and dynamics under external force. The process of evaporation of the ions from the ring upon temperature drop has been found, demonstrating a surprising feature—the uptake of ions by the nanoring increases with the temperature. The connection of this behavior to the dielectric constant of water, hydration and structural changes in the nanoring is discussed. Several properties of the nanoring, such as elastic and transport coefficients, have been determined. A measure of the tensile elasticity of the ring against its uniform 2D in-plane compression has been given, as K eff ≤ 0.01 GPa, which is a much lower value compared to typical values found for soft matter other than RNA.

Item Type:Article
ID Code:11292
Deposited By:Prof. Alexey Ivanov
Deposited On:01 Nov 2011 23:31
Last Modified:02 Nov 2011 00:47

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