Maxim Paliy et al 2009 Phys. Biol. 6 046003 doi:10.1088/1478-3975/6/4/046003
Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization
Maxim Paliy1,3, Roderick Melnik1,3 and Bruce A Shapiro2
Show affiliationsWe 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 Keff ≤ 0.01 GPa, which is a much lower value compared to typical values found for soft matter other than RNA.
- PACS
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87.15.H- Dynamics of biomolecules
- Subjects
- Dates
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Issue 4 (December 2009)
Received 7 July 2009, accepted for publication 13 August 2009
Published 10 September 2009
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Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization
Maxim Paliy et al 2009 Phys. Biol. 6 046003
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