Computational protocol: Selective nuclear localization of siRNA by metallic versus semiconducting single wall carbon nanotubes in keratinocytes

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Protocol publication

[…] The secondary and tertiary structure of siRNA was modeled using the software package Assemble []. Secondary structure interactions were determined using RNAplot [], followed by tertiary structure prediction through homology modeling. Two SWNT models were then generated using Visual Molecular Dynamics (VMD) nanotube modeler []. These included: a metallic nanotube (n = 9, m = 9) and a semiconducting nanotube (n = 11, m = 7), both having a diameter of 1.2 nm and length of 50 nm. Each SWNT was placed in a periodic simulation box with dimensions 50 × 50 × 50 nm and solvated for an initial minimization step. Production molecular dynamics runs of a SWNT with 15 gemini surfactant molecules and a single siRNA molecule were then performed using GROMACS 4.5.5 [] and a modified version of the OPLSaa force field accounting for the SWNT carbon and nucleic acid atom parameters. A steepest descents minimization, followed by 10 ns of constant NPT molecular dynamics was then performed. […]

Pipeline specifications

Software tools VMD, GROMACS
Application Protein structure analysis
Organisms Mus musculus
Chemicals Carbon