Simulations of Electrophoretic RNA Transport Through Transmembrane Carbon Nanotubes

Computational Science and Engineering Laboratory, ETH Zürich, Switzerland.
Biophysical Journal (Impact Factor: 3.97). 05/2008; 94(7):2546-57. DOI: 10.1529/biophysj.106.102467
Source: PubMed


The study of interactions between carbon nanotubes and cellular components, such as membranes and biomolecules, is fundamental for the rational design of nanodevices interfacing with biological systems. In this work, we use molecular dynamics simulations to study the electrophoretic transport of RNA through carbon nanotubes embedded in membranes. Decorated and naked carbon nanotubes are inserted into a dodecane membrane and a dimyristoylphosphatidylcholine lipid bilayer, and the system is subjected to electrostatic potential differences. The transport properties of this artificial pore are determined by the structural modifications of the membrane in the vicinity of the nanotube openings and they are quantified by the nonuniform electrostatic potential maps at the entrance and inside the nanotube. The pore is used to transport electrophoretically a short RNA segment and we find that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and unstacking process, affected by steric interactions with the membrane headgroups and by hydrophobic interaction with the walls of the nanotube. The RNA is structurally reorganized inside the nanotube, with its backbone solvated by water molecules near the axis of the tube and its bases aligned with the nanotube walls. Upon exiting the pore, the RNA interacts with the membrane headgroups and remains attached to the dodecane membrane while it is expelled into the solvent in the case of the lipid bilayer. The results of the simulations detail processes of molecular transport into cellular compartments through manufactured nanopores and they are discussed in the context of applications in biotechnology and nanomedicine.

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Available from: Petros Koumoutsakos
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    • "However, these coarse grained models are subject to periodic boundary conditions (BCs). Non-periodic BCs are often more appropriate in cases where the nanoscale domain interfaces a microscale flow or in cases where biomolecules are transported electrophoretically through membranes [2]. An approach is thus needed to couple mesoscopic descriptions to continuum ones. "
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    • "Very recently, the CNT was used to transport a short RNA segment and it was found that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and un-stacking process, affected by steric interactions with the membrane head groups and by hydrophobic interaction with the walls of the CNT[37]. Figure 5 The structure of nanotube-water model. "
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