Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes

Biophysical Journal
Urs Zimmerli, Petros Koumoutsakos

Abstract

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 ...Continue Reading

References

May 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·S M SimonG F Oster
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
May 31, 2001·Journal of Molecular Graphics & Modelling·B IsralewitzK Schulten
Feb 14, 2002·Trends in Biotechnology·Andrew Pohorille, David Deamer
May 23, 2002·Biophysical Journal·Bert L de GrootHelmut Grubmüller
May 25, 2002·European Biophysics Journal : EBJ·José D Faraldo-GómezMark S P Sansom
Jun 28, 2003·Biophysical Journal·Fangqiang Zhu, Klaus Schulten
Jul 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Amrit KalraGerhard Hummer
Apr 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Aleksij Aksimentiev, Klaus Schulten
Aug 11, 2004·Proceedings of the National Academy of Sciences of the United States of America·In-Chul Yeh, Gerhard Hummer
Sep 4, 2004·Biophysical Journal·Aleksij AksimentievKlaus Schulten
Sep 30, 2004·Angewandte Chemie·Davide PantarottoAlberto Bianco
Feb 22, 2005·Biophysical Journal·Carlos F LopezMichael L Klein
Mar 5, 2005·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·S Moein MoghimiJ Clifford Murray
May 12, 2005·Nano Letters·Gang LuEfthimios Kaxiras
Jun 10, 2005·Nano Letters·Urs ZimmerliPetros Koumoutsakos
Oct 13, 2005·Nano Letters·Jiunn B HengGregory Timp
Nov 4, 2005·Nature·Mainak MajumderBruce J Hinds
Nov 15, 2005·Biophysical Journal·J B HengG Timp
Feb 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Ravi SinghKostas Kostarelos
Feb 25, 2006·Cell·Mark Marsh, Ari Helenius
Apr 4, 2006·Physical Biology·Deyu LuKlaus Schulten
Jun 14, 2006·Proceedings of the National Academy of Sciences of the United States of America·Roderick Y H LimUeli Aebi
Jul 21, 2006·The Journal of Physical Chemistry. B·Deyu LuKlaus Schulten
Feb 15, 2007·Nano Letters·Tighe A Spurlin, Andrew A Gewirth
Feb 27, 2007·Science·Masanori KoshinoEiichi Nakamura
Feb 28, 2006·Nanotechnology·Somenath RoyWonbong Choi

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Citations

Feb 16, 2013·Chemical Reviews·Petr Král, Boyang Wang
Nov 5, 2013·The Journal of Chemical Physics·Takashi SumikamaIwao Ohmine
Jan 1, 2010·Biotechnology & Genetic Engineering Reviews·Babu ManjasettySantosh Panjikar
Mar 5, 2016·ACS Nano·Rebeca Garcia-FandiñoMark S P Sansom
Mar 1, 2009·IEEE Nanotechnology Magazine·Aleksei AksimentievKlaus Schulten
Aug 11, 2015·Langmuir : the ACS Journal of Surfaces and Colloids·Shuang ZhangJingyuan Li
Feb 23, 2013·International Journal of Molecular Sciences·Samaneh MashaghiAlireza Mashaghi
Feb 19, 2013·Small·Mickaël Lelimousin, Mark S P Sansom
Nov 13, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Valery N Kharkyanen, Semen O Yesylevskyy
Feb 12, 2009·Journal of the American Chemical Society·Peng XiuHaiping Fang

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