Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes.

Computational Science and Engineering Laboratory, ETH Zürich, Switzerland.
Biophysical Journal (Impact Factor: 3.83). 05/2008; 94(7):2546-57. DOI: 10.1529/biophysj.106.102467
Source: PubMed

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 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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    ABSTRACT: I. Introduction Ever since the unravelling of the double helix structure of DNA, the molecule has been considered as the building block of biological organisms. Because DNA is the agent that carries genetic information from one generation to the next, the knowledge of its physical and chemical properties is of paramount importance. Much of that information has to do with the way the nucleobases (NBs)—DNA's own building blocks—interact with their surrounding environment. Owing to their nanoscale dimensions, carbon nanotubes are able to selectively interact with DNA almost at the atomic level: homo- and heteropolymer ssDNA will readily adsorb onto the external walls of small diameter SWCNTs,1 according to a p–stacking mechanism of the NBs on the walls. We have already characterized the SWCNTs energetic landscape regarding exo- and endoadsorption, using small probe molecules.2,3 While exoadsorption on small diameter nanotubes (< 1 nm) is reasonably understood, confinement driven adsorption/binding is a phenomenon that remains quite unexplored. Okada4 determined the encapsulation energy of (in vacuum) ssDNA as a function of nanotube diameter, and suggested an intricate relationship between both, particularly in the range 1.25 < D (nm) < 1.8. As far as we are aware, there are no previous studies of intratubularly confined aqueous nucleobases. We shall address this issue using the well-tempered metadynamics scheme proposed by Parrinello,5 estimating the free-energy landscapes associated with the encapsulation process of Adenine (purine) and Thymine (pyrimidine) onto two different diameter (zig-zag) nanotubes, (16,0) with D = 1.25 nm and (23,0) with D = 1.8 nm. These two topologies correspond to the narrowest and largest nanopores obtained by electric-arc discharge.3 Because nanotubes can be electrically charged,6 the effect of charge density will be addressed considering purely hydrophobic solids and nanotubes with electric charges of q = + 0.05 e–/C. Physiological conditions (T=310K) are mimicked by explicitly including H2O molecules and Cl– ions in the calculations. II. Results and Discussion The encapsulation mechanism of both purine- and pyrimidine-types onto hydrophobic SWCNTs is energetically favorable and irreversible during the time windows spanned in the simulations (0.1 s); the resulting NB/SWCNT hybrids exhibit lower free energies compared to the unconfined systems (Fig.1). The highly symmetrical free-energy landscapes obtained are essentially one dimensionally isotropic regarding the x1 order parameter, in direct relationship to the nanotubes quasi 1-D symmetry. Once confined inside the nanotube, a nucleobase can explore a region whose boundaries are comprised between the entrances, 0.15 < x1 (nm) < Lz (where Lz is the SWCNT length), and the inner surface of the wall, never returning to the bulk. It is very interesting to observe that confinement effects are remarkably stronger at the nanopore center, where free energy differences are largest, [ x1, x2](16,0) = (1.1, 0.08) nm and [x1, x2](23,0) = (1.7, 0.08) nm. Independent umbrella sampling calculations identified a unique probability distribution maximum corresponding to a domain comprised between the solid walls and the nanopore center (Fig.2). Once confined, molecules are in direct contact with the walls at a minimum distance of closest approach of 0.26–0.28 nm. No layer of solvent could be observed between hydrophobic slabs. This is due to a robust pi-stacking mechanism of the NB onto the graphitic mesh, leading to strong dispersive energies of interaction with both the (16,0) and (23,0) topologies (Table I). These results have been compared with DFT and experimental data for graphene. Contrary to exoadsorption, intratubular binding affinity increases with nanotube curvature, as a result of enhanced interaction with the wall immediately opposite to the adsorptive one. We have estimated a diameter of D = 2.05 nm above which the SWCNT curvature mimics a flat graphene sheet and confinement effects tend to be negligible. Adenine and thymine evidence similar interaction energies with the hydrophobic nanopores, however, adenine confinement results in slightly favored energetics of ca. 0.9 – 1.4 kJ/mol (Table I). This previously unobserved finding indicate a binding affinity order: purines > pyrimidines. Electrically charged nanotubes evidence a completely different behavior. The narrowest nanopore employed here, (16,0), inhibits encapsulation of either the purine or pyrimidine moiety. Instead, that nanotube favors adsorption at a region very close to the pore entrance as indicated by the probability distribution maxima at W = 0.97 nm and W = 1.04 nm (Fig.2). When the nucleobases are put in contact with the (23,0) solids, several encapsulation/exit events can occur (Fig.3); moreover, the confined systems exhibit lower free energies. The probability distribution curves indicate two maxima: i) close to the pore center, overlapping the one obtained for the corresponding hydrophobic solid, and ii) at the pore entrance. This second region of confinement is energetically less stable than the pore center (Table I), particularly in the case of adenine where deltaE=40 kJ/mol. Because the pyrimidine molecule has a larger dipole moment, its exposure to the bulk solution carries smaller electrostatic penalties, and therefore its location at the pore center is stabilized by only ca. 12 kJ/mol compared to the entrance. Hydrophobic SWCNTs Charged SWCNTs FIGURE 1. Free energy landscapes, F(x1, x2), of the nucleobases in contact with (16,0) and (23,0) nanotubes. The two collective variables, x1 and x2, correspond to the distance between the nucleobase center of mass and the nanotube entrance or geometrical center, respectively, projected along the z-axis. For the hydrophobic solids, the absolute free energy minima at [ x1, x2](16,0) = (1.1, 0.08) nm and [x1, x2](23,0) = (1.7, 0.08) nm coincide almost exactly with the SWCNT center. When the SWCNTs are charged, two free energy minima can be observed: at the nanotube center [ x1, x2](16,0) = (1.09, 0.08) nm and [x1, x2](23,0) = (1.72, 0.08) nm, and at the entrance, [ x1, x2](16,0) = (0.08, 1.08) nm and [x1, x2](23,0) = (0.08–0.33, 1.41–1.70) nm. Note that the nanopore entrances are symmetrical about the SWCNTs center of mass and thus the sets of collective variables are equivalent: [x1, x2](16,0) = (0, 1.1) = [ x1, x2](16,0) = (2.2, 1.1) and [ x1, x2](23,0) = (0, 1.7) = [ x1, x2](23,0) = (3.4, 1.7). FIGURE 2. Potential of mean­­ force (PMF) and probability distribu­tion profiles: black) hydrophobic and red) electrically charged nanotubes. The order parameter, W, corresponds to the absolute distance between the center of mass of the nucleobase and that of the solid. Notice the parallel alignment of the nucleobases with the hydrophobic solid walls and the existence of two maxima in the probability curves for the electrically charged (23,0) nanotubes. FIGURE 3. Distance between a nucleobase and electrically charged SWCNT center: black) adenine, blue) thymine. The distance plateaus at ca. 1nm (16,0) and 1.35nm (23,0) essentially correspond to the nanopore entrances. Table I. Interaction energies between the nucleobases and the carbon nanotubes, Eint= Evdw+ ECoul, where Evdw is the dispersive energy and ECoul corresponds to the electrostatic contribution. Evdw (kJ/mol) ECoul (kJ/mol) Eint(kJ/mol) A T A T A T Unch. (16,0) -83.1 0.1 -82.2 0.1 0.0 0.0 -83.1 -82.2 (23,0) -68.6 0.1 -67.2 0.1 0.0 0.0 -68.6 -67.2 Charged (16,0)a -35.2 0.2 -31.8 0.3 -19.8 0.3 -20.6 0.3 -54.9 -52.3 (23,0)b -65.3 0.1 -51.4 0.3 -38.8 0.2 -37.6 0.3 -104.1 -89.0 (23,0)c -40.6 0.2 -45.8 0.3 -24.2 0.2 -31.4 0.3 -64.7 -77.2 aresults for the (16,0) electrically charged nanotubes correspond to exoadsorbed nucleobases. bconfinement close to the nanopore center and cat the pore entrance References ADDIN EN.REFLIST (1) Johnson, R. R.; Johnson, A. T. C.; Klein, M. L. Nano Letters 2008, 8, 69. (2) Cruz, F. J. A. L.; Mota, J. P. B. Phys. Rev. B 2009, 79, 165426. (3) Cruz, F. J. A. L.; Esteves, I. A. A. C.; Agnihotri, S.; Mota, J. P. B. J. Phys. Chem. C 2011, 115, 2622. (4) Kamiya, K.; Okada, S. Phys. Rev. B 2011, 83, 155444. (5) Barducci, A.; Bussi, G.; Parrinello, M. Phys. Rev. Let. 2008, 100, 020603. (6) Zhao, X.; Johnson, J. K. J. Am. Chem. Soc. 2007, 129, 10438.
    RSC Advances 11/2013; 4:1310. · 3.71 Impact Factor
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    ABSTRACT: Mechanism of ion permeation through an anion-doped carbon nanotube (ANT), a model of ion channel, is investigated. Using this model system, many trajectory calculations are performed to obtain the potential energy profile, in addition to the free energy profile, that enables to separate the energy and the entropic contributions, along the ion permeation. It is found that the mechanism of the transport is governed by the interplay between the energetic and the entropic forces. The rate of the ion permeation can be controlled by changing the balance between these contributions with altering, for example, the charge and/or the length of ANT, which increases the rate of the ion permeation by nearly two orders of magnitude. The dominant free energy barrier at the entrance of ANT is found to be caused by the entropy bottleneck due to the narrow phase space for the exchange of a water molecule and an incoming ion.
    The Journal of Chemical Physics 10/2013; 139(16):165106. · 3.12 Impact Factor
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    ABSTRACT: There is much interest in developing synthetic analogues of biological membrane channels with high efficiency and exquisite selectivity for transporting ions and molecules. Bottom-up and top-down methods can produce nanopores of a size comparable to that of endogenous protein channels, but replicating their affinity and transport properties remains challenging. In principle, carbon nanotubes (CNTs) should be an ideal membrane channel platform: they exhibit excellent transport properties and their narrow hydrophobic inner pores mimic structural motifs typical of biological channels. Moreover, simulations predict that CNTs with a length comparable to the thickness of a lipid bilayer membrane can self-insert into the membrane. Functionalized CNTs have indeed been found to penetrate lipid membranes and cell walls, and short tubes have been forced into membranes to create sensors, yet membrane transport applications of short CNTs remain underexplored. Here we show that short CNTs spontaneously insert into lipid bilayers and live cell membranes to form channels that exhibit a unitary conductance of 70-100 picosiemens under physiological conditions. Despite their structural simplicity, these 'CNT porins' transport water, protons, small ions and DNA, stochastically switch between metastable conductance substates, and display characteristic macromolecule-induced ionic current blockades. We also show that local channel and membrane charges can control the conductance and ion selectivity of the CNT porins, thereby establishing these nanopores as a promising biomimetic platform for developing cell interfaces, studying transport in biological channels, and creating stochastic sensors.
    Nature 10/2014; 514(7524):612-615. · 42.35 Impact Factor

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