Nanobubbles in Solid-State Nanopores

Smeets, Ralph M. M.; Keyser, Ulrich F.; Wu, Meng Yue; Dekker, Nynke H.; Dekker, Cees

doi:10.1103/physrevlett.97.088101

Cited by 140 publications

(153 citation statements)

References 20 publications

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“…This example might have some relevance for the modeling of solutes or cavities (e.g. nanobubbles) confined to one-dimensional channels or nanotubes in electrolyte solutions [21,22]. The calculations for this model system show that our main results are correct in form and do not depend on dimensionality.…”

Section: Introductionmentioning

confidence: 58%

Electrostatic Free Energy and Its Variations in Implicit Solvent Models

et al. 2008

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A mean-field approach to the electrostatics for solutes in electrolyte solution is revisited and rigorously justified. In this approach, an electrostatic free energy functional is constructed that depends solely on the local ionic concentrations. The unique set of such concentrations that minimize this free energy are given by the usual Boltzmann distributions through the electrostatic potential which is determined by the Poisson-Boltzmann equation. This approach is then applied to the variational implicit solvent description of the solvation of molecules McCammon, Phys. Rev. Lett., 96, 087802, 2006, and J. Chem. Phys., 124, 084905, 2006]. Care is taken for the singularities of the potential generated by the solute point charges. The variation of the electrostatic free energy with respect to the location change of solute-solvent interfaces, i.e., dielectric boundaries, is derived. Such a variation gives rise to the normal component of the effective surface force per unit surface area that is shown to be attractive to the fixed point charges in the solutes. Two examples of applications are given to validate the analytical results. The first one is a one-dimensional model system resembling, e.g., a charged solute or cavity in a one-dimensional channel. The second one, which is of its own interest, is the electrostatic free energy of a charged sphercal solute immersed in an ionic solution. An analytical formula is derived for the Debye-Hückel approximation of the free energy, extending the classical Born's formula to one that includes ionic

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Section: Introductionmentioning

confidence: 58%

Electrostatic Free Energy and Its Variations in Implicit Solvent Models

et al. 2008

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“…Laser light has been identified as a source of low frequency noise and variation in ionic current through silicon nitride nanopores. 21 Another challenge introduced in our geometry is the pausing during DNA translocation. Figure 4 shows several individual traces of this translocation process.…”

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confidence: 99%

Controlling DNA Capture and Propagation through Artificial Nanopores

et al. 2007

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Electrophorescing biopolymers across nanopores modulates the ionic current through the pore, revealing the polymer's diameter, length, and conformation. The rapidity of polymer translocation (∼30 000 bp/ms) in this geometry greatly limits the information that can be obtained for each base. Here we show that the translocation speed of λ-DNA through artificial nanopores can be reduced using optical tweezers. DNAs coupled to optically trapped beads were presented to nanopores. DNAs initially placed up to several micrometers from the pore could be captured. Subsequently, the optical tweezers reduced translocation speeds to 150 bp/ms, about 200-fold slower than free DNA. Moreover, the optical tweezers allowed us to "floss" single polymers back and forth through the pore. The combination of controlled sample presentation, greatly slowed translocation speeds, and repeated electrophoresis of single DNAs removes several barriers to using artificial nanopores for sequencing, haplotyping, and characterization of protein−DNA interactions.The characterization of single biopolymers is one of the potential applications of artificial nanopores 1,2 and nanochannels. [3][4][5] For example, artificial nanopores have been proposed as tools for rapid DNA sequencing. 1,2,[6][7][8][9][10] This approach is based on the modulation of the ionic current through the pore as a polymer traverses it, revealing the polymer's diameter, length, and conformation.1,2,6-10 A roadblock to single base resolution in such nanopore-based DNA sequencing approaches is a lack of control over translocation speeds. Speeds can be reduced by lowering the ionic strength or the driving voltage, 11 but this comes at the cost of decreased ionic current, reducing the signal-to-noise ratio.The widespread use of optical tweezers in single-molecule biophysics suggests their utility to control sample presentation to a pore or channel, reduce polymer propagation speeds without impairing ionic currents, and to repeatedly characterize one DNA molecule. The integration of optical trapping with synthetic nanopore translocation experiments was first demonstrated by Keyser et al. 12 These authors used optical force measurement to calculate the electrical force exerted on a DNA molecule in a nanopore as well as the effective charge of a DNA molecule in a nanopore. Here we extend their results by showing that this geometry can be used to reduce translocation rates by several hundred-fold and also repeatedly translocate and retract a single DNA.Optical tweezers are routinely used to study mechanical properties of biopolymers (for a review, see ref 13; the details of our optical tweezers instrument are described in ref 14 and in the Supporting Information). Typically, a molecule is connected by complementary chemistry to a micrometer-scale bead that can be manipulated in three dimensions by one or more highly focused laser beams. In our experiment, λ-DNAs were connected to 10 µm polystyrene beads via streptavidin-biotin linkage. As shown in the chamber schematic ( Figure...

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“…Hence, a thickness of few tens of nanometers provides a compromise between resolution and stability; this may partially explain why most of the conventional nanopores in solid state materials [35][36][37][38] have been sculpted in membranes with a thicknesses of ≈20 nm. The introduction of interfacial nanopores dramatically shifts this compromise: here the effective thickness of a nanopore with h = 100 nm is just ≈1.7 times higher than that of h = 4 nm; hence much thicker nanopores can be chosen without losing the resolution considerably.…”

Section: Bionanotechnologymentioning

confidence: 99%

Zero‐Depth Interfacial Nanopore Capillaries

et al. 2018

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Charged molecules can translocate through the nanopore. The instant passage of the molecule momentarily impacts the conductance by locally reducing the aperture size of the channel. The resulting variations of the ionic conductance depends on the local topology of the translocating molecule; particularly, portions of long chain molecules such as polymers, proteins or DNA mark the electronic readout with specific conductance blockade fingerprints, and ultimately allow for reconstructing the sequence of monomers composing the translocating strands. [10] Consequently, thinner pores, i.e., capillaries with shorter channels, are capable of resolving shorter portions of molecules, leading for instance toward highresolution sequencing devices. [1] Thus, the challenge toward high-resolution sequencing has driven the development of ultrashort channel nanopores. Historically, two major classes of nanopores, i.e., biological and solid state nanopores, have been considered. The thickness of these nanopores varies from a few nanometers, as for α-hemolysin biological nanopores, [11,12] up to tens of nanometers for solid-state nanopores. [13] A revolutionary breakthrough aiming at reducing the capillary length of nanopores was achieved by the introduction of 2D materials such as graphene, [14][15][16] hexagonal boron nitride, [17] and molybdenum disulfide. [18][19][20][21] Indeed, the monoatomic capillary length of 2D nanopores is expected to offer sequencing capabilities, [2] but has not been realized yet. Inferior mechanical stability is one of the downsides of thin membranes inherently limiting the sustainability of 2D nanopores. Moreover, the complex fabrication process, involving cleanroom facilities and electron beam lithography, [22][23][24] can be demanding to scale up to industrial production. The noise levels in such devices are also orders of magnitude higher than those for long capillary-based nanopores, thus hindering their application for sequencing. [25] To address these issues, we introduce the concept of interfacial nanopores, generated at the crossing of two trenches, as illustrated in Figure 1. Fundamentally, the cross-section of two 1D straight lines is a zero-dimensional entity defined as a point (Figure 1a). The addition of a second dimensionality implies the overlap of two components to become a surface (Figure 1b). Similarly, in a 3D space, the interface shared between two tangent rectangular parallelepipeds is a surface, hence mathematically 2D (Figure 1c). Unlike nanopores commonly fabricated in 2D materials-which notwithstanding still possess a finite thickness-the surface defined by the crossing parallelepipeds is strictly 2D and thus does not exhibit any thickness. A High-fidelity analysis of translocating biomolecules through nanopores demands shortening the nanocapillary length to a minimal value. Existing nanopores and capillaries, however, inherit a finite length from the parent membranes. Here, nanocapillaries of zero depth are formed by dissolving two superimposed and crossing metallic nanoro...

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Nanobubbles in Solid-State Nanopores

Cited by 140 publications

References 20 publications

Electrostatic Free Energy and Its Variations in Implicit Solvent Models

Electrostatic Free Energy and Its Variations in Implicit Solvent Models

Controlling DNA Capture and Propagation through Artificial Nanopores

Zero‐Depth Interfacial Nanopore Capillaries

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