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Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA.

Belkin M, Chao SH, Jonsson MP, Dekker C, Aksimentiev A - ACS Nano (2015)

Bottom Line: Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed.Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot.Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

ABSTRACT
With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

No MeSH data available.


Related in: MedlinePlus

MD simulation of dsDNA trapping in plasmonic nanopores. (a) All-atom model of a plasmonic nanopore. A cut-away view reveals a 3.5 nm diameter nanopore. The surface atoms of the bow tie and of the inorganic membrane are shown as yellow and gray spheres, respectively; atoms of DNA are colored according to the nucleotide type; water and ions are not shown. Hereafter, we visualize a plasmonic hot spot by drawing an isosurface of the average intensity of the plasmonic excitation (red); panels b and c provide zoomed-in views of the hot spots. Displacement of DNA through the nanopore is measured within a 2 nm slab in the middle of the membrane, depicted by the horizontal black lines. (b,c) Distribution of optical forces within the plasmonic hot spot. The arrows indicate the magnitude and direction of the plasmonic forces on a single non-hydrogen atom of DNA within the plane perpendicular (b) and parallel (c) to the nanopore axis. The forces were evaluated on a 2.5 (b) or 1.0 (c) Å grid; only the in-plane components of the forces are shown. The cyan arrows in the bottom right corners correspond to a 10 pN force under a 3.71 mW incident laser beam. In panel b, the dashed line indicates the plane in which the forces displayed in panel c were computed. The semitransparent surfaces indicate the isosurface of the optical field intensity for an optical enhancement of 30,000. (d) Simulated translocation of dsDNA in the absence of plasmonic excitations. Steps in the translocation traces indicate the stick–slip character of dsDNA motion. The three simulations began from the conformation shown in panel a. The inset plots the average rate of dsDNA translocation versus transmembrane bias. (e) Simulated translocation of dsDNA under a voltage bias of 0.35 V in the presence of plasmonic excitations of various strengths. To simplify comparison, the first 12 ns of the MD trajectories are not shown. (f) Average translocation rate versus the laser power. Squares and diamonds indicate single and dual trapping, respectively. Single-spot (g) and dual-spot (h) trapping of dsDNA.
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fig2: MD simulation of dsDNA trapping in plasmonic nanopores. (a) All-atom model of a plasmonic nanopore. A cut-away view reveals a 3.5 nm diameter nanopore. The surface atoms of the bow tie and of the inorganic membrane are shown as yellow and gray spheres, respectively; atoms of DNA are colored according to the nucleotide type; water and ions are not shown. Hereafter, we visualize a plasmonic hot spot by drawing an isosurface of the average intensity of the plasmonic excitation (red); panels b and c provide zoomed-in views of the hot spots. Displacement of DNA through the nanopore is measured within a 2 nm slab in the middle of the membrane, depicted by the horizontal black lines. (b,c) Distribution of optical forces within the plasmonic hot spot. The arrows indicate the magnitude and direction of the plasmonic forces on a single non-hydrogen atom of DNA within the plane perpendicular (b) and parallel (c) to the nanopore axis. The forces were evaluated on a 2.5 (b) or 1.0 (c) Å grid; only the in-plane components of the forces are shown. The cyan arrows in the bottom right corners correspond to a 10 pN force under a 3.71 mW incident laser beam. In panel b, the dashed line indicates the plane in which the forces displayed in panel c were computed. The semitransparent surfaces indicate the isosurface of the optical field intensity for an optical enhancement of 30,000. (d) Simulated translocation of dsDNA in the absence of plasmonic excitations. Steps in the translocation traces indicate the stick–slip character of dsDNA motion. The three simulations began from the conformation shown in panel a. The inset plots the average rate of dsDNA translocation versus transmembrane bias. (e) Simulated translocation of dsDNA under a voltage bias of 0.35 V in the presence of plasmonic excitations of various strengths. To simplify comparison, the first 12 ns of the MD trajectories are not shown. (f) Average translocation rate versus the laser power. Squares and diamonds indicate single and dual trapping, respectively. Single-spot (g) and dual-spot (h) trapping of dsDNA.

Mentions: Our all-atom MD simulations demonstrated the feasibility of arresting dsDNA translocation through a solid-state nanopore by means of plasmonic excitations. To carry out the simulations, we built an all-atom model containing the tips of the gold triangular prisms, the inorganic membrane, an hourglass nanopore, a 77 base pair fragment of dsDNA prethreaded through the pore, and 1 M KCl solution (Figure 2a). A constant electric field was applied to produce a transmembrane bias of a desired voltage difference.46 The effect of plasmonic excitations was accounted for by computing the local optical intensity enhancement factors I(r)/I0 for a continuum model of the plasmonic nanopore system27 using the finite difference time domain (FDTD) method.47 The optical intensity map was computed for a resonant EM pulse of a 788 nm wavelength; see Methods for details. The dimensions of the gold prisms’ tips, the thickness of the membrane, and the geometry of the nanopore were identical in the FDTD and all-atom MD models. Figure 2a–c illustrates the location of the volumes of the highest optical intensity resulting from the FDTD calculations. The optical forces were applied to DNA atoms in all-atom MD simulations according to the dipole approximation: Fopt = 1/2 α∇/E(r)/2, where α = 7.48 × 10–39 C m2 V–1 is the average polarizability of non-hydrogen DNA atoms estimated assuming 1.526 and 1.33 to be the indices of refraction of DNA and the surrounding environment, respectively. Figure 2b,c illustrates the distribution of optical forces in the hot spots; Supporting Information Figure S1 shows a typical optical intensity map at a larger scale. The absolute magnitude of the optical forces is determined by the power of the incident laser beam; see the Methods section for the derivation. Our simulations did not explicitly consider the effects of local heating,27,36,48−50 as those can be mitigated by integration of heat sinks with the plasmonic nanopore structure (see Supporting Information).


Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA.

Belkin M, Chao SH, Jonsson MP, Dekker C, Aksimentiev A - ACS Nano (2015)

MD simulation of dsDNA trapping in plasmonic nanopores. (a) All-atom model of a plasmonic nanopore. A cut-away view reveals a 3.5 nm diameter nanopore. The surface atoms of the bow tie and of the inorganic membrane are shown as yellow and gray spheres, respectively; atoms of DNA are colored according to the nucleotide type; water and ions are not shown. Hereafter, we visualize a plasmonic hot spot by drawing an isosurface of the average intensity of the plasmonic excitation (red); panels b and c provide zoomed-in views of the hot spots. Displacement of DNA through the nanopore is measured within a 2 nm slab in the middle of the membrane, depicted by the horizontal black lines. (b,c) Distribution of optical forces within the plasmonic hot spot. The arrows indicate the magnitude and direction of the plasmonic forces on a single non-hydrogen atom of DNA within the plane perpendicular (b) and parallel (c) to the nanopore axis. The forces were evaluated on a 2.5 (b) or 1.0 (c) Å grid; only the in-plane components of the forces are shown. The cyan arrows in the bottom right corners correspond to a 10 pN force under a 3.71 mW incident laser beam. In panel b, the dashed line indicates the plane in which the forces displayed in panel c were computed. The semitransparent surfaces indicate the isosurface of the optical field intensity for an optical enhancement of 30,000. (d) Simulated translocation of dsDNA in the absence of plasmonic excitations. Steps in the translocation traces indicate the stick–slip character of dsDNA motion. The three simulations began from the conformation shown in panel a. The inset plots the average rate of dsDNA translocation versus transmembrane bias. (e) Simulated translocation of dsDNA under a voltage bias of 0.35 V in the presence of plasmonic excitations of various strengths. To simplify comparison, the first 12 ns of the MD trajectories are not shown. (f) Average translocation rate versus the laser power. Squares and diamonds indicate single and dual trapping, respectively. Single-spot (g) and dual-spot (h) trapping of dsDNA.
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fig2: MD simulation of dsDNA trapping in plasmonic nanopores. (a) All-atom model of a plasmonic nanopore. A cut-away view reveals a 3.5 nm diameter nanopore. The surface atoms of the bow tie and of the inorganic membrane are shown as yellow and gray spheres, respectively; atoms of DNA are colored according to the nucleotide type; water and ions are not shown. Hereafter, we visualize a plasmonic hot spot by drawing an isosurface of the average intensity of the plasmonic excitation (red); panels b and c provide zoomed-in views of the hot spots. Displacement of DNA through the nanopore is measured within a 2 nm slab in the middle of the membrane, depicted by the horizontal black lines. (b,c) Distribution of optical forces within the plasmonic hot spot. The arrows indicate the magnitude and direction of the plasmonic forces on a single non-hydrogen atom of DNA within the plane perpendicular (b) and parallel (c) to the nanopore axis. The forces were evaluated on a 2.5 (b) or 1.0 (c) Å grid; only the in-plane components of the forces are shown. The cyan arrows in the bottom right corners correspond to a 10 pN force under a 3.71 mW incident laser beam. In panel b, the dashed line indicates the plane in which the forces displayed in panel c were computed. The semitransparent surfaces indicate the isosurface of the optical field intensity for an optical enhancement of 30,000. (d) Simulated translocation of dsDNA in the absence of plasmonic excitations. Steps in the translocation traces indicate the stick–slip character of dsDNA motion. The three simulations began from the conformation shown in panel a. The inset plots the average rate of dsDNA translocation versus transmembrane bias. (e) Simulated translocation of dsDNA under a voltage bias of 0.35 V in the presence of plasmonic excitations of various strengths. To simplify comparison, the first 12 ns of the MD trajectories are not shown. (f) Average translocation rate versus the laser power. Squares and diamonds indicate single and dual trapping, respectively. Single-spot (g) and dual-spot (h) trapping of dsDNA.
Mentions: Our all-atom MD simulations demonstrated the feasibility of arresting dsDNA translocation through a solid-state nanopore by means of plasmonic excitations. To carry out the simulations, we built an all-atom model containing the tips of the gold triangular prisms, the inorganic membrane, an hourglass nanopore, a 77 base pair fragment of dsDNA prethreaded through the pore, and 1 M KCl solution (Figure 2a). A constant electric field was applied to produce a transmembrane bias of a desired voltage difference.46 The effect of plasmonic excitations was accounted for by computing the local optical intensity enhancement factors I(r)/I0 for a continuum model of the plasmonic nanopore system27 using the finite difference time domain (FDTD) method.47 The optical intensity map was computed for a resonant EM pulse of a 788 nm wavelength; see Methods for details. The dimensions of the gold prisms’ tips, the thickness of the membrane, and the geometry of the nanopore were identical in the FDTD and all-atom MD models. Figure 2a–c illustrates the location of the volumes of the highest optical intensity resulting from the FDTD calculations. The optical forces were applied to DNA atoms in all-atom MD simulations according to the dipole approximation: Fopt = 1/2 α∇/E(r)/2, where α = 7.48 × 10–39 C m2 V–1 is the average polarizability of non-hydrogen DNA atoms estimated assuming 1.526 and 1.33 to be the indices of refraction of DNA and the surrounding environment, respectively. Figure 2b,c illustrates the distribution of optical forces in the hot spots; Supporting Information Figure S1 shows a typical optical intensity map at a larger scale. The absolute magnitude of the optical forces is determined by the power of the incident laser beam; see the Methods section for the derivation. Our simulations did not explicitly consider the effects of local heating,27,36,48−50 as those can be mitigated by integration of heat sinks with the plasmonic nanopore structure (see Supporting Information).

Bottom Line: Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed.Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot.Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

ABSTRACT
With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

No MeSH data available.


Related in: MedlinePlus