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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

SERS signal from DNA displaced in steps through a single plasmonic hot spot. (a) Schematic representation of a DNA fragment that displaced through a plasmonic hot spot in seven translocation (trapping) steps. Each nucleotide of every base pair contributes to the SERS intensity. For each translocation step, three nucleotides contributing the largest fractions of the total intensity in each frequency channel are highlighted using colors with opacities proportional to their contribution to the signal: the greater the contribution, the more intense background color; the colors are defined in panel b. Because the total intensity varies in each channel at each translocation step (panel b), coloring of the nucleotides can be discontinuous along the DNA strands. The SERS signals were computed for the all-atom MD trajectory of stepwise displacement obtained under the 5 ns on / 5 ns off plasmonic field pulse (Figure 4c); only the parts of the trajectory that had the trapping field on were used to compute the SERS signals. (b) Partitioning of the SERS signal among nucleotides of the DNA molecule. The average SERS intensity in each of the four frequency channels is plotted for each translocation step. For a given translocation step, the total height of the bar indicates the total SERS intensity; the segments of the bar indicate the contributions from individual nucleotides. The three nucleotides having the largest contributions to the total intensity in each channel are highlighted using colors and base pair indices; the white bar indicates the contribution from all other nucleotides of the same type. The height of the white bars does not vary considerably from one translocation step to the other and thus can be considered as a background offset for sequence determination purposes.
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fig7: SERS signal from DNA displaced in steps through a single plasmonic hot spot. (a) Schematic representation of a DNA fragment that displaced through a plasmonic hot spot in seven translocation (trapping) steps. Each nucleotide of every base pair contributes to the SERS intensity. For each translocation step, three nucleotides contributing the largest fractions of the total intensity in each frequency channel are highlighted using colors with opacities proportional to their contribution to the signal: the greater the contribution, the more intense background color; the colors are defined in panel b. Because the total intensity varies in each channel at each translocation step (panel b), coloring of the nucleotides can be discontinuous along the DNA strands. The SERS signals were computed for the all-atom MD trajectory of stepwise displacement obtained under the 5 ns on / 5 ns off plasmonic field pulse (Figure 4c); only the parts of the trajectory that had the trapping field on were used to compute the SERS signals. (b) Partitioning of the SERS signal among nucleotides of the DNA molecule. The average SERS intensity in each of the four frequency channels is plotted for each translocation step. For a given translocation step, the total height of the bar indicates the total SERS intensity; the segments of the bar indicate the contributions from individual nucleotides. The three nucleotides having the largest contributions to the total intensity in each channel are highlighted using colors and base pair indices; the white bar indicates the contribution from all other nucleotides of the same type. The height of the white bars does not vary considerably from one translocation step to the other and thus can be considered as a background offset for sequence determination purposes.

Mentions: Finally, we describe the type of SERS signals that could be obtained from a heterogeneous sequence DNA moving through a plasmonic hot spot. First, we consider the 5 ns on / 5 ns off trajectory of dsDNA stepwise displacement obtained under the single hot spot trapping condition (Figure 4c,d). Figure 7a shows the contribution of individual nucleotides to the overall SERS signal from the DNA molecule at the seven trapping phases of this all-atom MD trajectory. Figure 7b shows how the total SERS intensity in each frequency channel changes with the translocation step (which is the signal to be measured experimentally), as well as the contribution of individual nucleotides to the total intensity in each step. In each channel, the modulation of the total intensity is produced by three or less nucleotides, whereas the contribution from all other nucleotides is approximately constant (white bars in Figure 7b). As the DNA molecule is displaced through the hot spot in seven translocation steps, the contribution of the nucleotides to the overall SERS signal in each channel changes in accordance with the translocation direction prescribed by the transmembrane bias. The SERS intensity of the individual nucleotide is not a simple function of the DNA displacement because of the complex shape of the dsDNA molecule. Nevertheless, the change of the SERS intensity pattern covers without breaks the 20 base pair dsDNA fragment (base pairs 52 to 72) displaced through the hot spot.


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

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

SERS signal from DNA displaced in steps through a single plasmonic hot spot. (a) Schematic representation of a DNA fragment that displaced through a plasmonic hot spot in seven translocation (trapping) steps. Each nucleotide of every base pair contributes to the SERS intensity. For each translocation step, three nucleotides contributing the largest fractions of the total intensity in each frequency channel are highlighted using colors with opacities proportional to their contribution to the signal: the greater the contribution, the more intense background color; the colors are defined in panel b. Because the total intensity varies in each channel at each translocation step (panel b), coloring of the nucleotides can be discontinuous along the DNA strands. The SERS signals were computed for the all-atom MD trajectory of stepwise displacement obtained under the 5 ns on / 5 ns off plasmonic field pulse (Figure 4c); only the parts of the trajectory that had the trapping field on were used to compute the SERS signals. (b) Partitioning of the SERS signal among nucleotides of the DNA molecule. The average SERS intensity in each of the four frequency channels is plotted for each translocation step. For a given translocation step, the total height of the bar indicates the total SERS intensity; the segments of the bar indicate the contributions from individual nucleotides. The three nucleotides having the largest contributions to the total intensity in each channel are highlighted using colors and base pair indices; the white bar indicates the contribution from all other nucleotides of the same type. The height of the white bars does not vary considerably from one translocation step to the other and thus can be considered as a background offset for sequence determination purposes.
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Related In: Results  -  Collection

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fig7: SERS signal from DNA displaced in steps through a single plasmonic hot spot. (a) Schematic representation of a DNA fragment that displaced through a plasmonic hot spot in seven translocation (trapping) steps. Each nucleotide of every base pair contributes to the SERS intensity. For each translocation step, three nucleotides contributing the largest fractions of the total intensity in each frequency channel are highlighted using colors with opacities proportional to their contribution to the signal: the greater the contribution, the more intense background color; the colors are defined in panel b. Because the total intensity varies in each channel at each translocation step (panel b), coloring of the nucleotides can be discontinuous along the DNA strands. The SERS signals were computed for the all-atom MD trajectory of stepwise displacement obtained under the 5 ns on / 5 ns off plasmonic field pulse (Figure 4c); only the parts of the trajectory that had the trapping field on were used to compute the SERS signals. (b) Partitioning of the SERS signal among nucleotides of the DNA molecule. The average SERS intensity in each of the four frequency channels is plotted for each translocation step. For a given translocation step, the total height of the bar indicates the total SERS intensity; the segments of the bar indicate the contributions from individual nucleotides. The three nucleotides having the largest contributions to the total intensity in each channel are highlighted using colors and base pair indices; the white bar indicates the contribution from all other nucleotides of the same type. The height of the white bars does not vary considerably from one translocation step to the other and thus can be considered as a background offset for sequence determination purposes.
Mentions: Finally, we describe the type of SERS signals that could be obtained from a heterogeneous sequence DNA moving through a plasmonic hot spot. First, we consider the 5 ns on / 5 ns off trajectory of dsDNA stepwise displacement obtained under the single hot spot trapping condition (Figure 4c,d). Figure 7a shows the contribution of individual nucleotides to the overall SERS signal from the DNA molecule at the seven trapping phases of this all-atom MD trajectory. Figure 7b shows how the total SERS intensity in each frequency channel changes with the translocation step (which is the signal to be measured experimentally), as well as the contribution of individual nucleotides to the total intensity in each step. In each channel, the modulation of the total intensity is produced by three or less nucleotides, whereas the contribution from all other nucleotides is approximately constant (white bars in Figure 7b). As the DNA molecule is displaced through the hot spot in seven translocation steps, the contribution of the nucleotides to the overall SERS signal in each channel changes in accordance with the translocation direction prescribed by the transmembrane bias. The SERS intensity of the individual nucleotide is not a simple function of the DNA displacement because of the complex shape of the dsDNA molecule. Nevertheless, the change of the SERS intensity pattern covers without breaks the 20 base pair dsDNA fragment (base pairs 52 to 72) displaced through the hot spot.

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