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A low-noise solid-state nanopore platform based on a highly insulating substrate.

Lee MH, Kumar A, Park KB, Cho SY, Kim HM, Lim MC, Kim YR, Kim KB - Sci Rep (2014)

Bottom Line: The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution.The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40.Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
A solid-state nanopore platform with a low noise level and sufficient sensitivity to discriminate single-strand DNA (ssDNA) homopolymers of poly-A40 and poly-T40 using ionic current blockade sensing is proposed and demonstrated. The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution. The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40. Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis.

No MeSH data available.


Measurement of 40 nt ssDNA using different thickness nanopores.(a), Ionic conductance as a function of time with 40 nt ssDNA through different thickness nanopores with ~2.5 nm diameter and 200 mV. The translocation signals were enhanced in thinner nanopores, which provided us with a higher signal-to-noise ratio. (b), Concatenated sets of translocation events of 40 nt ssDNA. (c), Distribution of blockade current and dwell time of > 200 events for nanopores with various thicknesses.
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f4: Measurement of 40 nt ssDNA using different thickness nanopores.(a), Ionic conductance as a function of time with 40 nt ssDNA through different thickness nanopores with ~2.5 nm diameter and 200 mV. The translocation signals were enhanced in thinner nanopores, which provided us with a higher signal-to-noise ratio. (b), Concatenated sets of translocation events of 40 nt ssDNA. (c), Distribution of blockade current and dwell time of > 200 events for nanopores with various thicknesses.

Mentions: To investigate the signal-to-noise ratio of quartz-based solid-state nanopores, the signal characteristics derived from the translocation of 40 nt ssDNA homopolymers were analyzed. Figures 4a and 4b (concatenated plot) illustrate the ssDNA translocation event through nanopores with different membrane thicknesses and a diameter of ~2.5 nm at 200 mV. First, it is noted that the open pore current (I0) and blockade current (ΔIB) increase from 0.35, 0.81 and 1.64 nA and 0.11, 0.21 and 0.42 nA as the membrane thickness decreases to 20, 10 and 5 nm, respectively. However, the blockade fractions (ΔIB/I0) were similar regardless of the membrane thickness (29.5 ± 5.7% for 20 nm, 25.4 ± 4.5% for 10 nm, and 25.3 ± 3.3% for 5 nm thickness), suggesting that this fraction depends on the relative cross-sectional area of the DNA and nanopore rather than the membrane thickness. In contrast, the signal-to noise ratio (SNR) estimated using the formula ΔIB/ΔIRMS was observed to be 12.75 ± 2.39, 17.81 ± 3.18, and 47.50 ± 8.26 for 20, 10 and 5 nm thick SiNx membranes, respectively. An analogous improvement in the SNR with decreasing membrane thickness has also been reported, with an increase in the signal-to-noise ratio from 10 to 46 as the membrane thickness decreases from 25 to 6 nm17. Figure 4c shows the blockade current and dwell time plot estimated from DNA translocation data. The dwell time exhibits an ample variation ranging from 4 μsec up to approximately 1000 μsec, which indicates considerable fluctuation in the translocation time. A decrease in the membrane thickness leads to a large variation in the blockade current. However, this phenomenon is not clearly understood and is definitely another intriguing subject of study. The phenomenon of a broad blockade current in thinner nanopores was previously observed and explained as being the result of the varying interactions between the DNA and the edge of the nitride membrane during translocation3839.


A low-noise solid-state nanopore platform based on a highly insulating substrate.

Lee MH, Kumar A, Park KB, Cho SY, Kim HM, Lim MC, Kim YR, Kim KB - Sci Rep (2014)

Measurement of 40 nt ssDNA using different thickness nanopores.(a), Ionic conductance as a function of time with 40 nt ssDNA through different thickness nanopores with ~2.5 nm diameter and 200 mV. The translocation signals were enhanced in thinner nanopores, which provided us with a higher signal-to-noise ratio. (b), Concatenated sets of translocation events of 40 nt ssDNA. (c), Distribution of blockade current and dwell time of > 200 events for nanopores with various thicknesses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264027&req=5

f4: Measurement of 40 nt ssDNA using different thickness nanopores.(a), Ionic conductance as a function of time with 40 nt ssDNA through different thickness nanopores with ~2.5 nm diameter and 200 mV. The translocation signals were enhanced in thinner nanopores, which provided us with a higher signal-to-noise ratio. (b), Concatenated sets of translocation events of 40 nt ssDNA. (c), Distribution of blockade current and dwell time of > 200 events for nanopores with various thicknesses.
Mentions: To investigate the signal-to-noise ratio of quartz-based solid-state nanopores, the signal characteristics derived from the translocation of 40 nt ssDNA homopolymers were analyzed. Figures 4a and 4b (concatenated plot) illustrate the ssDNA translocation event through nanopores with different membrane thicknesses and a diameter of ~2.5 nm at 200 mV. First, it is noted that the open pore current (I0) and blockade current (ΔIB) increase from 0.35, 0.81 and 1.64 nA and 0.11, 0.21 and 0.42 nA as the membrane thickness decreases to 20, 10 and 5 nm, respectively. However, the blockade fractions (ΔIB/I0) were similar regardless of the membrane thickness (29.5 ± 5.7% for 20 nm, 25.4 ± 4.5% for 10 nm, and 25.3 ± 3.3% for 5 nm thickness), suggesting that this fraction depends on the relative cross-sectional area of the DNA and nanopore rather than the membrane thickness. In contrast, the signal-to noise ratio (SNR) estimated using the formula ΔIB/ΔIRMS was observed to be 12.75 ± 2.39, 17.81 ± 3.18, and 47.50 ± 8.26 for 20, 10 and 5 nm thick SiNx membranes, respectively. An analogous improvement in the SNR with decreasing membrane thickness has also been reported, with an increase in the signal-to-noise ratio from 10 to 46 as the membrane thickness decreases from 25 to 6 nm17. Figure 4c shows the blockade current and dwell time plot estimated from DNA translocation data. The dwell time exhibits an ample variation ranging from 4 μsec up to approximately 1000 μsec, which indicates considerable fluctuation in the translocation time. A decrease in the membrane thickness leads to a large variation in the blockade current. However, this phenomenon is not clearly understood and is definitely another intriguing subject of study. The phenomenon of a broad blockade current in thinner nanopores was previously observed and explained as being the result of the varying interactions between the DNA and the edge of the nitride membrane during translocation3839.

Bottom Line: The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution.The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40.Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea.

ABSTRACT
A solid-state nanopore platform with a low noise level and sufficient sensitivity to discriminate single-strand DNA (ssDNA) homopolymers of poly-A40 and poly-T40 using ionic current blockade sensing is proposed and demonstrated. The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution. The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40. Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis.

No MeSH data available.