nature LETTERS nanotechnology PUBLISHED ONLINE: 11 DECEMBER 2011 I DOL: 10. 1038/NNANO 2011.217 Local electrical potential detection of dna by nanowire-nanopore sensors Ping Xie, Qihua Xiong2, Ying Fang, Quan Qing and Charles M. Lieber15 Nanopores could potentially be used to perform single-molecule The integrated nanowire-nanopore FET sensor comprises a DNA sequencing at low cost and with high throughput-. short-channel silicon nanowire FET on a silicon nitride ( SiN Although single base resolution and differentiation have been membrane-based chip, with the nanopore extending through both demonstrated with nanopores using ionic current measure- the nanowire edge and the Sin membrane support(Fig. 1a, ments, direct sequencing has not been achieved because of Supplementary Fig. S1). The fabrication nanowire-n he difficulties in recording very small (pA) ionic currents at FET sensors involves several key steps( Supplementary Methods a bandwidth consistent with fast translocation speeds-3. Here, First, p-type silicon nanowires FETs were fabricated on SiN, we show that solid-state nanopores can be combined with membranes with nickel-metal source-drain contacts with a typical silicon nanowire field-effect transistors to create sensors in spacing of 1-2 um. To minimize signal attenuation due to Fet which detection is localized and self-aligned at the nanopore. channel series resistance, the active length of the silicon nanowire Well-defined field-effect transistor signals associated with was further reduced to less than 200 nm by solid-state diffusion to DNA translocation are recorded when an ionic strength form metallic nickel silicide(NiSi)contacts(Fig. 1b, gradient is imposed across the nanopores. Measurements Next, a focused electron beam(via transmission electron micros nd modelling show that field-effect transistor signals are TEM)was used to form a nanopore 2 through the edge generated by highly localized changes in the electrical silicon nanowire and the underlying membrane( Fig. 1b) potential during DNA translocation, and that nanowire- The sensitivity of nanowire-nanopore FET sensors fabricated nanopore sensors could enable large-scale integration with a in this way was characterized by scanning gate microscopy high intrinsic bandwidth. (SGM)(Supplementary Methods). A SGM map of the conductance Most current nanopore technology is based on detecting a change versus biased tip position for a silicon nanowire FET device modulation in the ionic current due to the partial blockade of a after nanopore formation(Fig. Ic)shows a pronounced peak of anopore during DNA translocation-. Significant progress has conductance change localized around the nanopore position been made towards direct DNA sequencing during translocation and no response from the NiSi region of the nanowire device. The through protein nanopore engineering and novel membrane sensitivity(conductance change/tip voltage) along the nanowire naterials7-,although some challenges remain. For example, the (Fig. ld, red line) exhibits a maximum of 18nSV-, which is DNA translocation speed, - l us base, is faster than the sharply localized and aligned with the nanopore position at bandwidth electronics available to amplify the small ionic current, approximately the midpoint along the length of the semiconductor and it is difficult to record ionic current from individual nanopores channel. We note that the sensitivity of this device before nanopore a highly parallel multiplexed format. To overcome these issues, formation is relatively constant (5-8 nSV; Fig. Id, black line) methods have been developed to better control the transloca- along the entire active silicon channel. The larger than twofold tiono-, thus enabling potential reductions in translocation sensitivity enhancement can be explained qualitatively by the peed that could facilitate ionic current detection Simultaneou ncrease in channel resistance of the ortion of th new detection designs have been proposed that could allow the silicon nanowire FET where silicon is removed. Although additional recording of larger and local signals from sensors integrated with work will be needed to quantify the factors contributing to the nanoporel-3. These integrated sensors include devices based this observed enhancement, the localized sensitivity makes the on the measurement of capacitive coupling 4 and tunnelling cur- nanowire-nanopore FET attractive for monitoring translocation rents s-, although none has roved upon traditional ionic events through the nanopore current detection in experiments. Field-effect transistors(FETs), Single-channel DNA translocation measurements were carried including nanowire and carbon-nanotube FETs, have demonstrated out with two polydimethylsiloxane(PDMS)solution chambers as high intrinsic speeds,19 and high sensitivities as chemical and trans and cis reservoirs above and below the Sin, membrane, biological sensors20-2, and thus might also function respectively. Both chambers were filled with 1 M KCl buffer, as integrated detectors for nanopores. However, the lack of a clear typically used in nanopore experiments24. 2. Following injection of mechanism for FET-based detection of DNA during nanopore 6 nM,2.6 kbps linear double-stranded DNA(dsDNA)(pUC19 translocation(where the relatively high solution ionic strength is Supplementary Methods)into the cis chamber, we observed trans- expected to screen the detection of molecular charge previously location events in the ionic current channel when the transmem- used in sensing experiments,) has left these detectors brane voltage reached -06V(Fig 2a, top panel). Simultaneous largely unexplored. recording of the nanowire FET conductance(Fig. 2a, lower panel) We investigated the possibility of integrating a FET with a nano- showed no noticeable translocation signals and only small and ore using synthesized silicon nanowires as the nanoscale FETs2-. slow conductance baseline shifts. However, if the trans Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA, Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, Division of Microelectronics, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 619798, Singapore, "National Center for Nanoscience and Technology, China, Beijing 100910, PR China, School of Engineering and Applied Sciences, Harvard University, Cambridge, massachusetts 02138, USA. e-mail: cml@cmliris. harvard. edu NaturENanotEchnOlogYIVol7IFebRuaRy2012Iwww.nature.com/naturenanotechnology o 2012 Macmillan Publishers Limited. All rights reserved
Local electrical potential detection of DNA by nanowire–nanopore sensors Ping Xie1 , Qihua Xiong2,3, Ying Fang4, Quan Qing1 and Charles M. Lieber1,5* Nanopores could potentially be used to perform single-molecule DNA sequencing at low cost and with high throughput1–4. Although single base resolution and differentiation have been demonstrated with nanopores using ionic current measurements5–7, direct sequencing has not been achieved because of the difficulties in recording very small (∼pA) ionic currents at a bandwidth consistent with fast translocation speeds1–3. Here, we show that solid-state nanopores can be combined with silicon nanowire field-effect transistors to create sensors in which detection is localized and self-aligned at the nanopore. Well-defined field-effect transistor signals associated with DNA translocation are recorded when an ionic strength gradient is imposed across the nanopores. Measurements and modelling show that field-effect transistor signals are generated by highly localized changes in the electrical potential during DNA translocation, and that nanowire– nanopore sensors could enable large-scale integration with a high intrinsic bandwidth. Most current nanopore technology is based on detecting a modulation in the ionic current due to the partial blockade of a nanopore during DNA translocation1–4. Significant progress has been made towards direct DNA sequencing during translocation through protein nanopore engineering5,6 and novel membrane materials7–9, although some challenges remain1,3. For example, the DNA translocation speed, 1 ms base21 , is faster than the bandwidth electronics available to amplify the small ionic current, and it is difficult to record ionic current from individual nanopores in a highly parallel multiplexed format. To overcome these issues, methods have been developed to better control the translocation4,10–13, thus enabling potential reductions in translocation speed that could facilitate ionic current detection. Simultaneously, new detection designs have been proposed that could allow the recording of larger and local signals from sensors integrated with the nanopore1–3. These integrated sensors include devices based on the measurement of capacitive coupling14 and tunnelling currents15–17, although none has yet improved upon traditional ionic current detection in experiments. Field-effect transistors (FETs), including nanowire and carbon-nanotube FETs, have demonstrated high intrinsic speeds18,19 and high sensitivities as chemical and biological sensors20–22, and thus might also function as integrated detectors for nanopores. However, the lack of a clear mechanism for FET-based detection of DNA during nanopore translocation (where the relatively high solution ionic strength is expected to screen the detection of molecular charge previously used in sensing experiments20,21) has left these detectors largely unexplored. We investigated the possibility of integrating a FET with a nanopore using synthesized silicon nanowires as the nanoscale FETs20–22. The integrated nanowire–nanopore FET sensor comprises a short-channel silicon nanowire FET on a silicon nitride (SiNx) membrane-based chip, with the nanopore extending through both the nanowire edge and the SiNx membrane support (Fig. 1a, Supplementary Fig. S1). The fabrication of nanowire–nanopore FET sensors involves several key steps (Supplementary Methods). First, p-type silicon nanowires FETs were fabricated on SiNx membranes with nickel-metal source–drain contacts with a typical spacing of 1–2 mm. To minimize signal attenuation due to FETchannel series resistance, the active length of the silicon nanowire was further reduced to less than 200 nm by solid-state diffusion to form metallic nickel silicide (NiSi) contacts19 (Fig. 1b, inset). Next, a focused electron beam (via transmission electron microscopy, TEM) was used to form a nanopore23 through the edge of the silicon nanowire and the underlying membrane (Fig. 1b). The sensitivity of nanowire–nanopore FET sensors fabricated in this way was characterized by scanning gate microscopy (SGM) (Supplementary Methods). A SGM map of the conductance change versus biased tip position for a silicon nanowire FET device after nanopore formation (Fig. 1c) shows a pronounced peak of conductance change localized around the nanopore position and no response from the NiSi region of the nanowire device. The sensitivity (conductance change/tip voltage) along the nanowire (Fig. 1d, red line) exhibits a maximum of 18 nS V21 , which is sharply localized and aligned with the nanopore position at approximately the midpoint along the length of the semiconductor channel. We note that the sensitivity of this device before nanopore formation is relatively constant (5–8 nS V21 ; Fig. 1d, black line) along the entire active silicon channel. The larger than twofold sensitivity enhancement can be explained qualitatively by the increase in channel resistance of the nanopore portion of the silicon nanowire FET where silicon is removed. Although additional work will be needed to quantify the factors contributing to this observed enhancement, the localized sensitivity makes the nanowire–nanopore FET attractive for monitoring translocation events through the nanopore. Single-channel DNA translocation measurements were carried out with two polydimethylsiloxane (PDMS) solution chambers as trans and cis reservoirs above and below the SiNx membrane, respectively. Both chambers were filled with 1 M KCl buffer, as typically used in nanopore experiments24,25. Following injection of 6 nM, 2.6 kbps linear double-stranded DNA (dsDNA) (pUC19; Supplementary Methods) into the cis chamber, we observed translocation events in the ionic current channel when the transmembrane voltage reached 0.6 V (Fig. 2a, top panel). Simultaneous recording of the nanowire FET conductance (Fig. 2a, lower panel) showed no noticeable translocation signals and only small and slow conductance baseline shifts. However, if the trans 1 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA, 2 Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore, 3 Division of Microelectronics, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 619798, Singapore, 4 National Center for Nanoscience and Technology, China, Beijing 100910, PR China, 5 School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA. *e-mail: cml@cmliris.harvard.edu LETTERS PUBLISHED ONLINE: 11 DECEMBER 2011 | DOI: 10.1038/NNANO.2011.217 NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology 119 © 2012 Macmillan Publishers Limited. All rights reserved.
ETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO 2011.217 NW-NP FET -100nS 0.5 Distance to nanopore (um) Figure 1 I Nanowire-nanopore transistor a, Schematic of the nanowire-nanopore measurement set-up Inset: zoom-in view around the nanopore. NW-NP nanowire-nanopore. b, High-resolution TEM image of a silicon nanowire with the nanopore off-axis at the nanowire edge Scale bar, 10 nm. Inset: larger-scale EM image of a nanowire-nanopore FeT device showing the central silicon nanowire connected to darker NiSi contacts, which are indicated by the white ashed line. The region where the high-resolution TEM image was recorded is indicated by the yellow dashed square Scale bar (inset), 50 nm. c SGM image of a silicon nanowire-nanopore device recorded with the tip voltage at -10 V. Scale bar, 1 um Nanopore position is indicated by the black circle. Nickel contacts are indicated by white dashed lines and the nanowire between the two contacts is indicated by the black dashed line. Inset: AFM topographic image of the device, with the Sgm image area indicated by the white square. Colour scale(-100 to 200 nS) corresponds to the conductance change. d, scanning gate sensitivity profile of the same device before and after nanopore formation, with the profile taken along the black dashed line in c and averaged over an -100 nm width perpendicular to the dashed line. (nanowire-nanopore FET side) and cis(back side)chambers are FETs(Fig. 4b) and other silicon nanowire FET sensors2b2 filled with solutions of different ionic strength(for example, demonstrate that much lower noise(and correspondingly higher 10 mM in the trans chamber and 1 M in cis chamber), clear FEt signal-to-noise ratio)can be achieved in general for nanowire- conductance signals with perfect time correlation to ionic current nanopore FETs. In addition, the relatively large(30 nA)trans- events can be observed(Fig. 2b) for a voltage of x2 V. location signal from the FET suggests the potential for higher- alitatively, a larger voltage is expected given the lower solution bandwidth recording than with smaller ionic-current resistance and therefore lower electric field on the cis side. which detection schemes determines DNA entry into the nanopore. With a further increase To understand the nanowire-nanopore detection mechanism in the voltage to 2.4 V( Fig. 2c), the duration of translocation events we first consider basic experimental facts. First, and as discussed in both ionic current and FET channels decreased, while the fre- above, it is possible to exclude direct charge sensing by the quency increased. These changes in duration and frequency are con- nanowire-nanopore FET202, because the negative charge on the sistent with the previous results reported for ionic current events DNA backbone should produce an increase in conductance recorded in other nanopore experiments. 4. Importantly, the for the p-type device during translocation instead of the hange in the FET signal during translocation-a decrease in con- observed decrease. Second, the importance of the differential ductance-is opposite to that expected for charge-based sensing buffer salt concentration suggests that solution resistance plays of the DNA with a p-type semiconductor 2, therefore implying a an important role in the signal generation. Specifically, under new detection mechanism alanced buffer conditions (1 M/1 M), the nanopore dominates The amplitude of the nanowire-nanopore FET signal in a non- the solution resistance and the voltage drops primarily across balanced buffer salt concentration can be compared to the ionic the nanopore. The potential around the nanowire-nanopore urrent signal by converting the FET conductance to a current. sensor is very close to ground, regardless of the change in This conversion shows that the FET current change is 30 nA solution resistance during DNA translocation. However, when mpared with the 3 nA ionic current changes during DNA the buffer concentration in the trans chamber containing the translocation. Although the noise in this nanowire-nanopore nanowire-nanopore sensor is lower than that of the cis chamber, FET(Fig. 2)is relatively high, other nanowire-nanopore the nanopore and trans chamber solution resistances are NatureNanotEchnOlogYIVol7IFebRuaRy2012Iwww.nature.com/naturenanotechnology o 2012 Macmillan Publishers Limited. All rights reserved
(nanowire–nanopore FET side) and cis (back side) chambers are filled with solutions of different ionic strength (for example, 10 mM in the trans chamber and 1 M in cis chamber), clear FET conductance signals with perfect time correlation to ionic current events can be observed (Fig. 2b) for a voltage of 2 V. Qualitatively, a larger voltage is expected given the lower solution resistance and therefore lower electric field on the cis side, which determines DNA entry into the nanopore3 . With a further increase in the voltage to 2.4 V (Fig. 2c), the duration of translocation events in both ionic current and FET channels decreased, while the frequency increased. These changes in duration and frequency are consistent with the previous results reported for ionic current events recorded in other nanopore experiments10,24. Importantly, the change in the FET signal during translocation—a decrease in conductance—is opposite to that expected for charge-based sensing of the DNA with a p-type semiconductor20, therefore implying a new detection mechanism. The amplitude of the nanowire–nanopore FET signal in a nonbalanced buffer salt concentration can be compared to the ionic current signal by converting the FET conductance to a current. This conversion shows that the FET current change is 30 nA compared with the 3 nA ionic current changes during DNA translocation. Although the noise in this nanowire–nanopore FET (Fig. 2) is relatively high, other nanowire–nanopore FETs (Fig. 4b) and other silicon nanowire FET sensors26,27 demonstrate that much lower noise (and correspondingly higher signal-to-noise ratio) can be achieved in general for nanowire– nanopore FETs. In addition, the relatively large (30 nA) translocation signal from the FET suggests the potential for higherbandwidth recording than with smaller ionic-current detection schemes. To understand the nanowire–nanopore detection mechanism we first consider basic experimental facts. First, and as discussed above, it is possible to exclude direct charge sensing by the nanowire–nanopore FET20,21, because the negative charge on the DNA backbone should produce an increase in conductance for the p-type device during translocation instead of the observed decrease. Second, the importance of the differential buffer salt concentration suggests that solution resistance plays an important role in the signal generation. Specifically, under balanced buffer conditions (1 M/1 M), the nanopore dominates the solution resistance and the voltage drops primarily across the nanopore. The potential around the nanowire–nanopore sensor is very close to ground, regardless of the change in solution resistance during DNA translocation. However, when the buffer concentration in the trans chamber containing the nanowire–nanopore sensor is lower than that of the cis chamber, the nanopore and trans chamber solution resistances are a c b SGM sensitivity (nS V−1) Distance to nanopore (μm) d Source Drain Cis Trans SiNx SiNx NW−NP FET Si chip Si Chip Nanowire Before nanopore After nanopore −1.0 −0.5 0.5 0 0 5 10 15 20 1.0 200nS −100nS NiSi NiSi Figure 1 | Nanowire–nanopore transistor. a, Schematic of the nanowire–nanopore measurement set-up. Inset: zoom-in view around the nanopore. NW–NP, nanowire–nanopore. b, High-resolution TEM image of a silicon nanowire with the nanopore off-axis at the nanowire edge. Scale bar, 10 nm. Inset: larger-scale TEM image of a nanowire–nanopore FET device showing the central silicon nanowire connected to darker NiSi contacts, which are indicated by the white dashed line. The region where the high-resolution TEM image was recorded is indicated by the yellow dashed square. Scale bar (inset), 50 nm. c, SGM image of a silicon nanowire–nanopore device recorded with the tip voltage at 210 V. Scale bar, 1 mm. Nanopore position is indicated by the black circle. Nickel contacts are indicated by white dashed lines and the nanowire between the two contacts is indicated by the black dashed line. Inset: AFM topographic image of the device, with the SGM image area indicated by the white square. Colour scale (2100 to 200 nS) corresponds to the conductance change. d, Scanning gate sensitivity profile of the same device before and after nanopore formation, with the profile taken along the black dashed line in c, and averaged over an 100 nm width perpendicular to the dashed line. LETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 120 NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology © 2012 Macmillan Publishers Limited. All rights reserved.
NATURE NANOTECHNOLOGY DOl: 10.1038/NNANO2011217 LETTERS 987 3000 4.000 494049504960 Time(ms) ge=2.0 V: cis: 1 M, trans: 10 mM bt 10 2360 1000 4,000 5000 4,7504,7604,770 oltage =2.4 V: cis: 1 M mM buffer 12 12 23900 523900 1000 3,000 423042404250 Time(ms) Figure 2 I Single-channel nanowire-nanopore FET detection of DNA translocation a-c, Left panels: simultaneously recorded ionic current and FET conductance signals with both chambers filled with 1 M kCI buffer, voltage 0.6 v and 6 nM puC 19 dsDNA in the cis chamber (a); simultaneously recorded ionic current and FET conductance signals at 2 V voltage(b); simultaneously recorded ionic current and FET conductance signals at 2.4 V voltage(c) Measurements in b and c were carried out with a trans chamber kcl buffer concentration of 10 mM, cis chamber kcl buffer concentration of 1 M, and 1.4 r oUC19 DNA Right panels: zoom-in views of single ionic current and FET conductance events at the time indicated by black arrows in the ionic current traces of the corresponding left panels comparable and the resistance of the cis chamber will be negligible. electrical potential change around the trans chamber nanopo Hence, changes in the solution resistance of the nanopore and opening (potential change signal)during DNA translocation ds 3 trans chamber during DNA translocation can result in a change in the potential around the nanowire-nanopore sensor, which is 2VA(41+d)(Cas/Ctrans -1) To understand quantitatively this proposed and unexpected In(Cas/Crans)(21+d)(d2(Cas/Ctrans -1)+4(21+d)r) detection mechanism for the nanowire-nanopore FET,we modelled the buffer concentration, electric potential and electric field distributions inside the solution of the nanopore and solution Here V, A, L, d, Ccis and r are the voltage, cross-sectional area chamber system( Fig 3a). The equivalent circuit(Fig. 3b) separates of the DNA, membrane thickness, nanopore diameter, cis and tran the total solution resistance into nanopore resistance(Reore), and cis chamber buffer salt concentrations and distance to the nanopore and trans chamber access resistances(Rtrans and ris respectively). opening, respectively The nanowire-nanopore FET sensor is simplified as a point-like To further analyse the potential change signal, we first plot th potential detector at the nanopore opening on the trans side. signal at the nanopore opening as a function of nanopore diameter Translocation of DNA molecules through the nanopore will par- and cis/trans chamber buffer concentration ratio(Fig. 3c).The ally block the nanopore, thus leading to a transient change in potential change is predicted to increase with decreasing nanopore nanopore resistance and both chamber access resistances. Detailed diameter, and can reach more than 10% of the applied voltage when calculations(Supplementary Methods, Fig S2)provide the solution the nanopore diameter is 2 nm. The maximal potential change NATURE NANOTECHNOLOGY I VOL 7 I FEBRUARY 2012 o 2012 Macmillan Publishers Limited. All rights reserved
comparable and the resistance of the cis chamber will be negligible. Hence, changes in the solution resistance of the nanopore and trans chamber during DNA translocation can result in a change in the potential around the nanowire–nanopore sensor, which is then detected. To understand quantitatively this proposed and unexpected detection mechanism for the nanowire–nanopore FET, we modelled the buffer concentration, electric potential and electric field distributions inside the solution of the nanopore and solution chamber system (Fig. 3a). The equivalent circuit (Fig. 3b) separates the total solution resistance into nanopore resistance (Rpore), and cis and trans chamber access resistances (Rtrans and Rcis respectively). The nanowire–nanopore FET sensor is simplified as a point-like potential detector at the nanopore opening on the trans side. Translocation of DNA molecules through the nanopore will partially block the nanopore, thus leading to a transient change in nanopore resistance and both chamber access resistances. Detailed calculations (Supplementary Methods, Fig. S2) provide the solution electrical potential change around the trans chamber nanopore opening (potential change signal) during DNA translocation as dV ≈ 2VA( ) 4l + d Ccis/Ctrans − 1 p ln Ccis/Ctrans ( ) 2l + d d2 Ccis/Ctrans − 1 + 4 2( ) l + d r (1) Here V, A, l, d, Ccis, Ctrans and r are the voltage, cross-sectional area of the DNA, membrane thickness, nanopore diameter, cis and trans chamber buffer salt concentrations and distance to the nanopore opening, respectively. To further analyse the potential change signal, we first plot the signal at the nanopore opening as a function of nanopore diameter and cis/trans chamber buffer concentration ratio (Fig. 3c). The potential change is predicted to increase with decreasing nanopore diameter, and can reach more than 10% of the applied voltage when the nanopore diameter is 2 nm. The maximal potential change a b c 6 7 8 9 0 1,000 2,000 3,000 4,000 5,000 900 1,000 1,100 1,200 1,300 Ionic current (nA) FET conductance (nS) Time (ms) Time (ms) 4,940 4,950 4,960 Voltage = 0.6 V; 1 M buffer in both chambers 10 12 14 0 1,000 2,000 3,000 4,000 5,000 23,700 23,900 24,100 Ionic current (nA) FET conductance (nS) Time (ms) Time (ms) Voltage = 2.4 V; cis: 1 M, trans: 10 mM buffer 8 9 10 11 0 1,000 2,000 3,000 4,000 5,000 23,400 23,500 23,600 23,700 Ionic current (nA) FET conductance (nS) 6 7 8 9 900 1,000 1,100 1,200 1,300 Ionic current (nA) FET conductance (nS) 10 12 14 23,700 23,900 24,100 Ionic current (nA) FET conductance (nS) 8 9 10 11 23,400 23,500 23,600 23,700 Ionic current (nA) FET conductance (nS) Time (ms) Time (ms) 4,750 4,760 4,770 Voltage = 2.0 V; cis: 1 M, trans: 10 mM buffer 4,230 4,240 4,250 Figure 2 | Single-channel nanowire–nanopore FET detection of DNA translocation. a–c, Left panels: simultaneously recorded ionic current and FET conductance signals with both chambers filled with 1 M KCl buffer, voltage 0.6 V and 6 nM pUC 19 dsDNA in the cis chamber (a); simultaneously recorded ionic current and FET conductance signals at 2 V voltage (b); simultaneously recorded ionic current and FET conductance signals at 2.4 V voltage (c). Measurements in b and c were carried out with a trans chamber KCl buffer concentration of 10 mM, cis chamber KCl buffer concentration of 1 M, and 1.4 nM pUC19 DNA. Right panels: zoom-in views of single ionic current and FET conductance events at the time indicated by black arrows in the ionic current traces of the corresponding left panels. NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 LETTERS NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology 121 © 2012 Macmillan Publishers Limited. All rights reserved.
ETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO 2011.217 SiNW SiNW Potential change (v) Potential change (v) 100100010.000100 Cis/trans concentration ratio X distance to pore opening(nm) 000 Voltage (v) Figure 3 I Nanowire-nanopore sensing mechanism. a, Schematic of the sensing circuit. b, equivalent circuit diagram for a SiNW, silicon nanowire. c, Calculated potential change at the nanopore opening in the trans chamber(using Supplementary equation (9)), due to translocation of one dsDNA molecule at a voltage of 1 v as a function of nanopore diameter and cis/trans chamber buffer concentration ratio. d, Calculated potential change distribution the trans chamber for a 10-nm-diameter nanopore at 1 V voltage (equation (1)). e, Experimental values of the Fet signal (black data points) and FET ignal/ ionic current signal ratio(red data points) under different voltages. signal for a given diameter nanopore is also predicted to occur at nanowire-nanopore sensors without crosstalk. Moreover, analysis he of the voltage drops across the nanopore and both chambers nanopore geometry used in our experiments( diameter, 7-10 nm; allows their solution resistances to be compared. To do so,we membrane thickness, 50 nm), the potential change signal can be plotted the potential distribution in both chambers at the optimal larger than 1%of the voltage at the optimal buffer concentration buffer concentration ratio(Supplementary Fig. S3), and found ratio(100: 1). We have tested the consistency of the model that the access resistance of the trans chamber and the resistance predictions with our experiments. Specifically, conversion of the of the nanopore are indeed within the same order of magnitude, FET conductance signal into potential change using the measured whereas the access resistance of the cis chamber is negligible lution-gated transconductance 2? yields a potential change of From the signal distribution, we can also roughly estimate the 25 mV(Fig. 2c), which agrees with our model calculations intrinsic bandwidth of the potential change signal (Supplementary 31-16 mV, with a 7-10-nm-diamter nanopore, and all other con- Methods, Fig. S4). A simple RC model suggests a potential signal ditions the same as in the experiment) bandwidth of -1 GHz under our experimental conditions In addition, the predicted distribution of the potential change in Finally, the different voltages required to initiate translocation at the trans chamber at this optimal condition(Fig. 3d)shows a highly 1:1 and 100: 1 buffer concentration ratios(Fig. 2)can be explained localized signal within several tens of nanometres of the quantitatively by our model: the onset of translocation is determined nanopore, suggesting the possibility of high-density integration of by the electric field at the nanopore opening in the cis chamber, which NatureNanotEchnOlogyIVol7iFebrUarY2012Iwww.nature.com/naturenanotechnology o 2012 Macmillan Publishers Limited. All rights reserved
signal for a given diameter nanopore is also predicted to occur at intermediate buffer concentration ratios. Specifically, for the nanopore geometry used in our experiments (diameter, 7–10 nm; membrane thickness, 50 nm), the potential change signal can be larger than 1% of the voltage at the optimal buffer concentration ratio (100:1). We have tested the consistency of the model predictions with our experiments. Specifically, conversion of the FET conductance signal into potential change using the measured solution-gated transconductance27 yields a potential change of 25 mV (Fig. 2c), which agrees with our model calculations (31–16 mV, with a 7–10-nm-diamter nanopore, and all other conditions the same as in the experiment). In addition, the predicted distribution of the potential change in the trans chamber at this optimal condition (Fig. 3d) shows a highly localized signal within several tens of nanometres of the nanopore, suggesting the possibility of high-density integration of nanowire–nanopore sensors without crosstalk. Moreover, analysis of the voltage drops across the nanopore and both chambers allows their solution resistances to be compared. To do so, we plotted the potential distribution in both chambers at the optimal buffer concentration ratio (Supplementary Fig. S3), and found that the access resistance of the trans chamber and the resistance of the nanopore are indeed within the same order of magnitude, whereas the access resistance of the cis chamber is negligible. From the signal distribution, we can also roughly estimate the intrinsic bandwidth of the potential change signal (Supplementary Methods, Fig. S4). A simple RC model suggests a potential signal bandwidth of 1 GHz under our experimental conditions. Finally, the different voltages required to initiate translocation at 1:1 and 100:1 buffer concentration ratios (Fig. 2) can be explained quantitatively by our model: the onset of translocation is determined by the electric field at the nanopore opening in the cis chamber, which e 2.0 2.1 2.2 2.3 2.4 2.5 100 150 200 250 300 FET/ionic current signal ratio (nS nA−1) FET signal (nS) Voltage (V) 0 20 40 60 b A Rcis Rpore Rtrans SiNW FET A a SiNxmembrane SiNxmembrane A Cis Trans SiNW SiNW A c 100 100 50 0 50 0 50 100 Potential change (V) d Nanopore diameter (nm) Cis/trans concentration ratio 1 1,000 10,000 10 100 10 8 6 4 2 0.001 0.01 0.1 X distance to pore opening (nm) Z distance to pore opening (nm) Potential change (V) 0 0.004 0.008 Figure 3 | Nanowire–nanopore sensing mechanism. a, Schematic of the sensing circuit. b, Equivalent circuit diagram for a. SiNW, silicon nanowire. c, Calculated potential change at the nanopore opening in the trans chamber (using Supplementary equation (9)), due to translocation of one dsDNA molecule at a voltage of 1 V as a function of nanopore diameter and cis/trans chamber buffer concentration ratio. d, Calculated potential change distribution in the trans chamber for a 10-nm-diameter nanopore at 1 V voltage (equation (1)). e, Experimental values of the FET signal (black data points) and FET signal/ionic current signal ratio (red data points) under different voltages. LETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 122 NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology © 2012 Macmillan Publishers Limited. All rights reserved.
NATURE NANOTECHNOLOGY DOl: 10.1038/NNANO2011217 LETTERS 9200 MnMT-wwlp 5.000 10.000 20000 7000 7200 7.400 7.600 ime(ms) Figure 4 I Multi-channel recording of DNa translocation with three nanowire-nanopore FET sensors. All measurements are made with 1 M KCI buffer in the cis chamber and 10 mM KCI buffer in the trans chamber, a voltage of 3 V, and 1.4 nM pUC19 DNA. a, Simultaneous recording of the total ionic current and three nanowire-nanopore FET conductance channels(Ch1-Ch3). b, Higher-resolution view of the multiplexed recording from the dashed rectangular area in a The dashed red trace in the upper panel corresponds to the reconstructed ionic current trace (offset 10 nA for clarity) calculated from the three FEt traces ulls the negatively charged DNA into the nanopore. We plotted the should not change significantly when the voltage changes. For the electric potential and field distribution inside the nanopore for both local potential sensing mechanism, however, the sensor signal is 1:1 and 100: 1 buffer concentration ratios( Supplementary Fig S5). predicted to be proportional to the voltage and can be regarded as the 1: 1 case, the field (-1. x 10'Vm )is uniformly distribu- the linear amplification of the ionic current signal. Hence, the ted within the nanopore, but for the 100: 1 case, the field(0.45 x ratio between the FET signal and the ionic current signal should 10'Vm )is smaller on the cis side because of the lower resistance be constant for a given nanopore geometry and buffer concentration (owing to higher buffer concentration) there. To produce the same( Supplementary Methods). This unique feature was experimentally tage applied for the 100: 1 case should e-8 na a val s by plotting the FET signal amplitude(Fig. 3e, black) and tested mately four times higher than the voltage for the 1: 1 case, current signal ratio( Fig. 3e, red)at different voltage quantitatively consistent with the observed onset of translocation values. Notably, the data show that the FET signal amplitude events at x2 V and 0.5-0.6 V, respectively(Fig. 2) increases, but the signal ratio is approximately constant with A crucial difference between our FET-based local potential increasing voltage, and thus provides strong support for sensing sing and other proposed DNA direct sensing mechanisms- by a local potential mechanism. the dependence of the FEt signal on the ionic current signal We have also carried out several additional experiments to test and the voltage. For DNA sensing mechanisms that rely on the the validity of our new model. First, DNA translocation experiments direct interaction between DNA and the sensor through electrical were carried out at different buffer salt concentrations in the oupling or quantum-mechanical tunnelling 5, 6, the signal is cis/trans chambers(Supplementary Methods, Figs S6, S7) typically not related directly to the ionic current or voltage and Measurements made at 3.3 M/33 mM(which equates to the san NATURE NANOTECHNOLOGY I VOL 7 I FEBRUARY 2012 o 2012 Macmillan Publishers Limited. All rights reserved
pulls the negatively charged DNA into the nanopore. We plotted the electric potential and field distribution inside the nanopore for both 1:1 and 100:1 buffer concentration ratios (Supplementary Fig. S5). For the 1:1 case, the field (1.8 × 107 V m21 ) is uniformly distributed within the nanopore, but for the 100:1 case, the field (0.45 × 107 V m21 ) is smaller on the cis side because of the lower resistance (owing to higher buffer concentration) there. To produce the same electric field, the voltage applied for the 100:1 case should be approximately four times higher than the voltage for the 1:1 case, which is quantitatively consistent with the observed onset of translocation events at 2 V and 0.5–0.6 V, respectively (Fig. 2). A crucial difference between our FET-based local potential sensing and other proposed DNA direct sensing mechanisms8–17 is the dependence of the FET signal on the ionic current signal and the voltage. For DNA sensing mechanisms that rely on the direct interaction between DNA and the sensor through electrical coupling8 or quantum-mechanical tunnelling15,16, the signal is typically not related directly to the ionic current or voltage and should not change significantly when the voltage changes. For the local potential sensing mechanism, however, the sensor signal is predicted to be proportional to the voltage and can be regarded as the linear amplification of the ionic current signal. Hence, the ratio between the FET signal and the ionic current signal should be constant for a given nanopore geometry and buffer concentration (Supplementary Methods). This unique feature was experimentally tested by plotting the FET signal amplitude (Fig. 3e, black) and FET/ionic current signal ratio (Fig. 3e, red) at different voltage values. Notably, the data show that the FET signal amplitude increases, but the signal ratio is approximately constant with increasing voltage, and thus provides strong support for sensing by a local potential mechanism. We have also carried out several additional experiments to test the validity of our new model. First, DNA translocation experiments were carried out at different buffer salt concentrations in the cis/trans chambers (Supplementary Methods, Figs S6,S7). Measurements made at 3.3 M/33 mM (which equates to the same a b 0 5,000 10,000 15,000 20,000 Ch1 FET conductance (nS) Ch2 FET conductance (nS) Ch3 FET conductance (nS) Time (ms) Total ionic current (nA) 7,000 7,200 7,400 7,600 7,800 8,000 Total ionic current (nA) Ch1 FET conductance (nS) Ch2 FET conductance (nS) Ch3 FET conductance (nS) Time (ms) Reconstructed ionic current (nA) 20 30 6,400 6,450 6,500 15,500 16,000 8,800 9,000 9,200 8,800 9,000 9,200 15,600 15,800 16,000 6,450 6,500 30 20 10 30 20 40 Figure 4 | Multi-channel recording of DNA translocation with three nanowire–nanopore FET sensors. All measurements are made with 1 M KCl buffer in the cis chamber and 10 mM KCl buffer in the trans chamber, a voltage of 3 V, and 1.4 nM pUC19 DNA. a, Simultaneous recording of the total ionic current and three nanowire–nanopore FET conductance channels (Ch1–Ch3). b, Higher-resolution view of the multiplexed recording from the dashed rectangular area in a. The dashed red trace in the upper panel corresponds to the reconstructed ionic current trace (offset 10 nA for clarity) calculated from the three FET traces. NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 LETTERS NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology 123 © 2012 Macmillan Publishers Limited. All rights reserved.
ETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO 2011.217 100: 1 ratio as for the results presented in Fig. 4 for 1 M/10 mM) Methods show that the signal amplitude is approximately constant when The silicon nanowires were synthesized by chemical vapour deposition(CVD) the buffer concentration changes proportionally in both chambers, methods as described previously".Electron-beam lithography(EBL)and solid-state conventional charge-based FET sensing mechanism. Furthermore, deposited by plama-enshanced cvp was ned to pais ate al metal meatrbodes when the cis/trans concentrat ratio is reduced to 10:1. the bef recorded translocation signal (Supplementary Fig S7)is reduced a JEOL 2010F field-emission TEM. The nanowire- s predicted by the model in Fig. 3c. Finally, translocation experiments carried using the formally neutral polymer polyethy lene glycol ( Supplementary Methods, Fig. S8)show correlated clamped-on PDMS chambers with a tight seal, which were filled with sterilized and filtered buffer solutions. DNA translocation measurements were made using ionic current and FET conductance signals similar to but linearized pUC19 FET and ionic current signals were fied and digitized using smaller in amplitude than recorded for DNA translocation. The standard electronics with the sen smaller FET signal is consistent with expectations for our model See supplementary information for full methods and any associated references. (given the smaller ionic current signal change)and,more importantly, the fact that we observe the same signal polarity in Receive September 2011; accepted 7 November 2011 the FET channel is inconsistent with a charge-based FET sensing publish ine 11 December 2011 mechanism but in complete agreement with our potential sensing mechanism References A key advantage of the nanowire-nanopore FET sensor is 1. Branton, D et al. The potential and challenges of nanopore sequencing. Nature biotech.26,1146-1153(2008) sis chamber without complex microfluidic systemas. Notably, 2. Nantkrt an B. .& 615-624 anopore sensors for nucleic acid analysis. simultaneous recording from three nanowire-nanopore devices 3. Zwolak, M.& Ventra, M D Colloquium: physical approaches to DNA observed in all three FET channels as well as for the total ionic 4. Dekker. ic ond detection. Rev. Mod. Phys 80, 141-163(2008) current channel. Closer examination of the three fet and total 5. Clarke, J et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotech. 4, 265-270 (2009). nic current signals (Fig. 4b)shows clearly that the three FET 6. Derrington, L M et al. Nanopore DNA sequencing with MspA.Proc. NatlAcad. channels operate independently, and every falling or rising edge ScL USA107,16060-16065(2010) apparent in the total ionic current channel can be uniquely corre- 7. Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane Nature lated to a corresponding edge in one of the three FET channels 467,190-19302010) Significantly, the total ionic current signal reconstructed from the 8. Merchant, C. A. et al. DNA translocation through graphene nanopores, data for the three FEt channels(dashed-red trace, top panel, 9. Schneider, G E et al. DNA translocation through graphene nanopores. ig, 4b)exhibits nearly perfect agreement with the measured total Nano Lett10,3163-3167(2010) ionic current(Supplementary Methods). In addition, a histogram 10. Fologea, D, Uplinger, J, Thomas, B, McNabb, D.S.& Li, J. Slowing D channel-specific ionic currents (Supplementary Methods, translocation in a solid-state nanopore. Nano Lett. 5, 1734-1737(2005). ig. S9)demonstrates that the ionic current signa litudes in 11. Peng, H& Ling X S Reverse DNA translocation throu solid-state nanopore different channels are also independent. As previous studies have 12. Olasagasti, E. et al. Replication of individual DNA molecules under electronic feT devices2with reproducible properties, and the local potential 13. Luan, B et al. Base-by-base ratcheting of single stranded DNA through a gnal decay length is as short as tens of nanometres, we expect nat it will also be possible to multiplex the nanowire-nanopore through a semiconductor nanopore-capacitor. Nanotedhnology 17, 622-633(2006). th FETs in much higher numbers and densities. Direct sequencing of long single-stranded DNA molecules using ys.Rev.Let95,2l6103(2005 FET-based nanopore sensors and the new potential change 16 Lagerqvist, J, Zwolak, M. Ventra, M D Fast DNA sequencing via transverse detection mechanism will require optimization of the signal-to- electronic transport. Nano Lett. 6, 779-782(2006) noise ratio associated with individual bases as well as improvement 11,279-285(2011) 17. Ivanov, A.P. et al. DNA tunnelling detector embedded in a nanopore Nano Left. in signal spatial resolution. Recognizing that direct base differen- 18. Chaste, I et al. Single carbon nanotube transistor at GHz frequency Nano Lett tiation by FET potential measurement is coupled to variations 8,525-528(2008). in the ionic current suggests that concepts proposed and demon- 19. Hu, Y, Xiang. J Liang, G, Yan, H. Lieber, C M Sub-100 nanometer channel strated for base-resolved ionic current measurements5-7 could successfully combined with our work. For example, it should be 20. Cui, Y. Wei, Q, Park, H. Lieber. C. M Nanowire nanosensors for highly possible to extend our nanowire-nanopore FET to atomically thin sensitive and selective detection of biological and chemical species. Science 293 graphene membranes- so as to achiev 1289-1292(2001) resolution, although the graphene nanopore would require precise 21 Patolsky, F et al Electrical detection of single viruses. Proc.Nat! Acad. Sci. USA structure engineering to enable differentiation of the distinct 101,14017-14022(2004) 22. Patolsky, F. et al Detection, stimulation, and inhibition of neuronal signals bases.Alternatively, coupling an engineered protein nanopore to with high-density nanowire transistor Science313,1100-1104(2006 the nanowire-nanopore FET could provide both the spatial and 23. Kim, M I, Wanunu, M. Bell, D. C. Meller, A Rapid fabrication of uniformly base resolution necessary for direct sequencing due to the localized sized nanopores and nanopore arrays for parallel DNA analysis. Adv. Mater. nanowire-nanopore FET sensor results and modelling strongly 24. Kasianowicz, - J Brandin, E, Branton, D &Deamer, D. WCharacterization of ad.Sa.UsA93,13770-13773(1996) urrent and other sensor-based detection schemes, including 25. Li, J et al. Ion-beam sculpting at nanometre length scales. Nature 412, rger measurement signals, high signal bandwidth with attractive 166-169(2001). nanopore-size scaling, and straightforward integration and multi- 26.Cohen-Karni,T,Timko,BP,Weiss,LE&Lieber,CMFlexible electrical plexing. We believe that this work provides a strong starting point reording from cells using nanowire transistor arrays. Proc Natl Acad. Sc: USA for a new class of nanopore sequencing devices with the capability 27. Tian, B et al. Three-dimensional, flexible nanoscale field-effect transistors as for fast direct sequencing and large-scale integration localised bioprobes. Science 329, 831-834(2010) NatureNanotEchnOlogYIVol7IFebRuaRy2012Iwww.nature.com/naturenanotechnology o 2012 Macmillan Publishers Limited. All rights reserved
100:1 ratio as for the results presented in Fig. 4 for 1 M/10 mM) show that the signal amplitude is approximately constant when the buffer concentration changes proportionally in both chambers, in agreement with the model predictions and in contrast to the conventional charge-based FET sensing mechanism. Furthermore, when the cis/trans concentration ratio is reduced to 10:1, the recorded translocation signal (Supplementary Fig. S7) is reduced as predicted by the model in Fig. 3c. Finally, translocation experiments carried using the formally neutral polymer polyethylene glycol (Supplementary Methods, Fig. S8) show correlated ionic current and FET conductance signals similar to but smaller in amplitude than recorded for DNA translocation. The smaller FET signal is consistent with expectations for our model (given the smaller ionic current signal change) and, more importantly, the fact that we observe the same signal polarity in the FET channel is inconsistent with a charge-based FET sensing mechanism but in complete agreement with our potential sensing mechanism. A key advantage of the nanowire–nanopore FET sensor is the potential for integration and multiplexing within a single analysis chamber without complex microfluidic systems28. Notably, simultaneous recording from three nanowire–nanopore devices (Fig. 4a) demonstrates that continuous translocation events are observed in all three FET channels as well as for the total ionic current channel. Closer examination of the three FET and total ionic current signals (Fig. 4b) shows clearly that the three FET channels operate independently, and every falling or rising edge apparent in the total ionic current channel can be uniquely correlated to a corresponding edge in one of the three FET channels. Significantly, the total ionic current signal reconstructed from the data for the three FET channels (dashed-red trace, top panel, Fig. 4b) exhibits nearly perfect agreement with the measured total ionic current (Supplementary Methods). In addition, a histogram of channel-specific ionic currents (Supplementary Methods, Fig. S9) demonstrates that the ionic current signal amplitudes in different channels are also independent. As previous studies have shown that it is possible to fabricate large numbers of nanowire– FET devices29 with reproducible properties, and the local potential signal decay length is as short as tens of nanometres, we expect that it will also be possible to multiplex the nanowire–nanopore FETs in much higher numbers and densities. Direct sequencing of long single-stranded DNA molecules using FET-based nanopore sensors and the new potential change detection mechanism will require optimization of the signal-tonoise ratio associated with individual bases as well as improvement in signal spatial resolution. Recognizing that direct base differentiation by FET potential measurement is coupled to variations in the ionic current suggests that concepts proposed and demonstrated for base-resolved ionic current measurements5–7 could be successfully combined with our work. For example, it should be possible to extend our nanowire–nanopore FET to atomically thin graphene membranes7–9 so as to achieve single base spatial resolution, although the graphene nanopore would require precise structure engineering to enable differentiation of the distinct bases. Alternatively, coupling an engineered protein nanopore to the nanowire–nanopore FET could provide both the spatial and base resolution necessary for direct sequencing due to the localized change of the potential at the nanopore opening (Fig. 3d). Our nanowire–nanopore FET sensor results and modelling strongly motivate such effort, given the advantages over direct ionic current and other sensor-based detection schemes, including larger measurement signals, high signal bandwidth with attractive nanopore-size scaling, and straightforward integration and multiplexing. We believe that this work provides a strong starting point for a new class of nanopore sequencing devices with the capability for fast direct sequencing and large-scale integration. Methods The silicon nanowires were synthesized by chemical vapour deposition (CVD) methods as described previously30. Electron-beam lithography (EBL) and solid-state diffusion of the nickel contact were used to fabricate short-channel devices on commercially available SiNx TEM membrane grid chips. A SiNx conformal thin film deposited by plasma-enhanced CVD was used to passivate all metal electrodes before final lift-off. Nanopores were drilled by focusing the 200 keV electron beam in a JEOL 2010F field-emission TEM. The nanowire–nanopore FET sensor chip was glued onto a home-made PCB chip carrier and electrically connected to the chip carrier by wire bonding. The chip carrier was sandwiched between mechanically clamped-on PDMS chambers with a tight seal, which were filled with sterilized and filtered buffer solutions. DNA translocation measurements were made using linearized pUC19. FET and ionic current signals were amplified and digitized using standard electronics with the sensor set-up mounted in a Faraday box. See supplementary information for full methods and any associated references. Received 16 September 2011; accepted 7 November 2011; published online 11 December 2011 References 1. Branton, D. et al. The potential and challenges of nanopore sequencing. Nature Biotechnol. 26, 1146–1153 (2008). 2. Venkatesan, B. M. & Bashir R. Nanopore sensors for nucleic acid analysis. Nature Nanotech. 6, 615–624 (2011). 3. Zwolak, M. & Ventra, M. D. Colloquium: physical approaches to DNA sequencing and detection. Rev. Mod. Phys. 80, 141–163 (2008). 4. Dekker, C. Solid-state nanopores. Nature Nanotech. 2, 209–215 (2007). 5. Clarke, J. et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotech. 4, 265–270 (2009). 6. Derrington, I. M. et al. Nanopore DNA sequencing with MspA. Proc. Natl Acad. Sci. USA 107, 16060–16065 (2010). 7. Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190–193 (2010). 8. Merchant, C. A. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 2915–2921 (2010). 9. Schneider, G. F. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 3163–3167 (2010). 10. Fologea, D., Uplinger, J., Thomas, B., McNabb, D. S. & Li, J. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 5, 1734–1737 (2005). 11. Peng, H. & Ling X. S. Reverse DNA translocation through a solid-state nanopore by magnetic tweezers. Nanotechnology 20, 185101 (2009). 12. Olasagasti, F. et al. Replication of individual DNA molecules under electronic control using a protein nanopore. Nature Nanotech. 5, 798–806 (2010). 13. Luan, B. et al. Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys. Rev. Lett. 104, 238103 (2010). 14. Gracheva, M. E. et al. Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor. Nanotechnology 17, 622–633 (2006). 15. King, G. M. & Golovchenko, J. A. Probing nanotube–nanopore interactions. Phys. Rev. Lett. 95, 216103 (2005). 16. Lagerqvist, J., Zwolak, M. & Ventra, M. D. Fast DNA sequencing via transverse electronic transport. Nano Lett. 6, 779–782 (2006). 17. Ivanov, A. P. et al. DNA tunnelling detector embedded in a nanopore. Nano Lett. 11, 279–285 (2011). 18. Chaste, J. et al. Single carbon nanotube transistor at GHz frequency. Nano Lett. 8, 525–528 (2008). 19. Hu, Y., Xiang, J., Liang, G., Yan, H. & Lieber, C. M. Sub-100 nanometer channel length Ge/Si nanowire transistors with potential for 2 THz switching speed. Nano Lett. 8, 925–930 (2008). 20. Cui, Y., Wei, Q., Park, H. & Lieber, C. M. Nanowire nanosensors for highly sensitive and selective detection of biological and chemical species. Science 293, 1289–1292 (2001). 21. Patolsky, F. et al. Electrical detection of single viruses. Proc. Natl Acad. Sci. USA 101, 14017–14022 (2004). 22. Patolsky, F. et al. Detection, stimulation, and inhibition of neuronal signals with high-density nanowire transistor arrays. Science 313, 1100–1104 (2006). 23. Kim, M. J., Wanunu, M., Bell, D. C. & Meller, A. Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Adv. Mater. 18, 3149–3153 (2006). 24. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770–13773 (1996). 25. Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 (2001). 26. Cohen-Karni, T., Timko, B. P., Weiss, L. E. & Lieber, C. M. Flexible electrical recording from cells using nanowire transistor arrays. Proc. Natl Acad. Sci. USA 106, 7309–7313 (2009). 27. Tian, B. et al. Three-dimensional, flexible nanoscale field-effect transistors as localised bioprobes. Science 329, 831–834 (2010). LETTERS NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 124 NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology © 2012 Macmillan Publishers Limited. All rights reserved
NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO2011217 LETTERS 28 Osaki, T, Suzuki H, Le Pioutle, B. Takeuchi, S Multichannel simultaneous Author contributions measurements of single-molecule translocation in a-hemolysin nanopore array. Px Q.x. Y F and C.M.L. designed the experiments. PX Q.X. and Y.E. performed the AnaL chem81,9866-9870(2009) 29. Yan, H et al. Programmable nanowire circuits for nanoprocessors Nature 470, program for data processing PX Q.x. Y.E. Q.Q. and C MLL analysed the data and wrote 40-244(2011) the manuscript 30. Cui, Y, Zhong, Z, Wang D, Wang, w.& Lieber, C M. High performance silicon nanowire field effect transistors. Nano Lett. 3, 149-152(2003) Additional information Acknowledgements The authors declare no cor ature. com/naturenanotechnology Reprints and Kempa for helpful discussions. C M L acknowledges support of this work from a NIE Directors Pioneer Award(SDPlOD003900). and requests for materials addressed to C.M. L NaturENanotEchnOlogYIVol7IFebRuaRy2012Iwww.nature.com/naturenanotechnology o 2012 Macmillan Publishers Limited. All rights reserved
28. Osaki, T., Suzuki H., Le Pioutle, B. & Takeuchi, S. Multichannel simultaneous measurements of single-molecule translocation in a-hemolysin nanopore array. Anal. Chem. 81, 9866–9870 (2009). 29. Yan, H. et al. Programmable nanowire circuits for nanoprocessors. Nature 470, 240–244 (2011). 30. Cui, Y., Zhong, Z., Wang D., Wang, W. & Lieber, C. M. High performance silicon nanowire field effect transistors. Nano Lett. 3, 149–152 (2003). Acknowledgements The authors thank A. Meller, M. Wanunu, D. Casanova, J. Huang, J. Cahoon and T.J. Kempa for helpful discussions. C.M.L. acknowledges support of this work from a NIH Director’s Pioneer Award (5DP1OD003900). Author contributions P.X., Q.X., Y.F. and C.M.L. designed the experiments. P.X., Q.X. and Y.F. performed the experiments. P.X. performed the modelling and calculation. P.X. and Q.Q. wrote the program for data processing. P.X., Q.X., Y.F., Q.Q. and C.M.L. analysed the data and wrote the manuscript. Additional information The authors declare no competing financial interests. Supplementary information accompanies this paper at www.nature.com/naturenanotechnology. Reprints and permission information is available online at http://www.nature.com/reprints. Correspondence and requests for materials should be addressed to C.M.L. NATURE NANOTECHNOLOGY DOI: 10.1038/NNANO.2011.217 LETTERS NATURE NANOTECHNOLOGY | VOL 7 | FEBRUARY 2012 | www.nature.com/naturenanotechnology 125 © 2012 Macmillan Publishers Limited. All rights reserved