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 reservedLocal 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 measure￾ments5–7, 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 transloca￾tion4,10–13, 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 cur￾rents15–17, 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 nano￾pore 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 FET￾channel 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 trans￾location events in the ionic current channel when the transmem￾brane 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.