Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing

It has recently been shown that solid-state nanometer-scale pores ('nanopores') can be used as highly sensitive single-molecule sensors. For example, electrophoretic translocation of DNA, RNA and proteins through such nanopores has enabled both detection and structural analysis of these complex biomolecules. Control over the nanopore size is critical as the pore must be comparable in size to the analyte molecule in question. The most widely used fabrication methods are based on focused electron or ion beams and thus require (scanning) transmission electron microscopy and focused ion beam (FIB) instrumentation. Even though very small pores have been made using these approaches, several issues remain. These include the requirement of being restricted to rather thin, mechanically less stable membranes, particularly for pore diameters in the single-digit nanometer range, lack of control of the surface properties at and inside the nanopore, and finally, the fabrication cost. In the proof-of-concept study, we report on a novel and simple route for fabricating metal nanopores with apparent diameters below 20 nm using electrodeposition and real-time ionic current feedback in solution. This fabrication approach inserts considerable flexibility into the kinds of platforms that can be used and the nanopore membrane material. Starting from much larger pores, which are straightforward to make using FIB or other semiconductor fabrication methods, we electrodeposit Pt at the nanopore interface while monitoring its ionic conductance at the same time in a bi-potentiostatic setup. Due to the deposition of Pt, the nanopore decreases in size, resulting in a decrease of the pore conductance. Once a desired pore conductance has been reached, the electrodeposition process is stopped by switching the potential of the membrane electrode and the fabrication process is complete. Furthermore, we demonstrate that these pores can be used for single-biomolecule analysis, such as that of λ-DNA, which we use in a proof-of-concept study. Importantly, our approach is applicable to single nanopores as well as nanopore arrays, and can easily be extended to deposits of metal other than Pt.

[1]  Peng Chen,et al.  Atomic Layer Deposition to Fine-Tune the Surface Properties and Diameters of Fabricated Nanopores. , 2004, Nano letters.

[2]  Meni Wanunu,et al.  Chemically modified solid-state nanopores. , 2007, Nano letters.

[3]  Matsuhiko Nishizawa,et al.  Metal Nanotubule Membranes with Electrochemically Switchable Ion-Transport Selectivity , 1995, Science.

[4]  S. Jacobson,et al.  Effect of conical nanopore diameter on ion current rectification. , 2009, The journal of physical chemistry. B.

[5]  J. Baumberg,et al.  Engineering SERS via absorption control in novel hybrid Ni/Au nanovoids. , 2009, Optics express.

[6]  Marija Drndic,et al.  Sub-10 nm device fabrication in a transmission electron microscope. , 2007, Nano letters.

[7]  Ryan J. White,et al.  Simultaneous alternating and direct current readout of protein ion channel blocking events using glass nanopore membranes. , 2008, Analytical chemistry.

[8]  Zuzanna S Siwy,et al.  Versatile ultrathin nanoporous silicon nitride membranes , 2009, Proceedings of the National Academy of Sciences.

[9]  Jiajun Gu,et al.  PROBING SINGLE DNA MOLECULE TRANSPORT USING FABRICATED NANOPORES. , 2004, Nano letters.

[10]  Bo Zhang,et al.  Electrostatic-gated transport in chemically modified glass nanopore electrodes. , 2006, Journal of the American Chemical Society.

[11]  H. Sakaue,et al.  Direct fabrication of nanopores in a metal foil using focused ion beam with in situ measurements of the penetrating ion beam current. , 2009, The Review of scientific instruments.

[12]  P. Kotula,et al.  Controlled fabrication of nanopores using a direct focused ion beam approach with back face particle detection , 2008, Nanotechnology.

[13]  Meni Wanunu,et al.  DNA translocation governed by interactions with solid-state nanopores. , 2008, Biophysical journal.

[14]  K. Schulten,et al.  Simulation of the electric response of DNA translocation through a semiconductor nanopore–capacitor , 2006 .

[15]  Zuzanna S Siwy,et al.  Conical nanopore membranes: controlling the nanopore shape. , 2006, Small.

[16]  J. Reiner,et al.  Nanoscopic porous sensors. , 2008, Annual review of analytical chemistry.

[17]  Rashid Bashir,et al.  Fabrication and characterization of solid-state nanopores using a field emission scanning electron microscope , 2006 .

[18]  D. Branton,et al.  Rapid nanopore discrimination between single polynucleotide molecules. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Ryan J. White,et al.  Glass nanopore-based ion-selective electrodes. , 2007, Analytical chemistry.

[20]  P. Batson,et al.  Formation of nanopores in a SiN/SiO2 membrane with an electron beam , 2005 .

[21]  Jonathan R. I. Lee,et al.  Localized Functionalization of Single Nanopores , 2006 .

[22]  C. Dekker Solid-state nanopores. , 2007, Nature nanotechnology.

[23]  G. Tonini,et al.  DNA-functionalized solid state nanopore for biosensing , 2010, Nanotechnology.

[24]  A. Ivanov,et al.  Nanopore/electrode structures for single-molecule biosensing , 2010 .

[25]  T. Sorsch,et al.  Nanopores in solid-state membranes engineered for single molecule detection , 2010, Nanotechnology.

[26]  C. Dekker,et al.  Fabrication of solid-state nanopores with single-nanometre precision , 2003, Nature materials.

[27]  Susan Daniel,et al.  Single ion-channel recordings using glass nanopore membranes. , 2007, Journal of the American Chemical Society.

[28]  A. Meller,et al.  Rapid Fabrication of Uniformly Sized Nanopores and Nanopore Arrays for Parallel DNA Analysis , 2006 .

[29]  Jongin Hong,et al.  Design of a solid-state nanopore-based platform for single-molecule spectroscopy. , 2008, Nanotechnology.

[30]  Shizhi Qian,et al.  Effects of Electroosmotic Flow on Ionic Current Rectification in Conical Nanopores , 2010 .

[31]  Michael J. Aziz,et al.  Ion-beam sculpting at nanometre length scales , 2001, Nature.

[32]  Ryan J. White,et al.  Bench-top method for fabricating glass-sealed nanodisk electrodes, glass nanopore electrodes, and glass nanopore membranes of controlled size. , 2007, Analytical chemistry.

[33]  A. Meller,et al.  Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores. , 2010, The Review of scientific instruments.

[34]  Alexey Bezryadin,et al.  Fabrication of symmetric sub-5 nm nanopores using focused ion and electron beams , 2006 .

[35]  P. Ramirez,et al.  Synthetic nanopores with fixed charges: an electrodiffusion model for ionic transport. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[36]  M. Gaitan,et al.  Microelectroplating Silver on Sharp Edges toward the Fabrication of Solid-State Nanopores , 2004 .

[37]  Aleksei Aksimentiev,et al.  Detection of DNA sequences using an alternating electric field in a nanopore capacitor. , 2008, Nano letters.

[38]  V. Radmilović,et al.  Formation of a few nanometer wide holes in membranes with a dual beam focused ion beam system , 2003 .

[39]  Hongbo Peng,et al.  Fabrication of nanopores in silicon chips using feedback chemical etching. , 2007, Small.

[40]  Nicholas N. Watkins,et al.  Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis , 2009, Advanced materials.

[41]  J. Zuo,et al.  DNA Sensing Using Nanocrystalline Surface‐Enhanced Al2O3 Nanopore Sensors , 2010, Advanced functional materials.

[42]  S. Howorka,et al.  Sequence-specific detection of individual DNA strands using engineered nanopores , 2001, Nature Biotechnology.

[43]  D. Branton,et al.  Characterization of nucleic acids by nanopore analysis. , 2002, Accounts of chemical research.

[44]  J. Leburton,et al.  p-n Semiconductor membrane for electrically tunable ion current rectification and filtering. , 2007, Nano letters.

[45]  Amit Meller,et al.  Single molecule measurements of DNA transport through a nanopore , 2002, Electrophoresis.

[46]  Z. Siwy,et al.  A nanodevice for rectification and pumping ions , 2004 .

[47]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.

[48]  T. Thornton,et al.  Fabrication of Cylindrical Nanopores and Nanopore Arrays in Silicon-On-Insulator Substrates , 2007, Journal of Microelectromechanical Systems.

[49]  U. Keyser,et al.  Salt dependence of ion transport and DNA translocation through solid-state nanopores. , 2006, Nano letters.

[50]  Min Jun Kim,et al.  Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope , 2007 .

[51]  In-Ho Lee,et al.  Nanopore sensor for fast label-free detection of short double-stranded DNAs. , 2007, Biosensors & bioelectronics.

[52]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Reimar Spohr,et al.  Diode-like single-ion track membrane prepared by electro-stopping , 2001 .

[54]  C. Mirkin,et al.  Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. , 2002, Journal of the American Chemical Society.

[55]  C. Dekker,et al.  Translocation of double-strand DNA through a silicon oxide nanopore. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[56]  Z. Siwy,et al.  Engineered voltage-responsive nanopores. , 2010, Chemical Society reviews.

[57]  J. Giérak,et al.  Direct FIB fabrication and integration of single nanopore devices for the manipulation of macromolecules , 2010 .

[58]  D. Deamer,et al.  Nanopores and nucleic acids: prospects for ultrarapid sequencing. , 2000, Trends in biotechnology.