Development of solid-state nanopore fabrication technologies

As the key components of nanopore-based nucleic acid sequencing systems, nanopores have drawn more and more scientific interests over these years. Although most of the early nanopore-based sequencers adopted biological nanopores, solid-state nanopores have been gradually growing in popularity due to their increased robustness and durability, control over pore geometry and surface properties, as well as compatibility with the existing semiconductor and microfluidics fabrication techniques. Besides acting as a platform for biomolecular analysis, solid-state nanopores also have great potential in many other fields such as near-field optics, nanostencil lithography and ionic logic circuitry, due to the possibility of parallel massive production. Therefore, many approaches for the fabrication of solid-state nanopores have been developed. This paper reviews the typical solid-state nanopore fabrication techniques reported to date and compares their advantages and disadvantages. The specific applications of each kind of solid-state nanopores are also summarized based on the carefully analysis of their unique morphologies and properties such as the feature size, inner structure and possibility of massive production.摘要作为基于纳米孔核酸测序系统的关键组成部分,近年来纳米孔在科研领域吸引了越来越多的研究兴趣。虽然早期基于纳米孔的测序系统大多数采用的是生物纳米孔,但由于固态纳米孔拥有更优异的鲁棒性和耐久性,且孔的几何结构及表面性质可控,并与现有的半导体和微流体制造技术相兼容等优势,因而愈来愈受到欢迎。由于高密度的固态纳米/纳米孔阵列可以被大规模的生产出来,固态纳米孔不但可以作为生物分子检测的平台,而且在很多其他领域也拥有广阔的应用前景,例如近场光学、纳米模板光刻和离子逻辑电路等。因此,研究人员已经开发出了各种各样的固态纳米孔制备方法。为了促进固态纳米孔制备技术的研究并拓展固态纳米孔的应用,本文对已经报道的各种典型的固态纳米孔制备方法进行了总结,详细剖析了各种固态纳米孔制备方法的工作机理,比较了各种方法在材料适用性、工艺可控性等各方面的优缺点。此外,在细致分析了各种固态纳米孔的特征,如纳米孔的极限尺寸、内部结构、能否并行大批量生产等的基础上,对不同固态纳米孔的潜在应用进行了总结。

[1]  Dusan Losic,et al.  Nanoporous anodic aluminium oxide: Advances in surface engineering and emerging applications , 2013 .

[2]  Leszek Zaraska,et al.  Synthesis of nanoporous tin oxide layers by electrochemical anodization , 2013 .

[3]  P. Schmuki,et al.  Transition from Nanopores to Nanotubes: Self-Ordered Anodic Oxide Structures on Titanium−Aluminides , 2008 .

[4]  Derek Stein,et al.  Ion-beam sculpting time scales. , 2002, Physical review letters.

[5]  S. Grigorescu,et al.  Various sized nanotubes on TiZr for antibacterial surfaces , 2013 .

[6]  M. Wanunu Nanopores: A journey towards DNA sequencing. , 2012, Physics of Life Reviews.

[7]  Zuzanna S Siwy,et al.  Detecting single porphyrin molecules in a conically shaped synthetic nanopore. , 2005, Nano letters.

[8]  Reinhard Neumann,et al.  Electro-responsive asymmetric nanopores in polyimide with stable ion-current signal , 2003 .

[9]  H. Osmanbeyoglu,et al.  Thin alumina nanoporous membranes for similar size biomolecule separation , 2009 .

[10]  A. Morrison,et al.  Solid-state nanopore technologies for nanopore-based DNA analysis. , 2007, Nanomedicine.

[11]  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.

[12]  P. Ajayan,et al.  Large Area Vapor Phase Growth and Characterization of MoS2 Atomic Layers on SiO2 Substrate , 2011, 1111.5072.

[13]  Gilles Patriarche,et al.  Sub-5nm FIB direct patterning of nanodevices , 2007 .

[14]  Kornelius Nielsch,et al.  Fast fabrication of long-range ordered porous alumina membranes by hard anodization , 2006, Nature materials.

[15]  Andreas Zürner,et al.  Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing. , 2010, Small.

[16]  Andrei Ghicov,et al.  Self-ordering electrochemistry: a review on growth and functionality of TiO2 nanotubes and other self-aligned MO(x) structures. , 2009, Chemical communications.

[17]  T. Xu,et al.  Size-dependent evolution of graphene nanopores under thermal excitation. , 2012, Small.

[18]  J. Georgiadis,et al.  Science and technology for water purification in the coming decades , 2008, Nature.

[19]  Andre K. Geim,et al.  Two-dimensional atomic crystals. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Sepideh Minagar,et al.  A review of the application of anodization for the fabrication of nanotubes on metal implant surfaces. , 2012, Acta biomaterialia.

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

[22]  Michael Zwolak,et al.  Fast DNA sequencing via transverse electronic transport. , 2006, Nano letters.

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

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

[25]  R. Bashir,et al.  Electron beam induced local crystallization of HfO2 nanopores for biosensing applications. , 2013, Nanoscale.

[26]  Yu-Chuan Lin,et al.  Growth of large-area and highly crystalline MoS2 thin layers on insulating substrates. , 2012, Nano letters.

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

[28]  A. Hall,et al.  Direct and transmission milling of suspended silicon nitride membranes with a focused helium ion beam. , 2012, Scanning.

[29]  A. Balan,et al.  Toward sensitive graphene nanoribbon-nanopore devices by preventing electron beam-induced damage. , 2013, ACS nano.

[30]  K. Saha,et al.  DNA base-specific modulation of $\mu$A transverse edge currents through a metallic graphene nanoribbon with a nanopore , 2012 .

[31]  S. Dai,et al.  Porous graphene as the ultimate membrane for gas separation. , 2009, Nano letters.

[32]  K. Shepard,et al.  Boron nitride substrates for high-quality graphene electronics. , 2010, Nature nanotechnology.

[33]  S. D. Collins,et al.  Nanopore formation by low-energy focused electron beam machining , 2010, Nanotechnology.

[34]  T. Deng,et al.  Fabrication of silicon nanopore arrays using a combination of dry and wet etching , 2012 .

[35]  A. Berg,et al.  Nanofluidics: Silicon for the perfect membrane , 2007, Nature.

[36]  H. Postma,et al.  Rapid sequencing of individual DNA molecules in graphene nanogaps. , 2008, Nano letters.

[37]  P. Schmuki,et al.  Preparation of Organized Ti Nanorods by Successive Electrochemical Processes in Aqueous Solution and Molten Salt , 2008 .

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

[39]  C. R. Martin,et al.  Developing synthetic conical nanopores for biosensing applications. , 2007, Molecular bioSystems.

[40]  J. Macák,et al.  Rapid anodic growth of TiO2 and WO3 nanotubes in fluoride free electrolytes , 2007 .

[41]  C. Dekker,et al.  Sculpting nanoelectrodes with a transmission electron beam for electrical and geometrical characterization of nanoparticles. , 2005, Nano letters.

[42]  Focused Ion-Beam Based Nanohole Modeling, Simulation, Fabrication, and Application , 2010 .

[43]  Josep Ferré-Borrull,et al.  Tuning the photonic stop bands of nanoporous anodic alumina-based distributed bragg reflectors by pore widening. , 2013, ACS applied materials & interfaces.

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

[45]  Christina Trautmann,et al.  An Asymmetric Polymer Nanopore for Single Molecule Detection , 2004 .

[46]  Waseem Asghar,et al.  Shrinking of Solid-state Nanopores by Direct Thermal Heating , 2011, Nanoscale research letters.

[47]  Derek Stein,et al.  Nanoscale volcanoes: accretion of matter at ion-sculpted nanopores. , 2006, Physical review letters.

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

[49]  W. Ko,et al.  A generalized theory of an electrolyte-insulator-semiconductor field-effect transistor , 1986, IEEE Transactions on Electron Devices.

[50]  Zeng-Qiang Wu,et al.  Solution‐pH‐Modulated Rectification of Ionic Current in Highly Ordered Nanochannel Arrays Patterned with Chemical Functional Groups at Designed Positions , 2013 .

[51]  Gilles Patriarche,et al.  Focused ion beam sculpted membranes for nanoscience tooling , 2006 .

[52]  Qun Cai,et al.  Nanopore sculpting with noble gas ions. , 2006, Journal of applied physics.

[53]  T. Ebbesen,et al.  Light in tiny holes , 2007, Nature.

[54]  DNA Translocation through Graphene Nanopores , 2011 .

[55]  Andre K. Geim,et al.  Electric Field Effect in Atomically Thin Carbon Films , 2004, Science.

[56]  Urs Staufer,et al.  Sensing protein molecules using nanofabricated pores , 2006 .

[57]  Dapeng Yu,et al.  Controlled deformation of Si3N4 nanopores using focused electron beam in a transmission electron microscope , 2011, Nanotechnology.

[58]  L. Qin,et al.  Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection , 2011, Nanotechnology.

[59]  Henny W. Zandbergen,et al.  Atomic-Scale Electron-Beam Sculpting of Defect-Free Graphene Nanostructures , 2011, Microscopy and Microanalysis.

[60]  A. Fedorov,et al.  A DLVO model for catalyst motion in metal-assisted chemical etching based upon controlled out-of-plane rotational etching and force-displacement measurements. , 2013, Nanoscale.

[61]  Lei Jiang,et al.  Energy Harvesting with Single‐Ion‐Selective Nanopores: A Concentration‐Gradient‐Driven Nanofluidic Power Source , 2010 .

[62]  Joseph A. Billo,et al.  Viscosity and surface-free energy effects in thermal shrinking of solid-state nanopores , 2012 .

[63]  Markus Brink,et al.  Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales. , 2014, Nanoscale.

[64]  D. Branton,et al.  Molecule-hugging graphene nanopores , 2013, Proceedings of the National Academy of Sciences.

[65]  Yanbiao Liu,et al.  Efficient photochemical water splitting and organic pollutant degradation by highly ordered TiO2 nanopore arrays , 2009 .

[66]  D. Gracias,et al.  Voltage-gated ion transport through semiconducting conical nanopores formed by metal nanoparticle-assisted plasma etching. , 2012, Nano letters.

[67]  J. Brugger,et al.  Fabrication and functionalization of nanochannels by electron-beam-induced silicon oxide deposition. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[68]  R. Fernandes,et al.  A one-step etching method to produce gold nanoparticle coated silicon microwells and microchannels , 2010, Analytical and bioanalytical chemistry.

[69]  P. Schmuki,et al.  Ideal Hexagonal Order: Formation of Self-Organized Anodic Oxide Nanotubes and Nanopores on a Ti–35Ta Alloy , 2010 .

[70]  Grégory Pandraud,et al.  Atomic-scale electron-beam sculpting of near-defect-free graphene nanostructures. , 2011, Nano letters.

[71]  J. Eijkel,et al.  A general model to describe the electrostatic potential at electrolyte oxide interfaces , 1996 .

[72]  Tao Xu,et al.  Fabrication of nanopores using electron beam , 2013, The 8th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems.

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

[74]  D. Higgins,et al.  Formation of self-organized nanoporous anodic oxide from metallic gallium. , 2012, Langmuir : the ACS journal of surfaces and colloids.

[75]  Joshua B Edel,et al.  Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. , 2013, Chemical Society reviews.

[76]  J. Leburton,et al.  Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor , 2006 .

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

[78]  J. Macák,et al.  Self-organized nanotubular oxide layers on Ti-6Al-7Nb and Ti-6Al-4V formed by anodization in NH4F solutions. , 2005, Journal of biomedical materials research. Part A.

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

[80]  Marija Drndic,et al.  Electron beam nanosculpting of suspended graphene sheets , 2008 .

[81]  Matthew B. Kerby,et al.  Landscape of next-generation sequencing technologies. , 2011, Analytical chemistry.

[82]  Patrik Schmuki,et al.  Formation of self-organized niobium porous oxide on niobium , 2005 .

[83]  M. Malac,et al.  Radiation damage in the TEM and SEM. , 2004, Micron.

[84]  Akihiko Hirata,et al.  Nanoporous metal/oxide hybrid electrodes for electrochemical supercapacitors. , 2011, Nature nanotechnology.

[85]  Derek Stein,et al.  Feedback-controlled ion beam sculpting apparatus , 2004 .

[86]  Aaron T. Kuan,et al.  Nanometer-thin solid-state nanopores by cold ion beam sculpting. , 2012, Applied physics letters.

[87]  J. Macák,et al.  Nanotube oxide coating on Ti–29Nb–13Ta–4.6Zr alloy prepared by self-organizing anodization , 2006 .

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

[89]  Sung-Wook Nam,et al.  Ionic field effect transistors with sub-10 nm multiple nanopores. , 2009, Nano letters.

[90]  Dimitrios H Roukos,et al.  From next-generation sequencing to nanopore sequencing technology: paving the way to personalized genomic medicine , 2013, Expert review of medical devices.

[91]  N. D. de Rooij,et al.  Label-free detection of single protein molecules and protein-protein interactions using synthetic nanopores. , 2008, Analytical chemistry.

[92]  Shikuan Yang,et al.  Surface patterning using templates: concept, properties and device applications. , 2011, Chemical Society reviews.

[93]  Michael F. Crommie,et al.  Hydrocarbon lithography on graphene membranes , 2008 .

[94]  Hui Li,et al.  Self-assembling subnanometer pores with unusual mass-transport properties , 2012, Nature Communications.

[95]  O. Hildreth,et al.  Vapor Phase Metal‐Assisted Chemical Etching of Silicon , 2013 .

[96]  Steven G. Louie,et al.  Graphene at the Edge: Stability and Dynamics , 2009, Science.

[97]  C Raillon,et al.  Detecting the translocation of DNA through a nanopore using graphene nanoribbons. , 2013, Nature nanotechnology.

[98]  Grégory Pandraud,et al.  DNA translocation through graphene nanopores. , 2010, Nano letters.

[99]  Jianbo Wang,et al.  Fabrication of faceted nanopores in magnesium , 2013 .

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

[101]  Kenji Fukuda,et al.  Ordered Metal Nanohole Arrays Made by a Two-Step Replication of Honeycomb Structures of Anodic Alumina , 1995, Science.

[102]  L. A. Baker,et al.  Conical nanopore membranes: solvent shaping of nanopores , 2006 .

[103]  Zewen Liu,et al.  Direct surface nanopatterning using pyramidal silicon nanopore arrays as templates , 2013 .

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

[105]  T. Deng,et al.  Controllable Fabrication of Pyramidal Silicon Nanopore Arrays and Nanoslits for Nanostencil Lithography , 2014 .

[106]  A. Reina,et al.  Graphene as a sub-nanometer trans-electrode membrane , 2010, Nature.

[107]  B. Chait,et al.  Artificial nanopores that mimic the transport selectivity of the nuclear pore complex , 2009, Nature.

[108]  Wei Guo,et al.  Biomimetic smart nanopores and nanochannels. , 2011, Chemical Society reviews.

[109]  Qing Zhao,et al.  Boron Nitride Nanopores: Highly Sensitive DNA Single‐Molecule Detectors , 2013, Advanced materials.

[110]  N. Pourmand,et al.  Immunoassays Using Artificial Nanopores , 2012 .

[111]  M. Drndić,et al.  DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore. , 2011, Nano letters.

[112]  Qiang Xu,et al.  Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation , 2013, Nature Communications.

[113]  K. Tsujino,et al.  Boring Deep Cylindrical Nanoholes in Silicon Using Silver Nanoparticles as a Catalyst , 2005 .

[114]  Takashi Taniguchi,et al.  Direct-bandgap properties and evidence for ultraviolet lasing of hexagonal boron nitride single crystal , 2004, Nature materials.

[115]  T. Deng,et al.  Fabrication of Inverted-Pyramid Silicon Nanopore Arrays with Three-Step Wet Etching , 2013 .

[116]  Cees Dekker,et al.  Fabrication and characterization of nanopore-based electrodes with radii down to 2 nm. , 2006, Nano letters.

[117]  A. Ouerghi,et al.  FIB carving of nanopores into suspended graphene films , 2012 .

[118]  J. Giérak,et al.  FIB patterning of dielectric, metallized and graphene membranes: A comparative study , 2014 .

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

[120]  Zhipeng Huang,et al.  Metal‐Assisted Chemical Etching of Silicon: A Review , 2011, Advanced materials.

[121]  Lin Liu,et al.  Comparison of Next-Generation Sequencing Systems , 2012, Journal of biomedicine & biotechnology.

[122]  Z. Siwy,et al.  Fabrication of a synthetic nanopore ion pump. , 2002, Physical review letters.

[123]  D. Dobrev,et al.  Etched Single-Ion-Track Templates for Single Nanowire Synthesis , 2004 .

[124]  D. C. Sun,et al.  A simple method for preparation of through-hole porous anodic alumina membrane , 2004 .

[125]  Jungsuk Kim,et al.  Recent advances in nanopore sequencing , 2012, Electrophoresis.

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

[127]  W. Lee,et al.  Porous anodic aluminum oxide: anodization and templated synthesis of functional nanostructures. , 2014, Chemical reviews.

[128]  Neil Peterman,et al.  DNA translocation through graphene nanopores. , 2010, Nano letters.

[129]  Rui Gao,et al.  Nanopore-based sequencing and detection of nucleic acids. , 2013, Angewandte Chemie.

[130]  P. Apel,et al.  Fabrication of nanopores in polymer foils with surfactant-controlled longitudinal profiles , 2007 .

[131]  A. Hirata,et al.  Nanoporous PdNi Bimetallic Catalyst with Enhanced Electrocatalytic Performances for Electro‐oxidation and Oxygen Reduction Reactions , 2011 .

[132]  Jing Kong,et al.  Synthesis of few-layer hexagonal boron nitride thin film by chemical vapor deposition. , 2010, Nano letters.

[133]  Zuzanna S Siwy,et al.  Resistive-pulse DNA detection with a conical nanopore sensor. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[134]  J. Leburton,et al.  Electrically tunable solid-state silicon nanopore ion filter , 2006, Nanoscale Research Letters.

[135]  C. Dekker,et al.  Biomimetic nanopores: learning from and about nature. , 2011, Trends in biotechnology.

[136]  E. Pop,et al.  Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes. , 2012, ACS nano.

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

[138]  C H Self,et al.  Advances in immunoassay technology. , 1996, Current opinion in biotechnology.

[139]  Zewen Liu,et al.  Controllable shrinking of inverted-pyramid silicon nanopore arrays by dry-oxygen oxidation , 2013, Nanotechnology.

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

[141]  Olivier Sudre,et al.  Control of ionic transport through gated single conical nanopores , 2009, Analytical and bioanalytical chemistry.

[142]  Michio Matsumura,et al.  Morphology of nanoholes formed in silicon by wet etching in solutions containing HF and H2O2 at different concentrations using silver nanoparticles as catalysts , 2007 .

[143]  Reimar Spohr,et al.  Pore geometry of etched ion tracks in polyimide , 1996 .

[144]  Ki-Bum Kim,et al.  Theoretical and experimental study of nanopore drilling by a focused electron beam in transmission electron microscopy , 2011, Nanotechnology.

[145]  M. Taniguchi,et al.  Fabrication of the gating nanopore device , 2009 .

[146]  O. Hildreth,et al.  3D Out‐of‐Plane Rotational Etching with Pinned Catalysts in Metal‐Assisted Chemical Etching of Silicon , 2011 .

[147]  R. Bashir,et al.  Nanopore sensors for nucleic acid analysis. , 2011, Nature nanotechnology.

[148]  M. Sendova-Vassileva,et al.  Preparation of thin porous silicon layers by stain etching , 1997 .

[149]  Zhipeng Huang,et al.  Extended arrays of vertically aligned sub-10 nm diameter [100] Si nanowires by metal-assisted chemical etching. , 2008, Nano letters.

[150]  Jongin Hong,et al.  Precise electrochemical fabrication of sub-20 nm solid-state nanopores for single-molecule biosensing , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[151]  Q. Ouyang,et al.  Controllable shrinking and shaping of silicon nitride nanopores under electron irradiation , 2007 .