Threading DNA through nanopores for biosensing applications

This review outlines the recent achievements in the field of nanopore research. Nanopores are typically used in single-molecule experiments and are believed to have a high potential to realize an ultra-fast and very cheap genome sequencer. Here, the various types of nanopore materials, ranging from biological to 2D nanopores are discussed together with their advantages and disadvantages. These nanopores can utilize different protocols to read out the DNA nucleobases. Although, the first nanopore devices have reached the market, many still have issues which do not allow a full realization of a nanopore sequencer able to sequence the human genome in about a day. Ways to control the DNA, its dynamics and speed as the biomolecule translocates the nanopore in order to increase the signal-to-noise ratio in the reading-out process are examined in this review. Finally, the advantages, as well as the drawbacks in distinguishing the DNA nucleotides, i.e., the genetic information, are presented in view of their importance in the field of nanopore sequencing.

[1]  Steven J. Gaik,et al.  DNA translocation through an array of kinked nanopores. , 2010, Nature materials.

[2]  Klaus Schulten,et al.  Graphene quantum point contact transistor for DNA sensing , 2013, Proceedings of the National Academy of Sciences.

[3]  Martin Z. Bazant,et al.  Fast ac electro-osmotic micropumps with nonplanar electrodes , 2006 .

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

[5]  Gianaurelio Cuniberti,et al.  Dynamic and electronic transport properties of DNA translocation through graphene nanopores. , 2013, Nano letters.

[6]  O. Otto,et al.  Voltage‐driven transport of ions and DNA through nanocapillaries , 2012, Electrophoresis.

[7]  Meni Wanunu,et al.  Nanopore based sequence specific detection of duplex DNA for genomic profiling. , 2010, Nano letters.

[8]  Rajeev Ahuja,et al.  Transverse conductance of DNA nucleotides in a graphene nanogap from first principles. , 2010, Nano letters.

[9]  Daisuke Fujita,et al.  Perspectives and challenges of emerging single-molecule DNA sequencing technologies. , 2009, Small.

[10]  Chun-Keung Loong,et al.  Anomalously soft dynamics of water in a nanotube: a revelation of nanoscale confinement. , 2004, Physical review letters.

[11]  Kwang S. Kim,et al.  Fast DNA sequencing with a graphene-based nanochannel device. , 2011, Nature nanotechnology.

[12]  K. Schulten,et al.  The electromechanics of DNA in a synthetic nanopore. , 2006, Biophysical journal.

[13]  G. Hummer,et al.  Water conduction through the hydrophobic channel of a carbon nanotube , 2001, Nature.

[14]  Sauro Succi,et al.  Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: theory and multiscale simulations. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  Michael Zwolak,et al.  Electronic signature of DNA nucleotides via transverse transport. , 2004, Nano letters.

[16]  D. Atkinson,et al.  Conformational analysis of apolipoprotein A-I and E-3 based on primary sequence and circular dichroism. , 1992, Biophysical journal.

[17]  M. Niederweis,et al.  Nucleotide Discrimination with DNA Immobilized in the MspA Nanopore , 2011, PloS one.

[18]  Zhijun Jiang,et al.  Fabrication of nanopores with embedded annular electrodes and transverse carbon nanotube electrodes , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[19]  Hsueh-Chia Chang,et al.  Nanoscale Electrokinetics and Microvortices: How Microhydrodynamics Affects Nanofluidic Ion Flux , 2012 .

[20]  N. Stellwagen,et al.  The free solution mobility of DNA. , 1997, Biopolymers.

[21]  P. Hagerman,et al.  Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). , 1999, Journal of molecular biology.

[22]  Michael L. Klein,et al.  Simulations of Phospholipids Using a Coarse Grain Model , 2001 .

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

[24]  J. Hansen,et al.  Permeation of nanopores by water: the effects of channel polarization , 2003 .

[25]  M. Di Ventra,et al.  Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport. , 2007, Biophysical journal.

[26]  Klaus Schulten,et al.  Computational investigation of DNA detection using graphene nanopores. , 2011, ACS nano.

[27]  Makusu Tsutsui,et al.  Thermophoretic manipulation of DNA translocation through nanopores. , 2013, ACS nano.

[28]  Gregory A Voth,et al.  Bridging microscopic and mesoscopic simulations of lipid bilayers. , 2002, Biophysical journal.

[29]  Nicholas A W Bell,et al.  DNA origami nanopores. , 2012, Nano letters.

[30]  Tae Song Kim,et al.  In situ real-time monitoring of biomolecular interactions based on resonating microcantilevers immersed in a viscous fluid , 2007 .

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

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

[33]  P. Kollman,et al.  Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation , 1993 .

[34]  G. Barkema,et al.  Passage times for polymer translocation pulled through a narrow pore. , 2007, Biophysical journal.

[35]  O. Otto,et al.  Correction to Detecting DNA Folding with Nanocapillaries , 2013 .

[36]  Axel Kohlmeyer,et al.  Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics. , 2009, Nano letters.

[37]  Makusu Tsutsui,et al.  Electrical detection of single methylcytosines in a DNA oligomer. , 2011, Journal of the American Chemical Society.

[38]  D. Branton,et al.  Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. , 1999, Biophysical journal.

[39]  S. Sligar,et al.  Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Marc Gershow,et al.  DNA molecules and configurations in a solid-state nanopore microscope , 2003, Nature materials.

[41]  Mark Bates,et al.  Dynamics of DNA molecules in a membrane channel probed by active control techniques. , 2003, Biophysical journal.

[42]  Yoshio Umezawa,et al.  Complementary base-pair-facilitated electron tunneling for electrically pinpointing complementary nucleobases. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Geunsik Lee,et al.  Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition. , 2014, ACS nano.

[44]  T. Albrecht.  How to understand and interpret current flow in nanopore/electrode devices. , 2011, ACS nano.

[45]  Stephen G. Sligar,et al.  Self-Assembly of Discoidal Phospholipid Bilayer Nanoparticles with Membrane Scaffold Proteins , 2002 .

[46]  M. Ventra.  Fast DNA sequencing by electrical means inches closer. , 2013 .

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

[48]  N. Aluru,et al.  Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes , 2003 .

[49]  A. Balan,et al.  Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. , 2013, ACS nano.

[50]  Juan J de Pablo,et al.  The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores. , 2008, The Journal of chemical physics.

[51]  Marc Gershow,et al.  Detecting single stranded DNA with a solid state nanopore. , 2005, Nano letters.

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

[53]  Y. Blanter,et al.  Carbon nanotubes as nanoelectromechanical systems , 2003 .

[54]  A. Meller,et al.  pH tuning of DNA translocation time through organically functionalized nanopores. , 2013, ACS nano.

[55]  H. Bayley,et al.  Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. , 2005, Angewandte Chemie.

[56]  S. Ghosal,et al.  Hydrodynamic flow in the vicinity of a nanopore induced by an applied voltage , 2013, Nanotechnology.

[57]  M. Dresselhaus,et al.  Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly , 2003, Science.

[58]  M. Muthukumar,et al.  Langevin dynamics simulations of ds-DNA translocation through synthetic nanopores. , 2006, The Journal of chemical physics.

[59]  Jianpeng Ma,et al.  Helical ice-sheets inside carbon nanotubes in the physiological condition , 2002 .

[60]  Ralph H. Scheicher,et al.  DNA sequencing with nanopores from an ab initio perspective , 2012, Journal of Materials Science.

[61]  Shot noise in parallel wires , 2004, cond-mat/0402180.

[62]  Y. Pershin,et al.  Effect of noise on DNA sequencing via transverse electronic transport. , 2009, Biophysical journal.

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

[64]  S. Lindsay,et al.  Optical and electrical detection of single-molecule translocation through carbon nanotubes. , 2013, ACS nano.

[65]  N. Peres,et al.  Field-Effect Tunneling Transistor Based on Vertical Graphene Heterostructures , 2011, Science.

[66]  Bo Zhang,et al.  Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. , 2010, Nano letters.

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

[68]  M. Strano,et al.  Near-infrared optical sensors based on single-walled carbon nanotubes , 2004, Nature materials.

[69]  Vivek V. Thacker,et al.  Studying DNA translocation in nanocapillaries using single molecule fluorescence. , 2012, Applied physics letters.

[70]  H. Dai,et al.  Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[71]  S. Sowerby,et al.  Differential adsorption of nucleic acid bases: Relevance to the origin of life. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[72]  K. Schulten,et al.  Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. , 2005, Biophysical journal.

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

[74]  Gerhard Hummer,et al.  Nucleic acid transport through carbon nanotube membranes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[75]  A. Jonas,et al.  Defined apolipoprotein A-I conformations in reconstituted high density lipoprotein discs. , 1989, The Journal of biological chemistry.

[76]  B. Ren,et al.  Preparation of gold tips suitable for tip-enhanced Raman spectroscopy and light emission by electrochemical etching , 2004 .

[77]  D. Branton,et al.  DNA conformation and base number simultaneously determined in a nanopore , 2007, Electrophoresis.

[78]  G. Anantharamaiah,et al.  Structural models of human apolipoprotein A-I. , 1995, Biochimica et biophysica acta.

[79]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[80]  Shibing Long,et al.  Enhanced DNA Sequencing Performance Through Edge‐Hydrogenation of Graphene Electrodes , 2010, 1012.0031.

[81]  Kyeong-Beom Park,et al.  A Low-Noise Solid-State Nanopore Platform Based on a Highly Insulating Substrate , 2014, Scientific Reports.

[82]  U. Keyser.  Controlling molecular transport through nanopores , 2011, Journal of The Royal Society Interface.

[83]  R. Ahuja,et al.  Physisorption of nucleobases on graphene : Density-functional calculations , 2007, 0704.1316.

[84]  M. Roukes,et al.  Zeptogram-scale nanomechanical mass sensing. , 2005, Nano letters.

[85]  M. Taniguchi,et al.  Identifying single nucleotides by tunnelling current. , 2010, Nature nanotechnology.

[86]  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.

[87]  R. Ahuja,et al.  Functionalized nanopore-embedded electrodes for rapid DNA sequencing , 2007, 0708.4011.

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

[89]  D. Furlong,et al.  Controlled wettability of quartz surfaces , 1982 .

[90]  M. Drndić,et al.  Fabrication and characterization of nanopores with insulated transverse nanoelectrodes for DNA sensing in salt solution , 2012, Electrophoresis.

[91]  C. Tropini,et al.  Multi-nanopore force spectroscopy for DNA analysis. , 2007, Biophysical journal.

[92]  H. Bayley,et al.  Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.

[93]  M. Boguski,et al.  On computer-assisted analysis of biological sequences: proline punctuation, consensus sequences, and apolipoprotein repeats. , 1986, Journal of lipid research.

[94]  T. Saiki,et al.  Optical detection of DNA translocation through silicon nanopore by ultraviolet light , 2014 .

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

[96]  Gerhard Hummer,et al.  Osmotic water transport through carbon nanotube membranes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[97]  Klaus Schulten,et al.  Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. , 2005, Biophysical journal.

[98]  Stijn van Dorp,et al.  Origin of the electrophoretic force on DNA in solid-state nanopores , 2009 .

[99]  Silvia Hernández-Ainsa,et al.  DNA origami nanopores for controlling DNA translocation. , 2013, ACS nano.

[100]  Arindam Ghosh,et al.  Graphene-MoS2 hybrid structures for multifunctional photoresponsive memory devices. , 2013, Nature nanotechnology.

[101]  B. K. Gupta,et al.  Artificially stacked atomic layers: toward new van der Waals solids. , 2012, Nano letters.

[102]  Fabrication and characterization of a solid-state nanopore with self-aligned carbon nanoelectrodes for molecular detection. , 2012, Nanotechnology.

[103]  M. Niederweis,et al.  Nanopore DNA sequencing with MspA , 2010, Proceedings of the National Academy of Sciences.

[104]  S. Lindsay,et al.  DNA translocating through a carbon nanotube can increase ionic current , 2012, Nanotechnology.

[105]  M. Roco.  Nanotechnology: convergence with modern biology and medicine. , 2003, Current opinion in biotechnology.

[106]  Theodore D. Moustakas,et al.  Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores , 2013, Nature nanotechnology.

[107]  B. Luan,et al.  Control and reversal of the electrophoretic force on DNA in a charged nanopore , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[108]  M. Taniguchi,et al.  Mechanism of how salt-gradient-induced charges affect the translocation of DNA molecules through a nanopore. , 2013, Biophysical journal.

[109]  Jin He,et al.  Identifying single bases in a DNA oligomer with electron tunnelling. , 2010, Nature nanotechnology.

[110]  N. Ashkenasy,et al.  The controlled fabrication of nanopores by focused electron-beam-induced etching , 2009, Nanotechnology.

[111]  Juekuan Yang,et al.  Molecular dynamics study of DNA translocation through graphene nanopores. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[112]  C. Pantano,et al.  Hydroxylation and Dehydroxylation Behavior of Silica Glass Fracture Surfaces , 2002 .

[113]  Klaus Schulten,et al.  Coarse grained protein-lipid model with application to lipoprotein particles. , 2006, The journal of physical chemistry. B.

[114]  Sung,et al.  Polymer Translocation through a Pore in a Membrane. , 1996, Physical review letters.

[115]  Electronic contribution to the energetics of helically wrapped nanotubes , 2006 .

[116]  Ilya A. Balabin,et al.  Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. , 2004, Biophysical journal.

[117]  S. Sligar,et al.  Thermotropic phase transition in soluble nanoscale lipid bilayers. , 2005, The journal of physical chemistry. B.

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

[119]  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.

[120]  V. Bansal,et al.  The importance of phase information for human genomics , 2011, Nature Reviews Genetics.

[121]  Makusu Tsutsui,et al.  Controlling DNA translocation through gate modulation of nanopore wall surface charges. , 2011, ACS nano.

[122]  Ulrich F Keyser,et al.  Detecting DNA folding with nanocapillaries. , 2010, Nano letters.

[123]  Ravindra Pandey,et al.  Electronic structure and quantum transport properties of trilayers formed from graphene and boron nitride. , 2012, Nanoscale.

[124]  Jin He,et al.  Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap , 2010, Nano letters.

[125]  K. Schulten,et al.  Sizing DNA using a nanometer-diameter pore. , 2004, Biophysical journal.

[126]  J. Joanny,et al.  Fast DNA translocation through a solid-state nanopore. , 2004, Nano letters.

[127]  Ravindra Pandey,et al.  First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes , 2007, Nanotechnology.

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

[129]  C. Dekker,et al.  DNA Translocations through Solid-State Plasmonic Nanopores , 2014, Nano letters.

[130]  Hagan Bayley,et al.  Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. , 2006 .

[131]  P. McEuen,et al.  A tunable carbon nanotube electromechanical oscillator , 2004, Nature.

[132]  J. Ramsey,et al.  Electrokinetically-driven transport of DNA through focused ion beam milled nanofluidic channels. , 2013, Analytical chemistry.

[133]  Klaus Schulten,et al.  Ion-nanotube terahertz oscillator. , 2005, Physical review letters.

[134]  T. Ala‐Nissila,et al.  Polymer translocation: the first two decades and the recent diversification. , 2014, Soft matter.

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

[136]  P. Marszalek,et al.  Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy. , 2007, Physical review letters.

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

[138]  S. Grimme,et al.  Structures and interaction energies of stacked graphene-nucleobase complexes. , 2008, Physical chemistry chemical physics : PCCP.

[139]  Y. Arakawa,et al.  The electronic properties of DNA bases. , 2007, Small.

[140]  Murali Krishna Ghatkesar,et al.  Micromechanical mass sensors for biomolecular detection in a physiological environment. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[141]  M. Wanunu,et al.  Programmed synthesis of freestanding graphene nanomembrane arrays. , 2015, Small.

[142]  S. Sligar,et al.  Phospholipid phase transitions in homogeneous nanometer scale bilayer discs , 2004, FEBS letters.

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

[144]  W. A. Steele,et al.  On the computer simulation of a hydrophobic vitreous silica surface , 1999 .

[145]  S. Sligar,et al.  Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers. , 2003, BioTechniques.

[146]  S. Sligar,et al.  Homotropic cooperativity of monomeric cytochrome P450 3A4 in a nanoscale native bilayer environment. , 2004, Archives of biochemistry and biophysics.

[147]  Mehran Kardar,et al.  Anomalous dynamics of forced translocation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[148]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[149]  C. Dekker,et al.  Plasmonic nanopore for electrical profiling of optical intensity landscapes. , 2013, Nano letters.

[150]  J. T. Rodgers,et al.  Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules. , 2003, Nucleic acids research.

[151]  Junqiang Lu,et al.  Nucleotide capacitance calculation for DNA sequencing. , 2008, Biophysical journal.

[152]  H. Dai,et al.  Nanotube molecular transporters: internalization of carbon nanotube-protein conjugates into Mammalian cells. , 2004, Journal of the American Chemical Society.

[153]  S. Sligar,et al.  Self‐assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers , 2003, Protein science : a publication of the Protein Society.

[154]  R. Scheicher,et al.  Silicene as a new potential DNA sequencing device , 2014, Nanotechnology.

[155]  Michiel Sprik,et al.  A polarizable model for water using distributed charge sites , 1988 .

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

[157]  J. Dobnikar,et al.  Counterion-mediated electrostatic interactions between helical molecules , 2008, 0807.1586.

[158]  K. Schulten,et al.  Microscopic Kinetics of DNA Translocation through synthetic nanopores. , 2004, Biophysical journal.

[159]  S. Lindsay,et al.  Identification of DNA basepairing via tunnel-current decay. , 2007, Nano letters.

[160]  G. Sivaraman,et al.  Chemically modified diamondoids as biosensors for DNA. , 2014, Nanoscale.

[161]  Colin Nuckolls,et al.  Translocation of Single-Stranded DNA Through Single-Walled Carbon Nanotubes , 2010, Science.

[162]  Klaus Schulten,et al.  Empirical nanotube model for biological applications. , 2005, The journal of physical chemistry. B.

[163]  David A. Sivak,et al.  Controlling DNA capture and propagation through artificial nanopores. , 2007, Nano letters.

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

[165]  O. Sankey,et al.  Tunneling readout of hydrogen-bonding based recognition , 2009, Nature nanotechnology.

[166]  Hugh E. Olsen,et al.  Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel , 2001, Nature Biotechnology.

[167]  G. Barkema,et al.  Through the eye of the needle: recent advances in understanding biopolymer translocation , 2013, Journal of physics. Condensed matter : an Institute of Physics journal.

[168]  S. Garofalini,et al.  Topological and bonding defects in vitreous silica surfaces , 1989 .

[169]  Ki-Bum Kim,et al.  Noise and its reduction in graphene based nanopore devices , 2013, Nanotechnology.

[170]  Tae Song Kim,et al.  Dynamical response of nanomechanical resonators to biomolecular interactions , 2007, 0706.3743.

[171]  Ralph H. Scheicher,et al.  Double-functionalized nanopore-embedded gold electrodes for rapid DNA sequencing , 2012 .

[172]  Erika Check Hayden,et al.  Technology: The $1,000 genome , 2014, Nature.

[173]  Mark Akeson,et al.  Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision1 , 2012, Nature Biotechnology.

[174]  Cees Dekker,et al.  Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores. , 2010, Nature nanotechnology.

[175]  Dongshan Wei,et al.  Unforced translocation of a polymer chain through a nanopore: the solvent effect. , 2007, The Journal of chemical physics.

[176]  K. Jensen,et al.  An atomic-resolution nanomechanical mass sensor. , 2008, Nature Nanotechnology.

[177]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[178]  H. Bayley,et al.  Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore. , 2012, Nano letters.

[179]  Kurt Binder,et al.  Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model. , 2004, The Journal of chemical physics.

[180]  Alexander Y. Grosberg,et al.  DNA capture into a nanopore: interplay of diffusion and electrohydrodynamics. , 2010, The Journal of chemical physics.

[181]  Charles M. Lieber,et al.  Local electrical potential detection of DNA by nanowire-nanopore sensors , 2011, Nature nanotechnology.

[182]  Silvia Hernández-Ainsa,et al.  Voltage-dependent properties of DNA origami nanopores. , 2014, Nano letters.

[183]  Ilkka Huopaniemi,et al.  Dynamical scaling exponents for polymer translocation through a nanopore. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[184]  S. Sligar,et al.  Co-incorporation of heterologously expressed Arabidopsis cytochrome P450 and P450 reductase into soluble nanoscale lipid bilayers. , 2004, Archives of biochemistry and biophysics.

[185]  Zhiping Weng,et al.  Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. , 2010, Nano letters.

[186]  M. Dresselhaus.  Carbon nanotubes , 1995 .

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

[188]  Davidson Ws,et al.  Apolipoprotein structural organization in high density lipoproteins: belts, bundles, hinges and hairpins. , 2005 .

[189]  Romain Quidant,et al.  Self -induced back-action optical trapping of dielectric nanoparticles , 2009 .

[190]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[191]  Miguel Fuentes-Cabrera,et al.  First-principles transversal DNA conductance deconstructed. , 2006, Biophysical journal.

[192]  K. Schulten,et al.  Control of the Selectivity of the Aquaporin Water Channel Family by Global Orientational Tuning , 2002, Science.

[193]  Anthony E. Klon,et al.  A Detailed Molecular Belt Model for Apolipoprotein A-I in Discoidal High Density Lipoprotein* , 1999, The Journal of Biological Chemistry.

[194]  Klaus Schulten,et al.  Water and proton conduction through carbon nanotubes as models for biological channels. , 2003, Biophysical journal.

[195]  S. Ghosal.  Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. , 2007, Physical review letters.

[196]  S. Iijima.  Helical microtubules of graphitic carbon , 1991, Nature.

[197]  Marc Gershow,et al.  Recapturing and trapping single molecules with a solid-state nanopore. , 2007, Nature nanotechnology.

[198]  David W. McComb,et al.  DNA Tunneling Detector Embedded in a Nanopore , 2010, Nano letters.

[199]  Petros Koumoutsakos,et al.  On the Water−Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes , 2003 .

[200]  N. Aluru,et al.  DNA base detection using a single-layer MoS2. , 2014, ACS nano.

[201]  Peiming Zhang,et al.  Nanopore DNA sequencing: Are we there yet? , 2015 .

[202]  Aleksei Aksimentiev,et al.  Slowing down DNA translocation through a nanopore in lithium chloride. , 2012, Nano letters.

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

[204]  M. Ventra,et al.  Colloquium: Physical approaches to DNA sequencing and detection , 2007, 0708.2724.

[205]  M. Niederweis,et al.  Single-molecule DNA detection with an engineered MspA protein nanopore , 2008, Proceedings of the National Academy of Sciences.

[206]  D. Branton,et al.  Voltage-driven DNA translocations through a nanopore. , 2001, Physical review letters.

[207]  Changhong Ke,et al.  Resonant pull-in of a double-sided driven nanotube-based electromechanical resonator , 2009 .

[208]  J. Gouaux,et al.  Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore , 1996, Science.

[209]  J. Segrest.  Amphipathic helixes and plasma lipoproteins: thermodynamic and geometric considerations. , 1977, Chemistry and physics of lipids.

[210]  Ke Liu,et al.  Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. , 2014, ACS nano.

[211]  C. Holm,et al.  Origin of current blockades in nanopore translocation experiments. , 2014, Physical review letters.

[212]  Yuhui He.  Graphene/hexagonal Boron Nitride/Graphene Nanopore for Electrical Detection of Single Molecules , 2013 .

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

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

[215]  Hagan Bayley,et al.  DNA strands from denatured duplexes are translocated through engineered protein nanopores at alkaline pH. , 2009, Nano letters.

[216]  J. Engler,et al.  Structural analysis of apolipoprotein A-I: effects of amino- and carboxy-terminal deletions on the lipid-free structure. , 1998, Biochemistry.

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

[218]  Ali Mani,et al.  Theory and experiments of concentration polarization and ion focusing at microchannel and nanochannel interfaces. , 2010, Chemical Society reviews.

[219]  W. Goddard,et al.  Charge equilibration for molecular dynamics simulations , 1991 .

[220]  H. Bayley,et al.  Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore. , 2010, Biophysical journal.

[221]  H. Craighead.  Future lab-on-a-chip technologies for interrogating individual molecules , 2006, Nature.

[222]  David Stoddart,et al.  Nucleobase recognition in ssDNA at the central constriction of the alpha-hemolysin pore. , 2010, Nano letters.

[223]  Alexander Y. Grosberg,et al.  Electrostatic Focusing of Unlabeled DNA into Nanoscale Pores using a Salt Gradient , 2009, Nature nanotechnology.

[224]  Tim Liedl,et al.  DNA Origami Nanopores , 2013 .

[225]  Alexander S. Mikheyev,et al.  A first look at the Oxford Nanopore MinION sequencer , 2014, Molecular ecology resources.

[226]  Juan G. Santiago,et al.  A review of micropumps , 2004 .

[227]  Cees Dekker,et al.  Direct force measurements on DNA in a solid-state nanopore , 2006 .

[228]  Aleksei Aksimentiev,et al.  Electro-osmotic screening of the DNA charge in a nanopore. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[229]  M. Furuhashi,et al.  Transverse electric field dragging of DNA in a nanochannel , 2012, Scientific Reports.

[230]  J. Wells,et al.  Characterization of the tunneling conductance across DNA bases. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[231]  M. Muthukumar,et al.  Theory of capture rate in polymer translocation. , 2010, The Journal of chemical physics.

[232]  Rashid Bashir,et al.  DNA-Mediated Fluctuations in Ionic Current through Silicon Oxide Nanopore Channels. Nano Lett., 4(8), 1551-1556 , 2004 .

[233]  T. Mitsui,et al.  Directly observing the motion of DNA molecules near solid-state nanopores. , 2012, ACS nano.

[234]  Jingmin Jin,et al.  Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. , 2010, Nature nanotechnology.

[235]  Peter Fischer,et al.  The self-assembly, aggregation and phase transitions of food protein systems in one, two and three dimensions , 2013, Reports on progress in physics. Physical Society.

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

[237]  Makusu Tsutsui,et al.  Single-Molecule Electrical Random Resequencing of DNA and RNA , 2012, Scientific Reports.

[238]  Adrien Nicolaï,et al.  DNA Translocation in Nanometer Thick Silicon Nanopores. , 2015, ACS nano.

[239]  Deepak Srivastava,et al.  Theory of transport of long polymer molecules through carbon nanotube channels. , 2003, Physical review letters.

[240]  Jin He,et al.  Tunnel conductance of Watson–Crick nucleoside–base pairs from telegraph noise , 2009, Nanotechnology.