DNA Sequencing Using Carbon Nanopores

  • Nianjun YangEmail author
  • Xin Jiang
Part of the Springer Series on Chemical Sensors and Biosensors book series (SSSENSORS, volume 17)


DNA sequence, the order and the type of four nucleotide bases (namely adenine, guanine, cytosine, and thymine) in a DNA molecule, offers genetic information at the molecular level. Visualization of DNA sequences by use of nanopores, so-named nanopore sequencing, is one of the most promising and revolutionary DNA sequencing technologies. In comparison to nanopores formed from solid-state membranes (e.g., silicon oxide, aluminum oxide, polymer membranes, glass, hafnium oxide, gold, etc.) and very recently 2D materials (e.g., boron nitride, molybdenum disulfide, etc.), those nanopores produced from carbon materials (e.g., graphene, carbon nanotubes (CNTs), diamond, etc.), especially those from graphene appear to be perfect for DNA sequencing. For example, the thickness of graphene nanopores can be as thin as 0.35 nm, resembling the height of the base spacing. Moreover, the sizes of graphene nanopores can be precisely fabricated and tuned to around 1.0 nm, the similar size of DNA molecules. Furthermore, carbon materials are chemically stable and feature rich surface chemistry. Therefore, various carbon nanopore sequencing techniques have been developed. Electrical detection, namely measuring ionic blockade, tunneling current, conductance, and voltage fluctuations when DNA molecules translocate through these carbon nanopores, is one of the most important approaches. In this chapter, the concept of nanopore sequencing as well as the nanopores employed for DNA sequencing are first introduced, followed by the summary of recent progress and achievements of carbon nanopore sequencing, covering: (1) the fabrication techniques of graphene, CNT, and diamond nanopores, (2) established strategies of DNA sequencing by use of these carbon nanopores, and (3) challenges and future perspectives for carbon nanopore sequencing.


Carbon materials Carbon nanotubes Diamond DNA sequencing Graphene Nanopores 



The author (N.Y.) thanks the financial support from German Research Foundation (DFG) under the project (grant no. YA344/1-1).


  1. 1.
    Franc LTC, Carrilho E, Kist TBL (2002) A review of DNA sequencing techniques. Q Rev Biophys 35:169–200Google Scholar
  2. 2.
    Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Ventra MD, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA (2008) The potential and challenges of nanopore sequencing. Nat Nanotechnol 26:1146–1153Google Scholar
  3. 3.
    Zwolak M, Ventra MD (2008) Colloquium: physical approaches to DNA sequencing and detection. Rev Mod Phys 80:141–165Google Scholar
  4. 4.
    Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedGoogle Scholar
  5. 5.
    Kasianowicz JJ, Robertson JWF, Chan ER, Reiner JE, Stanford VM (2008) Nanoscopic porous sensors. Annu Rev Anal Chem 1:737–766Google Scholar
  6. 6.
    Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46PubMedGoogle Scholar
  7. 7.
    Mirsaidov UM, Wang D, Timp W, Timp G (2010) Molecular diagnostics for personal medicine using a nanopore. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2:367–381PubMedPubMedCentralGoogle Scholar
  8. 8.
    Timp W, Mirsaidov UM, Wang D, Comer J, Aksimentiev A, Timp G (2010) Nanopore sequencing: electrical measurements of the code of life. IEEE Trans Nanotechnol 9:281–294PubMedPubMedCentralGoogle Scholar
  9. 9.
    Thompson JF, Milos PM (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12:217PubMedPubMedCentralGoogle Scholar
  10. 10.
    Venkatesan BM, Bashir R (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 6:615–624PubMedGoogle Scholar
  11. 11.
    Maitra RD, Kim J, Dunbar WB (2012) Recent advances in nanopore sequencing. Electrophoresis 33:3418–3428PubMedPubMedCentralGoogle Scholar
  12. 12.
    Schneider GF, Dekker C (2012) DNA sequencing with nanopores. Nat Biotechnol 30:326–328PubMedGoogle Scholar
  13. 13.
    Ying Y-L, Zhang J, Gao R, Long Y-T (2013) Nanopore-based sequencing and detection of nucleic acids. Angew Chem Int Ed 52:13154–13161Google Scholar
  14. 14.
    Feng Y, Zhang Y, Ying C, Wang D, Du C (2015) Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 13:4–16PubMedPubMedCentralGoogle Scholar
  15. 15.
    Lu H, Giordano F, Ning Z (2015) Oxford nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 14:265–279Google Scholar
  16. 16.
    Wanunu M (2012) Nanopores: a journey towards DNA sequencing. Phys Life Rev 9:125–158PubMedPubMedCentralGoogle Scholar
  17. 17.
    Yokota K, Tsutsuia M, Taniguchi M (2014) Electrode-embedded nanopores for label-free single-molecule sequencing by electric currents. RSC Adv 4:15886–15899Google Scholar
  18. 18.
    Taniguchi M (2015) Selective multidetection using nanopores. Anal Chem 87:188–199PubMedGoogle Scholar
  19. 19.
    Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, Kizek R (2015) Fabrication of solid-state nanopores and its perspectives. Electrophoresis 36:2367–2379PubMedGoogle Scholar
  20. 20.
    Haywood DG, Saha-Shah A, Baker LA, Jacobson SC (2015) Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem 87:172–187PubMedGoogle Scholar
  21. 21.
    Rhee M, Burns MA (2008) Nanopore sequencing technology: nanopore preparations. Trends Biotechnol 25:174–181Google Scholar
  22. 22.
    Ying Y-L, Chan C, Long Y-T (2014) Single molecule analysis by biological nanopore sensors. Analyst 139:3826–3835PubMedGoogle Scholar
  23. 23.
    Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A (2012) Modeling and simulation of ion channels. Chem Rev 112:6250–6284PubMedPubMedCentralGoogle Scholar
  24. 24.
    Arjmandi-Tash H, Belyaeva LA, Schneider GF (2016) Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond. Chem Soc Rev 45:476–493PubMedGoogle Scholar
  25. 25.
    Liu S, Lu B, Zhao Q, Li J, Gao T, Chen Y, Zhang Y, Liu Z, Fan Z, Yang F, You L, Yu D (2013) Boron nitride nanopores: highly sensitive DNA single-molecule detectors. Adv Mater 25:4549–4554PubMedGoogle Scholar
  26. 26.
    Gu Z, Zhang Y, Luan B, Zhou R (2016) DNA translocation through single-layer boron nitride nanopores. Soft Matter 12:817–823PubMedGoogle Scholar
  27. 27.
    Farimani AB, Min K, Aluru NR (2014) DNA base detection using a single-layer MoS2. ACS Nano 8:7914–7922PubMedGoogle Scholar
  28. 28.
    Liu K, Feng J, Kis A, Radenovic A (2014) Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8:2504–2511PubMedGoogle Scholar
  29. 29.
    Amorim RG, Scheicher RH (2015) Silicene as a new potential DNA sequencing device. Nanotechnology 26:154002PubMedGoogle Scholar
  30. 30.
    Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93:13770–13773PubMedPubMedCentralGoogle Scholar
  31. 31.
    Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouauxt JE (1996) Structure of staphylococcal α-hemoIysin, a heptameric transmembrane pore. Science 274:1859–1865PubMedGoogle Scholar
  32. 32.
    Stefureac R, Long YT, Kraatz HB, Howard P, Lee JS (2006) Transport of α-helical peptides through α-hemolysin and aerolysin pores. Biochemistry 45:9172–9179PubMedGoogle Scholar
  33. 33.
    Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, Pavlenok M, Niederweis M, Gundlach JH (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30(4):349–353PubMedPubMedCentralGoogle Scholar
  34. 34.
    Soskine M, Biesemans A, Moeyaert B, Cheley S, Bayley H, Maglia G (2012) An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. Nano Lett 12:4895–4900PubMedPubMedCentralGoogle Scholar
  35. 35.
    Mohammad MM, Iyer R, Howard KR, McPike MP, Borer PN, Movileanu L (2012) Engineering a rigid protein tunnel for biomolecular detection. J Am Chem Soc 134:9521–9531PubMedPubMedCentralGoogle Scholar
  36. 36.
    Wendell D, Jing P, Geng J, Subramaniam V, Lee TJ, Montemagno C, Guo P (2009) Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores. Nat Nanotechnol 4:765–772PubMedPubMedCentralGoogle Scholar
  37. 37.
    Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys J 77:3227–3233PubMedPubMedCentralGoogle Scholar
  38. 38.
    Meller A, Nivon L, Brandin E, Golovchenko JJ, Branton D (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci U S A 97:1079–1084PubMedPubMedCentralGoogle Scholar
  39. 39.
    Li J, Gershow M, Stein D, Brandin E, Golovchenko JA (2003) DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater 2:611–615PubMedGoogle Scholar
  40. 40.
    Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169PubMedGoogle Scholar
  41. 41.
    Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540PubMedGoogle Scholar
  42. 42.
    Deng T, Li M, Wang Y, Liu Z (2015) Development of solid-state nanopore fabrication technologies. Sci Bull 60:304–319Google Scholar
  43. 43.
    Hlawacek G, Veligura V, van Gastel R, Poelsema B (2014) Helium ion microscopy. J Vac Sci Technol B 32:020801Google Scholar
  44. 44.
    Kwok H, Waugh M, Bustamante J, Briggs K, Tabard-Cossa V (2014) Long passage times of short ssDNA molecules through metallized nanopores fabricated by controlled breakdown. Adv Funct Mater 24:7745–7753Google Scholar
  45. 45.
    Tseng AA (2005) Recent developments in nanofabrication using focused ion beams. Small 1:924–939PubMedGoogle Scholar
  46. 46.
    Bai J, Wang D, Nam SW, Peng H, Bruce R, Gignac L, Brink M, Kratschmer E, Rossnagel S, Waggoner P, Reuter K, Wang C, Astier Y, Balagurusamy V, Luan B, Kwark Y, Joseph E, Guillorn M, Polonsky S, Royyuru A, Papa Rao S, Stolovitzky G (2014) Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales. Nanoscale 6:8900–8906PubMedGoogle Scholar
  47. 47.
    Rollings RC, Kuan AT, Golovchenko JA (2016) Ion selectivity of graphene nanopores. Nat Commun 7:11408PubMedPubMedCentralGoogle Scholar
  48. 48.
    Tapasztó L, Dobrik G, Lambin P, Biró LP (2008) Tailoring the atomic structure of graphene nanoribbons by scanning tunnelling microscope lithography. Nat Nanotechnol 3:397–401PubMedGoogle Scholar
  49. 49.
    Venkatesan BM, Dorvel B, Yemenicioglu S, Watkins N, Petrov I, Bashir R (2009) Highly sensitive, mechanically stable nanopore sensors for DNA analysis. Adv Mater 21:2771–2776PubMedPubMedCentralGoogle Scholar
  50. 50.
    Gierak J, Madouri A, Biance AL, Bourhis E, Patriarche G, Ulysse C, Lucot D, Lafosse X, Auvray L, Bruchhaus L, Jede R (2007) Sub-5 nm FIB direct patterning of nanodevices. Microelectron Eng 84:779–783Google Scholar
  51. 51.
    Nilsson J, Lee JRI, Ratto TV, Létant SE (2016) Localized functionalization of single nanopores. Adv Mater 18:427–431Google Scholar
  52. 52.
    Zhang J, You L, Ye H, Yu D (2007) Fabrication of ultrafine nanostructures with single- nanometre precision in a high-resolution transmission electron microscope. Nanotechnology 18:155303Google Scholar
  53. 53.
    Knez M, Nielsch K, Niinistö L (2007) Synthesis and surface engineering of complex nanostructures by atomic layer deposition. Adv Mater 19:3425–3438Google Scholar
  54. 54.
    Lepoitevin M, Ma T, Bechelany M, Janot J-M, Balme S (2017) Functionalization of single solid state nanopores to mimic biological ion channels: a review. Adv Colloid Interface Sci 250:195–213PubMedGoogle Scholar
  55. 55.
    Carson S, Wanunu M (2015) Challenges in DNA motion control and sequence readout using nanopore devices. Nanotechnology 26:074004PubMedPubMedCentralGoogle Scholar
  56. 56.
    Hall AR, Scott A, Rotem D, Mehta KK, Bayley H, Dekker C (2010) Hybrid pore formation by directed insertion of [alpha]-haemolysin into solid-state nanopores. Nat Nanotechnol 5:874–877PubMedPubMedCentralGoogle Scholar
  57. 57.
    Keyser U (2011) Controlling molecular transport through nanopores. J R Soc Interface 8:1369–1378PubMedPubMedCentralGoogle Scholar
  58. 58.
    Wanunu M, Meller A (2007) Chemically modified solid-state nanopores. Nano Lett 7:1580–1585PubMedGoogle Scholar
  59. 59.
    Bell NAW, Thacker VV, Hernández-Ainsa S, Fuentes-Perez ME, Moreno-Herrero F, Liedlc T, Keyser UF (2013) Multiplexed ionic current sensing with glass nanopores. Lab Chip 13:1859–1862PubMedGoogle Scholar
  60. 60.
    Farimani AB, Dibaeinia P, Aluru NR (2017) DNA origami-graphene hybrid nanopore for DNA detection. ACS Appl Mater Interfaces 9:92–100Google Scholar
  61. 61.
    Comer J, Aksimentiev A (2016) DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. Nanoscale 8:9600–9613PubMedPubMedCentralGoogle Scholar
  62. 62.
    Park HJ, Ryu GH, Lee Z (2015) Hole defects on two-dimensional materials formed by electron beam irradiation: toward nanopore devices. Appl Microsc 45:107–114Google Scholar
  63. 63.
    Heerema SJ, Dekker C (2016) Graphene nanodevices for DNA sequencing. Nat Nanotechnol 11:127–136PubMedGoogle Scholar
  64. 64.
    Chen W, Liu G-C, Ouyang J, Gao M-J, Li B, Zhao Y-D (2017) Graphene nanopore toward DNA sequencing: a review of experimental aspects. Sci China Chem 60:721–729Google Scholar
  65. 65.
    Yang N, Jiang X (2017) Nanocarbons for DNA sequencing: a review. Carbon 115:293–311Google Scholar
  66. 66.
    Bayley H (2010) Holes with an edge. Nature 467:164–165PubMedGoogle Scholar
  67. 67.
    Banerjee S, Shim J, Rivera J, Jin X, Estrada D, Solovyeva V, You X, Pak J, Pop E, Aluru N, Bashir R (2013) Electrochemistry at the edge of a single graphene layer in a nanopore. ACS Nano 7:834–843PubMedGoogle Scholar
  68. 68.
    Heerema SJ, Schneider GF, Rozemuller M, Vicarelli L, Zandbergen HW, Dekker C (2015) 1/f noise in graphene nanopores. Nanotechnology 26:074001PubMedGoogle Scholar
  69. 69.
    Kumar A, Park K-B, Kim H-M, Kim K-B (2013) Noise and its reduction in graphene based nanopore devices. Nanotechnology 24:495503PubMedGoogle Scholar
  70. 70.
    Robertson AW, Lee G-D, He K, Gong C, Chen Q, Yoon E, Kirkland AI, Warner JH (2015) Atomic structure of graphene subnanometer pores. ACS Nano 9:11599–11607PubMedGoogle Scholar
  71. 71.
    Tang L, Wang Y, Li J (2015) The graphene/nucleic acid nanobiointerface. Chem Soc Rev 44:6954–6980PubMedGoogle Scholar
  72. 72.
    Min SK, Kim WY, Cho Y, Kim KS (2011) Fast DNA sequencing with a graphene-based nanochannel device. Nat Nanotechnol 6:162–165PubMedGoogle Scholar
  73. 73.
    Wells DB, Belkin M, Comer J, Aksimentiev A (2012) Assessing graphene nanopores for sequencing DNA. Nano Lett 12:4117–4123PubMedPubMedCentralGoogle Scholar
  74. 74.
    Fan S, Chapline MG, Franklin NR, Tombler TW, Cassell AM, Dai H (1999) Self-oriented regular arrays of carbon nanotubes and their field emission properties. Science 283:512–514PubMedGoogle Scholar
  75. 75.
    Sun L, Crooks RM (2000) Single carbon nanotube membranes: a well-defined model for studying mass transport through nanoporous materials. J Am Chem Soc 122:12340–12345Google Scholar
  76. 76.
    Yang N, Swain GM, Jiang X (2016) Nanocarbon electrochemistry and electroanalysis: current status and future perspectives. Electroanalysis 28:27–34Google Scholar
  77. 77.
    Yang N, Jiang X, Pang D-W (eds) (2016) Carbon nanoparticles and nanostructures. Springer, New YorkGoogle Scholar
  78. 78.
    Yang N (ed) (2015) Novel aspects of diamond: from growth to applications. Springer, New YorkGoogle Scholar
  79. 79.
    Brilla E, Martinez-Huitle CA (2011) Synthetic diamond films: preparation, electrochemistry, characterization, and applications. Wiley, HobokenGoogle Scholar
  80. 80.
    Schneider GF, Kowalczyk SW, Calado VE, Pandraud G, Zandbergen HW, Vandersypen LMK, Dekker C (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163–3167PubMedGoogle Scholar
  81. 81.
    Merchant CA, Healy K, Wanunu M, Ray V, Peterman N, Bartel J, Fischbein MD, Venta K, Luo Z, Johnson ATC, Drndic M (2010) DNA translocation through graphene nanopores. Nano Lett 10:2915–2921PubMedGoogle Scholar
  82. 82.
    Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko JA (2010) Graphene as a subnanometre transelectrode membrane. Nature 467:190–193PubMedPubMedCentralGoogle Scholar
  83. 83.
    Nam S, Choi I, Fu C-C, Kim K, Hong S, Choi Y, Zettl A, Lee LP (2014) Graphene nanopore with a self-integrated optical antenna. Nano Lett 14:5584–5589PubMedGoogle Scholar
  84. 84.
    Russo CJ, Golovchenko JA (2012) Atom-by-atom nucleation and growth of graphene nanopores. Proc Natl Acad Sci U S A 109:5953–5957PubMedPubMedCentralGoogle Scholar
  85. 85.
    Cao Y, Dong S, Liu S, He L, Gan L, Yu X, Steigerwald ML, Wu X, Liu Z, Guo X (2012) Building high-throughput molecular junctions using indented graphene point contacts. Angew Chem Int Ed 124:12394–12398Google Scholar
  86. 86.
    Xu Q, Wu M-Y, Schneider GF, Houben L, Malladi SK, Dekker C, Yucelen E, Dunin-Borkowski RE, Zandbergen HW (2013) Controllable atomic scale patterning of freestanding monolayer graphene at elevated temperature. ACS Nano 7:1566–1572PubMedGoogle Scholar
  87. 87.
    Venkatesan BM, Estrada D, Banerjee S, Jin X, Dorgan VE, Bae M-H, Aluru NR, Pop E, Bashir R (2012) Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DANN-protein complexes. ACS Nano 6:441–450PubMedGoogle Scholar
  88. 88.
    Song B, Schneider GF, Xu Q, Pandraud G, Dekker C, Zandbergen H (2011) Atomic-scale electron-beam sculpting of near defect-free graphene nanostructures. Nano Lett 11:2247–2250PubMedGoogle Scholar
  89. 89.
    Wu X, Zhao H, Pei J (2015) Fabrication of nanopore in graphene by electron and ion beam irradiation: influence of graphene thickness and substrate. Comput Mater Sci 102:258–266Google Scholar
  90. 90.
    Bai Z, Zhang L, Li H, Liu L (2016) Nanopore creation in graphene by ion beam irradiation: geometry, quality, and efficiency. ACS Appl Mater Interfaces 8:24803–24809PubMedGoogle Scholar
  91. 91.
    Fischbein MD, Drndic M (2008) Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett 93:113107Google Scholar
  92. 92.
    Crick CR, Sze JYY, Rosillo-Lopez M, Salzmann CG, Edel JB (2015) Selectively sized graphene-based nanopores for in situ single molecule sensing. ACS Appl Mater Interfaces 7:18188–18194PubMedPubMedCentralGoogle Scholar
  93. 93.
    Prins F, Barreiro A, Ruitenberg JW, Seldenthuis JS, Aliaga-Alcalde N, Vandersypen LMK, van der Zant HSJ (2011) Room-temperature gating of molecular junctions using few-layer graphene nanogap electrodes. Nano Lett 11:4607–4611PubMedGoogle Scholar
  94. 94.
    Nef C, Pósa L, Makk P, Fu W, Halbritter A, Schönenberger C, Calame M (2014) High-yield fabrication of nm-size gaps in monolayer CVD graphene. Nanoscale 6:7249–7254PubMedGoogle Scholar
  95. 95.
    Sadeghi H, Mol JA, Lau CS, Briggs GAD, Warner J, Lambert CJ (2015) Conductance enlargement in picoscale electroburnt graphene nanojunctions. Proc Natl Acad Sci U S A 112:2658–2663PubMedPubMedCentralGoogle Scholar
  96. 96.
    Island JO, Holovchenko A, Koole M, Alkemade PFA, Menelaou M, Aliaga-Alcalde N, Burzurí E, van der Zant HSJ (2014) Fabrication of hybrid molecular devices using multi-layer graphene break junctions. J Phys Condens Matter 26:474205PubMedGoogle Scholar
  97. 97.
    Jia X, Campos-Delgado J, Terrones M, Meunier V, Dresselhaus MS (2011) Graphene edges: a review of their fabrication and characterization. Nanoscale 3:86–95PubMedGoogle Scholar
  98. 98.
    Puster M, Rodríguez-Manzo JA, Balan A, Drndić M (2013) Toward sensitive graphene nanoribbon-nanopore devices by preventing electron beam-induced damage. ACS Nano 7:11283–11289PubMedGoogle Scholar
  99. 99.
    Qi ZJ, Rodríguez-Manzo JA, Botello-Méndez AR, Hong SJ, Stach EA, Park YW, Charlier J-C, Drndić M, Johnson ATC (2014) Correlating atomic structure and transport in suspended graphene nanoribbons. Nano Lett 14:4238–4244PubMedPubMedCentralGoogle Scholar
  100. 100.
    Qi ZJ, Daniels C, Hong SJ, Park YW, Meunier V, Drndić M, Johnson ATC (2015) Electronic transport of recrystallized freestanding graphene nanoribbons. ACS Nano 9:3510–3520PubMedGoogle Scholar
  101. 101.
    Kato T, Hatakeyama R (2012) Site- and alignment-controlled growth of graphene nanoribbons from nickel nanobars. Nat Nanotechnol 7:651–656PubMedGoogle Scholar
  102. 102.
    Wang X, Dai H (2010) Etching and narrowing of graphene from the edges. Nat Chem 2:661–665PubMedGoogle Scholar
  103. 103.
    Park S, Ruoff RS (2009) Chemical methods for the production of graphenes. Nat Nanotechnol 4:217–224PubMedPubMedCentralGoogle Scholar
  104. 104.
    Allen MJ, Tung VC, Kaner RB (2010) Honeycomb carbon: a review of graphene. Chem Rev 110:132–145PubMedGoogle Scholar
  105. 105.
    Zhang Y, Zhang L, Zhou C (2016) Review of chemical vapor deposition of graphene and related applications. Acc Chem Res 46:2329–2339Google Scholar
  106. 106.
    Bell DC, Lemme MC, Stern LA, Williams JR, Marcus CM (2009) Precision cutting and patterning of graphene with helium ions. Nanotechnology 20:455301PubMedGoogle Scholar
  107. 107.
    Lemme MC, Bell DC, Williams JR, Stern LA, Baugher BWH, Jarillo-Herrero P, Marcus CM (2009) Etching of graphene devices with a helium ion beam. ACS Nano 3:2674–2676PubMedGoogle Scholar
  108. 108.
    Hemamouche A, Morin A, Bourhis E, Toury B, Tarnaud E, Mathé J, Guégan P, Madouri A, Lafosse X, Ulysse C, Guilet S, Patriarche G, Auvray L, Montel F, Wilmart Q, Plaçais B, Yates J, Gierak J (2014) FIB patterning of dielectric, metallized and graphene membranes: a comparative study. Microelectron Eng 121:87–91Google Scholar
  109. 109.
    Zan R, Bangert U, Ramasse Q, Novoselov KS (2012) Interaction of metals with suspended graphene observed by transmission electron microscopy. J Phys Chem Lett 3:953–958PubMedGoogle Scholar
  110. 110.
    Ramasse QM, Zan R, Bangert U, Boukhvalov DW, Son YW, Novoselov KS (2012) Direct experimental evidence of metal-mediated etching of suspended graphene. ACS Nano 6:4063–4071PubMedGoogle Scholar
  111. 111.
    Egerton RF, Li P, Malac M (2004) Radiation damage in the TEM and SEM. Micron 35:399–409PubMedGoogle Scholar
  112. 112.
    Meyer JC, Girit CO, Crommie MF, Zettl A (2008) Hydrocarbon lithography on graphene membranes. Appl Phys Lett 92:123110Google Scholar
  113. 113.
    Schneider GF, Xu Q, Hage S, Luik S, Spoor JNH, Malladi S, Zandbergen H, Dekker C (2013) Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation. Nat Commun 4:2619PubMedGoogle Scholar
  114. 114.
    Freedman KJ, Ahn CW, Kim MJ (2013) Detection of long and short DNA using nanopores with graphitic polyhedral edges. ACS Nano 7:5008–5016PubMedGoogle Scholar
  115. 115.
    Xu T, Yin K, Xie X, He L, Wang B, Sun L (2012) Size-dependent evolution of graphene nanopores under thermal excitation. Small 8:3422–3426PubMedGoogle Scholar
  116. 116.
    Barreiro A, Boerrnert F, Avdoshenko SM, Rellinghaus B, Cuniberti G, Ruemmeli MH, Vandersypen LMK (2013) Understanding the catalyst-free transformation of amorphous carbon into graphene by current-induced annealing. Sci Rep 3:1115PubMedCentralGoogle Scholar
  117. 117.
    Ataca C, Ciraci S (2011) Perpendicular growth of carbon chains on graphene from first-principles. Phys Rev B 83:235417Google Scholar
  118. 118.
    Tsetseris L, Pantelides ST (2009) Adatom complexes and self-healing mechanisms on graphene and single-wall carbon nanotubes. Carbon 47:901–908Google Scholar
  119. 119.
    Kuan AT, Lu B, Xie P, Szalay T, Golovchenko JA (2015) Electrical pulse fabrication of graphene nanopores in electrolyte solution. Appl Phys Lett 106:203109PubMedPubMedCentralGoogle Scholar
  120. 120.
    Liu H, He J, Tang J, Liu H, Pang P, Cao D, Krstic P, Joseph S, Lindsay S, Nuckolls C (2010) Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327:64–67PubMedPubMedCentralGoogle Scholar
  121. 121.
    Liu L, Yang C, Zhao K, Li J, Wu H-C (2013) Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor. Nat Commun 4:2989PubMedPubMedCentralGoogle Scholar
  122. 122.
    Ito T, Sun L, Henriquez RR, Crooks RM (2004) A carbon nanotube-based coulter nanoparticle counter. Acc Chem Res 37:937–945PubMedGoogle Scholar
  123. 123.
    Arash B, Wang Q, Wu N (2012) Gene detection with carbon nanotubes. J Nanotechnol Eng Med 3:020902Google Scholar
  124. 124.
    Henriquez RR, Ito T, Sun L, Crooks RM (2004) The resurgence of Coulter counting for analyzing nanoscale objects. Analyst 129:478–482PubMedGoogle Scholar
  125. 125.
    Ito T, Sun L, Crooks RM (2003) Observation of DNA transport through a single carbon nanotube channel using fluorescence microscopy. Chem Commun 12:1482–1483Google Scholar
  126. 126.
    Mehedi H-A, Arnault J-C, Eon D, Hébert C, Carole D, Omnes F, Gheeraert E (2013) Etching mechanism of diamond by Ni nanoparticles for fabrication of nanopores. Carbon 59:448–456Google Scholar
  127. 127.
    Smirnov W, Hees J, Brink D, Müller-Sebert W, Kriele A, Williams OA, Nebel C (2010) Anisotropic etching of diamond by molten Ni particles. Appl Phys Lett 97:073117Google Scholar
  128. 128.
    Takasu Y, Konishi S, Sugimoto W, Murakami Y (2006) Catalytic formation of nanochannels in the surface layers of diamonds by metal nanoparticles. Electrochem Solid St 9:C114–C117Google Scholar
  129. 129.
    Mehedi H-A, Hébert C, Ruffinatto S, Eon D, Omnès F, Gheeraert E (2012) Formation of oriented nanostructures in diamond using metallic nanoparticles. Nanotechnology 23:455302PubMedGoogle Scholar
  130. 130.
    Masuda H, Yasui K, Watanabe M, Nishio K, Nakao M, Tamamura T, Rao TN, Fujishima A (2001) Fabrication of through-hole diamond membranes by plasma etching using anodic porous alumina mask. Electrochem Solid St 4(11):G101–G103Google Scholar
  131. 131.
    Aharonovich I, Greentree AD, Prawer S (2011) Diamond photonics. Nat Photonics 5:397–405Google Scholar
  132. 132.
    Mahé E, Devilliers D, Comninellis C (2005) Electrochemical reactivity at graphitic micro- domains on polycrystalline boron doped diamond thin-films electrodes. Electrochim Acta 50:2263–2277Google Scholar
  133. 133.
    Zhuang H, Yang N, Fu H, Zhang L, Wang C, Huang N, Jiang X (2015) Diamond network: template-free fabrication and properties. ACS Appl Mater Interfaces 7:5384–5390PubMedGoogle Scholar
  134. 134.
    Yang N, Foord JS, Jiang X (2016) Diamond electrochemistry at the nanoscale: a review. Carbon 99:90–110Google Scholar
  135. 135.
    Webb JR, Martin AA, Johnson RP, Joseph MB, Newton ME, Aharonovich I, Toth M, Macpherson JV (2017) Fabrication of a single sub-micron pore spanning a single crystal (100) diamond membrane and impact on particle translocation. Carbon 122:319–328Google Scholar
  136. 136.
    McNally B, Singer A, Liu Z, Sun Y, Wenig Z, Meller A (2010) Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett 10:2237–2244PubMedPubMedCentralGoogle Scholar
  137. 137.
    Keyser UF, Koeleman BN, Dorp SV, Krapf D, Smeets RMM, Lemay SG, Dekker NH, Dekker C (2006) Direct force measurements on DNA in a solid-state nanopore. Nat Phys 2:473–477Google Scholar
  138. 138.
    Sathe C, Zou XQ, Leburton JP, Schulten K (2011) Computational investigation of DNA detection using graphene nanopores. ACS Nano 5:8842–8851PubMedPubMedCentralGoogle Scholar
  139. 139.
    Garaj S, Liu S, Golovchenko JA, Branton D (2013) Molecule-hugging graphene nanopores. Proc Natl Acad Sci U S A 110:12192–12196PubMedPubMedCentralGoogle Scholar
  140. 140.
    Peng S, Yang Z, Ni X, Zhang H, Ouyang J, Fangping O (2014) DNA translocation through graphene nanopores: a first-principles study. Mater Res Express 1:015044Google Scholar
  141. 141.
    Lv W, Liu S, Li X, Wu R (2014) Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore. Electrophoresis 35:1144–1151PubMedGoogle Scholar
  142. 142.
    Sadeghi H, Algaragholy L, Pope T, Bailey S, Visontai D, Manrique D, Ferrer J, Garcia-Suarez V, Sangtarash S, Lambert CJ (2014) Graphene sculpturene nanopores for DNA nucleobase sensing. J Phys Chem B 118:6908–6914PubMedGoogle Scholar
  143. 143.
    Shankla M, Aksimentiev A (2014) Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene. Nat Commun 5:5171PubMedPubMedCentralGoogle Scholar
  144. 144.
    Suk ME, Aluru NR (2014) Ion transport in sub-5-nm graphene nanopores. J Chem Phys 140:084707PubMedGoogle Scholar
  145. 145.
    Avdoshenko SM, Nozaki D, da Rocha CG, González JW, Lee MH, Gutierrez R, Cuniberti G (2013) Dynamic and electronic transport properties of DNA translocation through graphene nanopores. Nano Lett 13:1969–1976PubMedGoogle Scholar
  146. 146.
    Liang L, Cui P, Wu T, Agren H, Tu Y (2013) Theoretical study on key factors in DNA sequencing with graphene nanopores. RSC Adv 3:2445–2453Google Scholar
  147. 147.
    Hu G, Mao M, Ghosal S (2012) Ion transport through a graphene nanopore. Nanotechnology 23:395501PubMedPubMedCentralGoogle Scholar
  148. 148.
    Zhao S, Xue J, Kang W (2013) Ion selection of charge-modified large nanopores in a graphene sheet. J Chem Phys 139:114702PubMedGoogle Scholar
  149. 149.
    Liang L, Zhang Z, Shen J, Zhe K, Wang Q, Wu T, Agren H, Tu Y (2015) Theoretical studies on the dynamics of DNA fragment translocation through multilayer graphene nanopores. RSC Adv 4:50494–50502Google Scholar
  150. 150.
    Shi C, Kong Z, Sun TT, Liang L, Shen J, Zhao Z, Wang Q, Kang Z, Agren H, Tu Y (2015) Molecular dynamics simulations indicate that DNA bases using graphene nanopores can be identified by their translocation times. RSC Adv 5:9389–9395Google Scholar
  151. 151.
    Becton M, Zhang L, Wang X (2014) Molecular dynamics study of programmable nanoporous graphene. J Nanomech Micromech 4:B4014002Google Scholar
  152. 152.
    Zhang Z, Shen J, Wang H, Wang Q, Zhang J, Liang L, Agren H, Tu Y (2014) Effects of graphene nanopore geometry on DNA sequencing. J Phys Chem Lett 5:1602–1607PubMedGoogle Scholar
  153. 153.
    Qiu H, Guo W (2012) Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: a molecular dynamics study. Appl Phys Lett 100:083106Google Scholar
  154. 154.
    Kang Y, Zhang Z, Shi H, Zhang J, Liang L, Wang Q, Agren H, Tu Y (2014) Na+ and K+ ion selectivity by size-controlled biomimetic graphene nanopores. Nanoscale 6:10666–10672PubMedGoogle Scholar
  155. 155.
    Lv W, Chen M, Wu R (2013) The impact of the number of layers of a graphene nanopore on DNA translocation. Soft Matter 9:960–966Google Scholar
  156. 156.
    Banerjee S, Wilson J, Shim J, Shankla M, Corbin EA, Aksimentiev A, Bashir R (2015) Slowing DNA transport using graphene–DNA interactions. Adv Funct Mater 25:936–946PubMedGoogle Scholar
  157. 157.
    Ventra MD, Tanigichi M (2016) Decoding DNA, RNA and peptides with quantum tunnelling. Nat Nanotechnol 11:117–126PubMedGoogle Scholar
  158. 158.
    Tsutsui M, Taniguchi M, Yokota K, Kawai T (2010) Identifying single nucleotides by tunnelling current. Nat Nanotechnol 5:286–290PubMedGoogle Scholar
  159. 159.
    Ohshiro T, Tsutsui M, Yokota K, Furuhashi M, Taniguchi M, Kawai T (2014) Detection of post-translational modifications in single peptides using electron tunnelling currents. Nat Nanotechnol 9:835–840PubMedGoogle Scholar
  160. 160.
    Gracheva ME, Xiong A, Aksimentiev A, Schulten K, Timp G, Leburton JP (2006) Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor. Nanotechnology 17:622–633Google Scholar
  161. 161.
    Siwy ZS, Howorka S (2010) Engineered voltage-responsive nanopores. Chem Soc Rev 39:1115–1132PubMedGoogle Scholar
  162. 162.
    Tanaka H, Kawai T (2003) Visualization of detailed structures within DNA. Surf Sci 539:L531–L536Google Scholar
  163. 163.
    Lee JW, Meller A (2007) In: Mitchelson K (ed) Perspectives in bioanalysis. Elsevier, AmsterdamGoogle Scholar
  164. 164.
    Zwolak M, Ventra MD (2005) Electronic signature of DNA nucleotides via transverse transport. Nano Lett 5:421–424PubMedGoogle Scholar
  165. 165.
    Prasongkit J, Grigoriev A, Pathak B, Ahuja R, Scheicher RH (2011) Transverse conductance of DNA nucleotides in a graphene nanogap from first principles. Nano Lett 11:1941–1945PubMedGoogle Scholar
  166. 166.
    Postma HW (2010) Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett 10:420–425PubMedGoogle Scholar
  167. 167.
    Zhao Q, Wang Y, Dong J, Zhao L, Rui XF, Yu D (2012) Nanopore-based DNA analysis via graphene electrodes. J Nanomater 2012:318950Google Scholar
  168. 168.
    He Y, Tsutsui M, Scheicher RH, Taniguchi M (2012) Bilayer graphene lateral contacts for DNA. arXiv:1206.4199v1Google Scholar
  169. 169.
    Jeong H, Kim HS, Lee S-H, Lee D, Kim YH, Huh N (2013) Quantum interference in DNA bases probed by graphene nanoribbons. Appl Phys Lett 103:023701Google Scholar
  170. 170.
    Prasongkit J, Grigoriev A, Pathak B, Ahuja R, Scheicher RH (2013) Theoretical study of electronic transport through DNA nucleotides in a double-functionalized graphene nanogap. J Phys Chem C 117:15421–15428Google Scholar
  171. 171.
    Waduge P, Larkin J, Upmanyu M, Kar S, Wanunu M (2015) Synthesis of freestanding graphene nanomembrane arrays. Small 11:597–603PubMedGoogle Scholar
  172. 172.
    Nelson T, Zhang B, Prezhdo OV (2010) Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. Nano Lett 10:3237–3242PubMedGoogle Scholar
  173. 173.
    Ouyang F-P, Peng S-L, Zhang H, Weng L-B, Xu H (2011) A biosensor based on graphene nanoribbon with nanopores: a first-principles devices-design. Chin Phys B 20:058504Google Scholar
  174. 174.
    Saha KK, Drndić M, Nikolić BK (2012) DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore. Nano Lett 12:50–55PubMedGoogle Scholar
  175. 175.
    Ahmed T, Haraldsen JT, Zhu J-X, Balatsky AV (2014) Next-generation epigenetic detection technique: identifying methylated cytosine using graphene nanopore. J Phys Chem Lett 5:2601–2607PubMedGoogle Scholar
  176. 176.
    Ahmed T, Haraldsen JT, Rehr JJ, Ventra MD, Schuller I, Balatsky AV (2014) Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases. Nanotechnology 25:125705PubMedGoogle Scholar
  177. 177.
    Zhang H, Xu H, Ni X, Peng SL, Liu Q, OuYang FP (2014) Detection of nucleic acids by graphene-based devices: a first-principles study. J Appl Phys 115:133701Google Scholar
  178. 178.
    Liu N, Yang Z, Ou X, Wie B, Zhang J, Jia Y, Xia F (2016) Nanopore-based analysis of biochemical species. Microchim Acta 183:955–963Google Scholar
  179. 179.
    Girdhar A, Sathe C, Schulten K, Leburton J-P (2013) Graphene quantum point contact transistor for DNA sensing. Proc Natl Acad Sci U S A 110:16748–16753PubMedPubMedCentralGoogle Scholar
  180. 180.
    Prasongkit J, Feliciano GT, Rocha AR, He Y, Osotchan T, Ahuja R, Scheicher RH (2015) Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene. Sci Rep 5:17560PubMedPubMedCentralGoogle Scholar
  181. 181.
    Sathe C, Girdhar A, Leburton J-P, Schulten K (2014) Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores. Nanotechnology 25:445105PubMedPubMedCentralGoogle Scholar
  182. 182.
    He Y, Scheicher RH, Grigoriev A, Ahuja R, Long S, Huo Z, Liu M (2011) Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes. Adv Funct Mater 21:2674–2679Google Scholar
  183. 183.
    McFarland HL, Ahmed T, Zhu J-X, Balatsky AV, Haraldsen JT (2015) First-principles investigation of nanopore sequencing using variable voltage bias on graphene-based nanoribbons. J Phys Chem Lett 6:2616–2621PubMedGoogle Scholar
  184. 184.
    Paulechka E, Wassenaar TA, Kroenlein K, Kazakova A, Smolyanitsky A (2016) Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing. Nanoscale 8:1861–1867PubMedGoogle Scholar
  185. 185.
    Mahmood MAI, Ali W, Adnan A, Iqbal SM (2014) 3D structural integrity and interactions of single-stranded protein-binding DNA in a functionalized nanopore. J Phys Chem B 118:5799–5806PubMedGoogle Scholar
  186. 186.
    He H, Scheicher RH, Pandey R, Rocha AR, Sanvito S, Grigoriev A, Ahuja R, Karna SP (2008) Functionalized nanopore-embedded electrodes for rapid DNA sequencing. J Phys Chem C 112:3456–3459Google Scholar
  187. 187.
    Traversi F, Raillon C, Benameur SM, Liu K, Khlybov S, Tosun M, Krasnozhon D, Kis A, Radenovic A (2013) Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat Nanotechnol 8:939–945PubMedGoogle Scholar
  188. 188.
    Liu L, Xie J, Li T, Wu H-C (2015) Fabrication of nanopores with ultrashort single-walled carbon nanotubes inserted in a lipid bilayer. Nat Protoc 10:1670–1678PubMedGoogle Scholar
  189. 189.
    Lee CY, Choi W, Han J-H, Strano MS (2010) Coherence resonance in a single-walled carbon nanotube ion channel. Science 329:1320–1324PubMedGoogle Scholar
  190. 190.
    Chen X, Rungger I, Pemmaraju CD, Schwingenschlögl U, Sanvito S (2012) First principles study of high-conductance DNA sequencing with carbon nanotube electrodes. Phys Rev B 85:115436Google Scholar
  191. 191.
    Li J, Zhang Y, Yang J, Bi K, Ni Z, Li D, Chen Y (2013) Molecular dynamics study of DNA translocation through graphene nanopores. Phys Rev E 87:062707Google Scholar
  192. 192.
    Iliafar S, Wagner K, Manohar S, Jagota A, Vezenov D (2012) Quantifying interactions between DNA oligomers and graphite surface using single molecule force spectroscopy. J Phys Chem C 116:13896–13903Google Scholar
  193. 193.
    Gowtham S, Scheicher R, Ahuja R, Pandey R, Karna S (2007) Physisorption of nucleobases on graphene: density-functional calculations. Phys Rev B 76:033401Google Scholar
  194. 194.
    Akca S, Foroughi A, Frochtzwajg D, Postma HWC (2011) Competing interactions in DNA assembly on graphene. PLoS One 6:e18442PubMedPubMedCentralGoogle Scholar
  195. 195.
    Lee J-H, Choi Y-K, Kim H-J, Scheicher RH, Cho J-H (2013) Physisorption of DNA nucleobases on h-BN and graphene: vdW-corrected DFT calculations. J Phys Chem C 117:13435–13441Google Scholar
  196. 196.
    Antony J, Grimme S (2008) Structures and interaction energies of stacked graphene-nucleobase complexes. Phys Chem Chem Phys 10:2722–2729PubMedGoogle Scholar
  197. 197.
    Varghese N, Mogera U, Govindaraj A, Das A, Maiti PK, Sood AK, Rao CNR (2009) Binding of DNA nucleobases and nucleosides with graphene. Chem Phys Chem 10:206–210PubMedGoogle Scholar
  198. 198.
    Umadevi D, Sastry GN (2011) Quantum mechanical study of physisorption of nucleobases on carbon materials: graphene versus carbon nanotubes. J Phys Chem Lett 2:1572–1576Google Scholar
  199. 199.
    Le D, Kara A, Schröder F, Hyldgaard P, Rahman TS (2012) Physisorption of nucleobases on graphene: a comparative van der Waals study. J Phys Condens Matter 24:424210PubMedGoogle Scholar
  200. 200.
    Smeets RMM, Keyser UF, Dekker NH, Dekker C (2008) Noise in solid-state nanopores. Proc Natl Acad Sci U S A 105:417–421PubMedPubMedCentralGoogle Scholar
  201. 201.
    Tabard-Cossa V, Trivedi D, Wiggin M, Jetha NN, Marziali A (2007) Noise analysis and reduction in solid-state nanopores. Nanotechnology 18:305505Google Scholar
  202. 202.
    Kong Z, Zheng W, Wang Q, Wang H, Xi F, Liang L, Shen J-W (2015) Charge-tunable absorption behavior of DNA on graphene. J Mater Chem B 3:4814–4820Google Scholar
  203. 203.
    Kundu S, Karmakar SN (2016) Detection of base-pair mismatches in DNA using graphene-based nanopore device. Nanotechnology 27:135101PubMedGoogle Scholar
  204. 204.
    Qiu H, Girdhar A, Schulten K, Leburton JP (2016) Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores. ACS Nano 10:4482–4488PubMedPubMedCentralGoogle Scholar
  205. 205.
    Fotouhi B, Ahmadi V, Abasifard M, Roohi R (2016) Interband π plasmon of graphene nanopores: a potential sensing mechanism for DNA nucleotides. J Phys Chem C 120:13693–13700Google Scholar
  206. 206.
    Wen C, Zeng S, Zhang Z, Hjort K, Scheicher R, Zhang SL (2016) On nanopore DNA sequencing by signal and noise analysis of ionic current. Nanotechnology 27:215502PubMedGoogle Scholar
  207. 207.
    Al-Dirini F, Mohammed MA, Hossain MS, Hossain FM, Nirmalathas A, Skafidas E (2016) Tuneable graphene nanopores for single biomolecule detection. Nanoscale 8:10066–10077PubMedGoogle Scholar
  208. 208.
    Guo Y-D, Yan X-H, Xiao Y (2012) Computational investigation of DNA detection using single-electron transistor-based nanopore. J Phys Chem B 116:21609–21614Google Scholar
  209. 209.
    Mirsaidov U, Comer J, Dimitrov V, Aksimentiev A, Timp G (2010) Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix. Nanotechnology 21:395501PubMedGoogle Scholar
  210. 210.
    Kastner MA (1992) The single-electron transistor. Rev Mod Phys 64:849–858Google Scholar
  211. 211.
    Kaasbjerg K, Flensberg K (2008) Strong polarization-induced reduction of addition energies in single-molecule nanojunctions. Nano Lett 8:3809–3814PubMedGoogle Scholar
  212. 212.
    Leroux A, Destine J, Vanderheyden B, Gracheva ME, Leburton J (2010) Spice circuit simulation of the electrical response of a semiconductor membrane to a single-stranded DNA translocating through a nanopore. IEEE Trans Nanotechnol 9:322–329Google Scholar
  213. 213.
    Gracheva ME, Vidal J, Leburton JP (2007) p-n semiconductor membrane for electrically tunable ion current rectification and filtering. Nano Lett 7:1717–1722PubMedPubMedCentralGoogle Scholar
  214. 214.
    Nikolaev A, Gracheval ME (2011) Simulation of ionic current through the nanopore in a double-layered semiconductor membrane. Nanotechnology 22:165202PubMedGoogle Scholar
  215. 215.
    Melnikov DV, Leburton J-P, Gracheva ME (2012) Slowing down and stretching DNA with an electrically tunable nanopore in a p-n semiconductor membrane. Nanotechnology 23:255501PubMedGoogle Scholar
  216. 216.
    Jou IA, Melnikov DV, McKinney CR, Gracheva ME (2012) DNA translocation through a nanopore in a single-layered doped semiconductor membrane. Phys Rev E 86:061906Google Scholar
  217. 217.
    Jou IA, Melnikov DV, Nadtochiy A, Gracheva ME (2014) Charged particle separation by an electrically tunable nanoporous membrane. Nanotechnology 25:145201PubMedGoogle Scholar
  218. 218.
    Chinappi M, Luchian T, Cecconi F (2015) Nanopore tweezers: voltage-controlled trapping and releasing of analytes. Phys Rev E 92:032714Google Scholar
  219. 219.
    Murray KM (1996) DNA sequencing by mass spectrometry. J Mass Spectrom 31:1203–1215PubMedGoogle Scholar
  220. 220.
    Kirpekar F, Nordhoff E, Larsen LK, Kristiansen K, Roepstorff P, Hillenkamp F (1998) DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res 26:554–2559Google Scholar
  221. 221.
    Edwards JR, Ruparel H, Ju J (2005) Mass-spectrometry DNA sequencing. Mutat Res 573:3–12PubMedGoogle Scholar
  222. 222.
    Tost J, Gut IG (2006) DNA analysis by mass spectrometry – past, present, and future. J Mass Spectrom 41:981–995PubMedGoogle Scholar
  223. 223.
    Tretyakova N, Villalta PW, Kotapati S (2013) Mass spectrometry of structurally modified DNA. Chem Rev 113:2395–2436PubMedPubMedCentralGoogle Scholar
  224. 224.
    Maulbetsch W, Wiener B, Poole W, Bush J, Stein D (2016) Preserving the sequence of a biopolymer’s monomers as they enter an electrospray mass spectrometer. Phys Rev Applied 6:054006Google Scholar
  225. 225.
    Lu Y, Merchant CA, Drndić M, Johnson ATC (2011) In situ electronic characterization of graphene nanoconstrictions fabricated in a transmission electron microscope. Nano Lett 11:5184–5188PubMedPubMedCentralGoogle Scholar
  226. 226.
    Dontschuk N, Stacey A, Tadich A, Rietwyk KJ, Schenk A, Edmonds MT, Shimonil O, Pakes CI, Prawer S, Cervenka J (2014) A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases. Nat Commun 6:6563Google Scholar
  227. 227.
    Liu L, Wu H-C (2016) DNA-based nanopore sensing. Angew Chem Int Ed 55:15216–15222Google Scholar
  228. 228.
    Cho Y, Min SK, Kim WY, Kim KS (2011) The origin of dips for the graphene-based DNA sequencing device. Phys Chem Chem Phys 13:14293–14296PubMedGoogle Scholar
  229. 229.
    Song B, Cuniberti G, Sanvito S, Fang H (2012) Nucleobase adsorbed at graphene devices: enhance bio-sensorics. Appl Phys Lett 100:063101Google Scholar
  230. 230.
    Bobadilla AD, Seminario JM (2013) Assembly of a noncovalent DNA junction on graphene sheets and electron transport characteristics. J Phys Chem C 117:26441–26453Google Scholar
  231. 231.
    Cai J, Ruffieux P, Jaafar R, Bieri M, Braun T, Blankenburg S, Muoth M, Seitsonen AP, Saleh M, Feng X, Müllen K, Fasel R (2010) Atomically precise bottom-up fabrication of graphene nanoribbons. Nature 466:470–473PubMedGoogle Scholar
  232. 232.
    Ahmed T, Kilina S, Das T, Haraldsen JT, Rehr JJ, Balatsky AV (2012) Electronic fingerprints of DNA bases on graphene. Nano Lett 12:927–931PubMedGoogle Scholar
  233. 233.
    Tanaka H, Kawai T (2009) Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 4:518–522PubMedGoogle Scholar
  234. 234.
    Vicarelli L, Heerema SJ, Dekker C, Zandbergen HW (2015) Controlling defects in graphene for optimizing the electrical properties of graphene nanodevices. ACS Nano 9:3428–3435PubMedPubMedCentralGoogle Scholar

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Materials Engineering, University of SiegenSiegenGermany

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