Skip to main content
SpringerLink
Log in

DNA Sequencing Using Carbon Nanopores

  • Chapter
  • First Online:
Book cover Carbon-Based Nanosensor Technology

Part of the book series: Springer Series on Chemical Sensors and Biosensors ((SSSENSORS,volume 17))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 349.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 449.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Franc LTC, Carrilho E, Kist TBL (2002) A review of DNA sequencing techniques. Q Rev Biophys 35:169–200

    Article  CAS  Google Scholar 

  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 26:1146–1153

    CAS  Google Scholar 

  3. Zwolak M, Ventra MD (2008) Colloquium: physical approaches to DNA sequencing and detection. Rev Mod Phys 80:141–165

    Article  Google Scholar 

  4. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145

    Article  CAS  PubMed  Google Scholar 

  5. Kasianowicz JJ, Robertson JWF, Chan ER, Reiner JE, Stanford VM (2008) Nanoscopic porous sensors. Annu Rev Anal Chem 1:737–766

    Article  CAS  Google Scholar 

  6. Metzker ML (2010) Sequencing technologies – the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  7. Mirsaidov UM, Wang D, Timp W, Timp G (2010) Molecular diagnostics for personal medicine using a nanopore. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2:367–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 9:281–294

    Article  PubMed  PubMed Central  Google Scholar 

  9. Thompson JF, Milos PM (2011) The properties and applications of single-molecule DNA sequencing. Genome Biol 12:217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Venkatesan BM, Bashir R (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 6:615–624

    Article  CAS  PubMed  Google Scholar 

  11. Maitra RD, Kim J, Dunbar WB (2012) Recent advances in nanopore sequencing. Electrophoresis 33:3418–3428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Schneider GF, Dekker C (2012) DNA sequencing with nanopores. Nat Biotechnol 30:326–328

    Article  CAS  PubMed  Google Scholar 

  13. Ying Y-L, Zhang J, Gao R, Long Y-T (2013) Nanopore-based sequencing and detection of nucleic acids. Angew Chem Int Ed 52:13154–13161

    Article  CAS  Google Scholar 

  14. Feng Y, Zhang Y, Ying C, Wang D, Du C (2015) Nanopore-based fourth-generation DNA sequencing technology. Genomics Proteomics Bioinformatics 13:4–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lu H, Giordano F, Ning Z (2015) Oxford nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 14:265–279

    Article  Google Scholar 

  16. Wanunu M (2012) Nanopores: a journey towards DNA sequencing. Phys Life Rev 9:125–158

    Article  PubMed  PubMed Central  Google Scholar 

  17. Yokota K, Tsutsuia M, Taniguchi M (2014) Electrode-embedded nanopores for label-free single-molecule sequencing by electric currents. RSC Adv 4:15886–15899

    Article  CAS  Google Scholar 

  18. Taniguchi M (2015) Selective multidetection using nanopores. Anal Chem 87:188–199

    Article  CAS  PubMed  Google Scholar 

  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 36:2367–2379

    Article  CAS  PubMed  Google Scholar 

  20. Haywood DG, Saha-Shah A, Baker LA, Jacobson SC (2015) Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem 87:172–187

    Article  CAS  PubMed  Google Scholar 

  21. Rhee M, Burns MA (2008) Nanopore sequencing technology: nanopore preparations. Trends Biotechnol 25:174–181

    Article  CAS  Google Scholar 

  22. Ying Y-L, Chan C, Long Y-T (2014) Single molecule analysis by biological nanopore sensors. Analyst 139:3826–3835

    Article  CAS  PubMed  Google Scholar 

  23. Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A (2012) Modeling and simulation of ion channels. Chem Rev 112:6250–6284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 45:476–493

    Article  CAS  PubMed  Google Scholar 

  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 25:4549–4554

    Article  CAS  PubMed  Google Scholar 

  26. Gu Z, Zhang Y, Luan B, Zhou R (2016) DNA translocation through single-layer boron nitride nanopores. Soft Matter 12:817–823

    Article  CAS  PubMed  Google Scholar 

  27. Farimani AB, Min K, Aluru NR (2014) DNA base detection using a single-layer MoS2. ACS Nano 8:7914–7922

    Article  CAS  PubMed  Google Scholar 

  28. Liu K, Feng J, Kis A, Radenovic A (2014) Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano 8:2504–2511

    Article  CAS  PubMed  Google Scholar 

  29. Amorim RG, Scheicher RH (2015) Silicene as a new potential DNA sequencing device. Nanotechnology 26:154002

    Article  PubMed  CAS  Google Scholar 

  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 93:13770–13773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouauxt JE (1996) Structure of staphylococcal α-hemoIysin, a heptameric transmembrane pore. Science 274:1859–1865

    Article  CAS  PubMed  Google Scholar 

  32. Stefureac R, Long YT, Kraatz HB, Howard P, Lee JS (2006) Transport of α-helical peptides through α-hemolysin and aerolysin pores. Biochemistry 45:9172–9179

    Article  CAS  PubMed  Google Scholar 

  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):349–353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 12:4895–4900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 134:9521–9531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 4:765–772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 77:3227–3233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 97:1079–1084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Li J, Gershow M, Stein D, Brandin E, Golovchenko JA (2003) DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater 2:611–615

    Article  CAS  PubMed  Google Scholar 

  40. Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169

    Article  CAS  PubMed  Google Scholar 

  41. Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540

    Article  CAS  PubMed  Google Scholar 

  42. Deng T, Li M, Wang Y, Liu Z (2015) Development of solid-state nanopore fabrication technologies. Sci Bull 60:304–319

    Article  CAS  Google Scholar 

  43. Hlawacek G, Veligura V, van Gastel R, Poelsema B (2014) Helium ion microscopy. J Vac Sci Technol B 32:020801

    Article  CAS  Google Scholar 

  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 24:7745–7753

    Article  CAS  Google Scholar 

  45. Tseng AA (2005) Recent developments in nanofabrication using focused ion beams. Small 1:924–939

    Article  CAS  PubMed  Google Scholar 

  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 6:8900–8906

    Article  CAS  PubMed  Google Scholar 

  47. Rollings RC, Kuan AT, Golovchenko JA (2016) Ion selectivity of graphene nanopores. Nat Commun 7:11408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Tapasztó L, Dobrik G, Lambin P, Biró LP (2008) Tailoring the atomic structure of graphene nanoribbons by scanning tunnelling microscope lithography. Nat Nanotechnol 3:397–401

    Article  PubMed  CAS  Google Scholar 

  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 21:2771–2776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 84:779–783

    Article  CAS  Google Scholar 

  51. Nilsson J, Lee JRI, Ratto TV, Létant SE (2016) Localized functionalization of single nanopores. Adv Mater 18:427–431

    Article  CAS  Google Scholar 

  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 18:155303

    Article  CAS  Google Scholar 

  53. Knez M, Nielsch K, Niinistö L (2007) Synthesis and surface engineering of complex nanostructures by atomic layer deposition. Adv Mater 19:3425–3438

    Article  CAS  Google Scholar 

  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 250:195–213

    Article  CAS  PubMed  Google Scholar 

  55. Carson S, Wanunu M (2015) Challenges in DNA motion control and sequence readout using nanopore devices. Nanotechnology 26:074004

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 5:874–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Keyser U (2011) Controlling molecular transport through nanopores. J R Soc Interface 8:1369–1378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wanunu M, Meller A (2007) Chemically modified solid-state nanopores. Nano Lett 7:1580–1585

    Article  CAS  PubMed  Google Scholar 

  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 13:1859–1862

    Article  CAS  PubMed  Google Scholar 

  60. Farimani AB, Dibaeinia P, Aluru NR (2017) DNA origami-graphene hybrid nanopore for DNA detection. ACS Appl Mater Interfaces 9:92–100

    Article  CAS  Google Scholar 

  61. Comer J, Aksimentiev A (2016) DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. Nanoscale 8:9600–9613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Park HJ, Ryu GH, Lee Z (2015) Hole defects on two-dimensional materials formed by electron beam irradiation: toward nanopore devices. Appl Microsc 45:107–114

    Article  Google Scholar 

  63. Heerema SJ, Dekker C (2016) Graphene nanodevices for DNA sequencing. Nat Nanotechnol 11:127–136

    Article  CAS  PubMed  Google Scholar 

  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 60:721–729

    Article  CAS  Google Scholar 

  65. Yang N, Jiang X (2017) Nanocarbons for DNA sequencing: a review. Carbon 115:293–311

    Article  CAS  Google Scholar 

  66. Bayley H (2010) Holes with an edge. Nature 467:164–165

    Article  CAS  PubMed  Google Scholar 

  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 7:834–843

    Article  CAS  PubMed  Google Scholar 

  68. Heerema SJ, Schneider GF, Rozemuller M, Vicarelli L, Zandbergen HW, Dekker C (2015) 1/f noise in graphene nanopores. Nanotechnology 26:074001

    Article  CAS  PubMed  Google Scholar 

  69. Kumar A, Park K-B, Kim H-M, Kim K-B (2013) Noise and its reduction in graphene based nanopore devices. Nanotechnology 24:495503

    Article  PubMed  CAS  Google Scholar 

  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 9:11599–11607

    Article  CAS  PubMed  Google Scholar 

  71. Tang L, Wang Y, Li J (2015) The graphene/nucleic acid nanobiointerface. Chem Soc Rev 44:6954–6980

    Article  CAS  PubMed  Google Scholar 

  72. Min SK, Kim WY, Cho Y, Kim KS (2011) Fast DNA sequencing with a graphene-based nanochannel device. Nat Nanotechnol 6:162–165

    Article  CAS  PubMed  Google Scholar 

  73. Wells DB, Belkin M, Comer J, Aksimentiev A (2012) Assessing graphene nanopores for sequencing DNA. Nano Lett 12:4117–4123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 283:512–514

    Article  CAS  PubMed  Google Scholar 

  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 122:12340–12345

    Article  CAS  Google Scholar 

  76. Yang N, Swain GM, Jiang X (2016) Nanocarbon electrochemistry and electroanalysis: current status and future perspectives. Electroanalysis 28:27–34

    Article  CAS  Google Scholar 

  77. Yang N, Jiang X, Pang D-W (eds) (2016) Carbon nanoparticles and nanostructures. Springer, New York

    Google Scholar 

  78. Yang N (ed) (2015) Novel aspects of diamond: from growth to applications. Springer, New York

    Google Scholar 

  79. Brilla E, Martinez-Huitle CA (2011) Synthetic diamond films: preparation, electrochemistry, characterization, and applications. Wiley, Hoboken

    Google Scholar 

  80. Schneider GF, Kowalczyk SW, Calado VE, Pandraud G, Zandbergen HW, Vandersypen LMK, Dekker C (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163–3167

    Article  CAS  PubMed  Google Scholar 

  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 10:2915–2921

    Article  CAS  PubMed  Google Scholar 

  82. Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko JA (2010) Graphene as a subnanometre transelectrode membrane. Nature 467:190–193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 14:5584–5589

    Article  CAS  PubMed  Google Scholar 

  84. Russo CJ, Golovchenko JA (2012) Atom-by-atom nucleation and growth of graphene nanopores. Proc Natl Acad Sci U S A 109:5953–5957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 124:12394–12398

    Article  Google Scholar 

  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 7:1566–1572

    Article  CAS  PubMed  Google Scholar 

  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 6:441–450

    Article  CAS  PubMed  Google Scholar 

  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 11:2247–2250

    Article  CAS  PubMed  Google Scholar 

  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 102:258–266

    Article  CAS  Google Scholar 

  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 8:24803–24809

    Article  CAS  PubMed  Google Scholar 

  91. Fischbein MD, Drndic M (2008) Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett 93:113107

    Article  CAS  Google Scholar 

  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 7:18188–18194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 11:4607–4611

    Article  CAS  PubMed  Google Scholar 

  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 6:7249–7254

    Article  CAS  PubMed  Google Scholar 

  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 112:2658–2663

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 26:474205

    Article  CAS  PubMed  Google Scholar 

  97. Jia X, Campos-Delgado J, Terrones M, Meunier V, Dresselhaus MS (2011) Graphene edges: a review of their fabrication and characterization. Nanoscale 3:86–95

    Article  CAS  PubMed  Google Scholar 

  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 7:11283–11289

    Article  CAS  PubMed  Google Scholar 

  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 14:4238–4244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 9:3510–3520

    Article  CAS  PubMed  Google Scholar 

  101. Kato T, Hatakeyama R (2012) Site- and alignment-controlled growth of graphene nanoribbons from nickel nanobars. Nat Nanotechnol 7:651–656

    Article  CAS  PubMed  Google Scholar 

  102. Wang X, Dai H (2010) Etching and narrowing of graphene from the edges. Nat Chem 2:661–665

    Article  CAS  PubMed  Google Scholar 

  103. Park S, Ruoff RS (2009) Chemical methods for the production of graphenes. Nat Nanotechnol 4:217–224

    Article  CAS  PubMed  Google Scholar 

  104. Allen MJ, Tung VC, Kaner RB (2010) Honeycomb carbon: a review of graphene. Chem Rev 110:132–145

    Article  CAS  PubMed  Google Scholar 

  105. Zhang Y, Zhang L, Zhou C (2016) Review of chemical vapor deposition of graphene and related applications. Acc Chem Res 46:2329–2339

    Article  CAS  Google Scholar 

  106. Bell DC, Lemme MC, Stern LA, Williams JR, Marcus CM (2009) Precision cutting and patterning of graphene with helium ions. Nanotechnology 20:455301

    Article  CAS  PubMed  Google Scholar 

  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 3:2674–2676

    Article  CAS  PubMed  Google Scholar 

  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 121:87–91

    Article  CAS  Google Scholar 

  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 3:953–958

    Article  CAS  PubMed  Google Scholar 

  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 6:4063–4071

    Article  CAS  PubMed  Google Scholar 

  111. Egerton RF, Li P, Malac M (2004) Radiation damage in the TEM and SEM. Micron 35:399–409

    Article  CAS  PubMed  Google Scholar 

  112. Meyer JC, Girit CO, Crommie MF, Zettl A (2008) Hydrocarbon lithography on graphene membranes. Appl Phys Lett 92:123110

    Article  CAS  Google Scholar 

  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 4:2619

    Article  PubMed  CAS  Google Scholar 

  114. Freedman KJ, Ahn CW, Kim MJ (2013) Detection of long and short DNA using nanopores with graphitic polyhedral edges. ACS Nano 7:5008–5016

    Article  CAS  PubMed  Google Scholar 

  115. Xu T, Yin K, Xie X, He L, Wang B, Sun L (2012) Size-dependent evolution of graphene nanopores under thermal excitation. Small 8:3422–3426

    Article  CAS  PubMed  Google Scholar 

  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 3:1115

    Article  PubMed Central  CAS  Google Scholar 

  117. Ataca C, Ciraci S (2011) Perpendicular growth of carbon chains on graphene from first-principles. Phys Rev B 83:235417

    Article  CAS  Google Scholar 

  118. Tsetseris L, Pantelides ST (2009) Adatom complexes and self-healing mechanisms on graphene and single-wall carbon nanotubes. Carbon 47:901–908

    Article  CAS  Google Scholar 

  119. Kuan AT, Lu B, Xie P, Szalay T, Golovchenko JA (2015) Electrical pulse fabrication of graphene nanopores in electrolyte solution. Appl Phys Lett 106:203109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 327:64–67

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 4:2989

    Article  PubMed  CAS  Google Scholar 

  122. Ito T, Sun L, Henriquez RR, Crooks RM (2004) A carbon nanotube-based coulter nanoparticle counter. Acc Chem Res 37:937–945

    Article  CAS  PubMed  Google Scholar 

  123. Arash B, Wang Q, Wu N (2012) Gene detection with carbon nanotubes. J Nanotechnol Eng Med 3:020902

    Article  CAS  Google Scholar 

  124. Henriquez RR, Ito T, Sun L, Crooks RM (2004) The resurgence of Coulter counting for analyzing nanoscale objects. Analyst 129:478–482

    Article  CAS  PubMed  Google Scholar 

  125. Ito T, Sun L, Crooks RM (2003) Observation of DNA transport through a single carbon nanotube channel using fluorescence microscopy. Chem Commun 12:1482–1483

    Article  CAS  Google Scholar 

  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 59:448–456

    Article  CAS  Google Scholar 

  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 97:073117

    Article  CAS  Google Scholar 

  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–C117

    Article  CAS  Google Scholar 

  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 23:455302

    Article  PubMed  CAS  Google Scholar 

  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–G103

    Article  CAS  Google Scholar 

  131. Aharonovich I, Greentree AD, Prawer S (2011) Diamond photonics. Nat Photonics 5:397–405

    Article  CAS  Google Scholar 

  132. Mahé E, Devilliers D, Comninellis C (2005) Electrochemical reactivity at graphitic micro- domains on polycrystalline boron doped diamond thin-films electrodes. Electrochim Acta 50:2263–2277

    Article  CAS  Google Scholar 

  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 7:5384–5390

    Article  CAS  PubMed  Google Scholar 

  134. Yang N, Foord JS, Jiang X (2016) Diamond electrochemistry at the nanoscale: a review. Carbon 99:90–110

    Article  CAS  Google Scholar 

  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 122:319–328

    Article  CAS  Google Scholar 

  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 10:2237–2244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 2:473–477

    Article  CAS  Google Scholar 

  138. Sathe C, Zou XQ, Leburton JP, Schulten K (2011) Computational investigation of DNA detection using graphene nanopores. ACS Nano 5:8842–8851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Garaj S, Liu S, Golovchenko JA, Branton D (2013) Molecule-hugging graphene nanopores. Proc Natl Acad Sci U S A 110:12192–12196

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 1:015044

    Article  CAS  Google Scholar 

  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 35:1144–1151

    Article  CAS  PubMed  Google Scholar 

  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 118:6908–6914

    Article  CAS  PubMed  Google Scholar 

  143. Shankla M, Aksimentiev A (2014) Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene. Nat Commun 5:5171

    Article  CAS  PubMed  Google Scholar 

  144. Suk ME, Aluru NR (2014) Ion transport in sub-5-nm graphene nanopores. J Chem Phys 140:084707

    Article  PubMed  CAS  Google Scholar 

  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 13:1969–1976

    Article  CAS  PubMed  Google Scholar 

  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 3:2445–2453

    Article  CAS  Google Scholar 

  147. Hu G, Mao M, Ghosal S (2012) Ion transport through a graphene nanopore. Nanotechnology 23:395501

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Zhao S, Xue J, Kang W (2013) Ion selection of charge-modified large nanopores in a graphene sheet. J Chem Phys 139:114702

    Article  PubMed  CAS  Google Scholar 

  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 4:50494–50502

    Article  CAS  Google Scholar 

  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 5:9389–9395

    Article  CAS  Google Scholar 

  151. Becton M, Zhang L, Wang X (2014) Molecular dynamics study of programmable nanoporous graphene. J Nanomech Micromech 4:B4014002

    Article  Google Scholar 

  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 5:1602–1607

    Article  CAS  PubMed  Google Scholar 

  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 100:083106

    Article  CAS  Google Scholar 

  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 6:10666–10672

    Article  CAS  PubMed  Google Scholar 

  155. Lv W, Chen M, Wu R (2013) The impact of the number of layers of a graphene nanopore on DNA translocation. Soft Matter 9:960–966

    Article  CAS  Google Scholar 

  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 25:936–946

    Article  CAS  PubMed  Google Scholar 

  157. Ventra MD, Tanigichi M (2016) Decoding DNA, RNA and peptides with quantum tunnelling. Nat Nanotechnol 11:117–126

    Article  PubMed  CAS  Google Scholar 

  158. Tsutsui M, Taniguchi M, Yokota K, Kawai T (2010) Identifying single nucleotides by tunnelling current. Nat Nanotechnol 5:286–290

    Article  CAS  PubMed  Google Scholar 

  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 9:835–840

    Article  CAS  PubMed  Google Scholar 

  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 17:622–633

    Article  CAS  Google Scholar 

  161. Siwy ZS, Howorka S (2010) Engineered voltage-responsive nanopores. Chem Soc Rev 39:1115–1132

    Article  CAS  PubMed  Google Scholar 

  162. Tanaka H, Kawai T (2003) Visualization of detailed structures within DNA. Surf Sci 539:L531–L536

    Article  CAS  Google Scholar 

  163. Lee JW, Meller A (2007) In: Mitchelson K (ed) Perspectives in bioanalysis. Elsevier, Amsterdam

    Google Scholar 

  164. Zwolak M, Ventra MD (2005) Electronic signature of DNA nucleotides via transverse transport. Nano Lett 5:421–424

    Article  CAS  PubMed  Google Scholar 

  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 11:1941–1945

    Article  CAS  PubMed  Google Scholar 

  166. Postma HW (2010) Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett 10:420–425

    Article  CAS  PubMed  Google Scholar 

  167. Zhao Q, Wang Y, Dong J, Zhao L, Rui XF, Yu D (2012) Nanopore-based DNA analysis via graphene electrodes. J Nanomater 2012:318950

    Google Scholar 

  168. He Y, Tsutsui M, Scheicher RH, Taniguchi M (2012) Bilayer graphene lateral contacts for DNA. arXiv:1206.4199v1

    Google Scholar 

  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 103:023701

    Article  CAS  Google Scholar 

  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 117:15421–15428

    Article  CAS  Google Scholar 

  171. Waduge P, Larkin J, Upmanyu M, Kar S, Wanunu M (2015) Synthesis of freestanding graphene nanomembrane arrays. Small 11:597–603

    Article  CAS  PubMed  Google Scholar 

  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 10:3237–3242

    Article  CAS  PubMed  Google Scholar 

  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 20:058504

    Article  CAS  Google Scholar 

  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 12:50–55

    Article  CAS  PubMed  Google Scholar 

  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 5:2601–2607

    Article  CAS  PubMed  Google Scholar 

  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 25:125705

    Article  PubMed  CAS  Google Scholar 

  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 115:133701

    Article  CAS  Google Scholar 

  178. Liu N, Yang Z, Ou X, Wie B, Zhang J, Jia Y, Xia F (2016) Nanopore-based analysis of biochemical species. Microchim Acta 183:955–963

    Article  CAS  Google Scholar 

  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 110:16748–16753

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 5:17560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 25:445105

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  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 21:2674–2679

    Article  CAS  Google Scholar 

  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 6:2616–2621

    Article  CAS  PubMed  Google Scholar 

  184. Paulechka E, Wassenaar TA, Kroenlein K, Kazakova A, Smolyanitsky A (2016) Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing. Nanoscale 8:1861–1867

    Article  CAS  PubMed  Google Scholar 

  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 118:5799–5806

    Article  CAS  PubMed  Google Scholar 

  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 112:3456–3459

    Article  CAS  Google Scholar 

  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 8:939–945

    Article  CAS  PubMed  Google Scholar 

  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 10:1670–1678

    Article  CAS  PubMed  Google Scholar 

  189. Lee CY, Choi W, Han J-H, Strano MS (2010) Coherence resonance in a single-walled carbon nanotube ion channel. Science 329:1320–1324

    Article  CAS  PubMed  Google Scholar 

  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 85:115436

    Article  CAS  Google Scholar 

  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 87:062707

    Article  CAS  Google Scholar 

  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 116:13896–13903

    Article  CAS  Google Scholar 

  193. Gowtham S, Scheicher R, Ahuja R, Pandey R, Karna S (2007) Physisorption of nucleobases on graphene: density-functional calculations. Phys Rev B 76:033401

    Article  CAS  Google Scholar 

  194. Akca S, Foroughi A, Frochtzwajg D, Postma HWC (2011) Competing interactions in DNA assembly on graphene. PLoS One 6:e18442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 117:13435–13441

    Article  CAS  Google Scholar 

  196. Antony J, Grimme S (2008) Structures and interaction energies of stacked graphene-nucleobase complexes. Phys Chem Chem Phys 10:2722–2729

    Article  CAS  PubMed  Google Scholar 

  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 10:206–210

    Article  CAS  PubMed  Google Scholar 

  198. Umadevi D, Sastry GN (2011) Quantum mechanical study of physisorption of nucleobases on carbon materials: graphene versus carbon nanotubes. J Phys Chem Lett 2:1572–1576

    Article  CAS  Google Scholar 

  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 24:424210

    Article  PubMed  CAS  Google Scholar 

  200. Smeets RMM, Keyser UF, Dekker NH, Dekker C (2008) Noise in solid-state nanopores. Proc Natl Acad Sci U S A 105:417–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Tabard-Cossa V, Trivedi D, Wiggin M, Jetha NN, Marziali A (2007) Noise analysis and reduction in solid-state nanopores. Nanotechnology 18:305505

    Article  CAS  Google Scholar 

  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 3:4814–4820

    Article  CAS  PubMed  Google Scholar 

  203. Kundu S, Karmakar SN (2016) Detection of base-pair mismatches in DNA using graphene-based nanopore device. Nanotechnology 27:135101

    Article  PubMed  CAS  Google Scholar 

  204. Qiu H, Girdhar A, Schulten K, Leburton JP (2016) Electrically tunable quenching of DNA fluctuations in biased solid-state nanopores. ACS Nano 10:4482–4488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 120:13693–13700

    Article  CAS  Google Scholar 

  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 27:215502

    Article  PubMed  CAS  Google Scholar 

  207. Al-Dirini F, Mohammed MA, Hossain MS, Hossain FM, Nirmalathas A, Skafidas E (2016) Tuneable graphene nanopores for single biomolecule detection. Nanoscale 8:10066–10077

    Article  CAS  PubMed  Google Scholar 

  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 116:21609–21614

    Article  CAS  Google Scholar 

  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 21:395501

    Article  PubMed  CAS  Google Scholar 

  210. Kastner MA (1992) The single-electron transistor. Rev Mod Phys 64:849–858

    Article  Google Scholar 

  211. Kaasbjerg K, Flensberg K (2008) Strong polarization-induced reduction of addition energies in single-molecule nanojunctions. Nano Lett 8:3809–3814

    Article  CAS  PubMed  Google Scholar 

  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 9:322–329

    Article  Google Scholar 

  213. Gracheva ME, Vidal J, Leburton JP (2007) p-n semiconductor membrane for electrically tunable ion current rectification and filtering. Nano Lett 7:1717–1722

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Nikolaev A, Gracheval ME (2011) Simulation of ionic current through the nanopore in a double-layered semiconductor membrane. Nanotechnology 22:165202

    Article  PubMed  Google Scholar 

  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 23:255501

    Article  PubMed  CAS  Google Scholar 

  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 86:061906

    Article  CAS  Google Scholar 

  217. Jou IA, Melnikov DV, Nadtochiy A, Gracheva ME (2014) Charged particle separation by an electrically tunable nanoporous membrane. Nanotechnology 25:145201

    Article  PubMed  CAS  Google Scholar 

  218. Chinappi M, Luchian T, Cecconi F (2015) Nanopore tweezers: voltage-controlled trapping and releasing of analytes. Phys Rev E 92:032714

    Article  CAS  Google Scholar 

  219. Murray KM (1996) DNA sequencing by mass spectrometry. J Mass Spectrom 31:1203–1215

    Article  CAS  PubMed  Google Scholar 

  220. Kirpekar F, Nordhoff E, Larsen LK, Kristiansen K, Roepstorff P, Hillenkamp F (1998) DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res 26:554–2559

    Article  Google Scholar 

  221. Edwards JR, Ruparel H, Ju J (2005) Mass-spectrometry DNA sequencing. Mutat Res 573:3–12

    Article  CAS  PubMed  Google Scholar 

  222. Tost J, Gut IG (2006) DNA analysis by mass spectrometry – past, present, and future. J Mass Spectrom 41:981–995

    Article  CAS  PubMed  Google Scholar 

  223. Tretyakova N, Villalta PW, Kotapati S (2013) Mass spectrometry of structurally modified DNA. Chem Rev 113:2395–2436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 6:054006

    Article  CAS  Google Scholar 

  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 11:5184–5188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 6:6563

    Article  CAS  Google Scholar 

  227. Liu L, Wu H-C (2016) DNA-based nanopore sensing. Angew Chem Int Ed 55:15216–15222

    Article  CAS  Google Scholar 

  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 13:14293–14296

    Article  CAS  PubMed  Google Scholar 

  229. Song B, Cuniberti G, Sanvito S, Fang H (2012) Nucleobase adsorbed at graphene devices: enhance bio-sensorics. Appl Phys Lett 100:063101

    Article  CAS  Google Scholar 

  230. Bobadilla AD, Seminario JM (2013) Assembly of a noncovalent DNA junction on graphene sheets and electron transport characteristics. J Phys Chem C 117:26441–26453

    Article  CAS  Google Scholar 

  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 466:470–473

    Article  CAS  PubMed  Google Scholar 

  232. Ahmed T, Kilina S, Das T, Haraldsen JT, Rehr JJ, Balatsky AV (2012) Electronic fingerprints of DNA bases on graphene. Nano Lett 12:927–931

    Article  CAS  PubMed  Google Scholar 

  233. Tanaka H, Kawai T (2009) Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 4:518–522

    Article  CAS  PubMed  Google Scholar 

  234. Vicarelli L, Heerema SJ, Dekker C, Zandbergen HW (2015) Controlling defects in graphene for optimizing the electrical properties of graphene nanodevices. ACS Nano 9:3428–3435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

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

Author information

Authors and Affiliations

  1. Institute of Materials Engineering, University of Siegen, Siegen, Germany

    Nianjun Yang & Xin Jiang

Authors
  1. Nianjun Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xin Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nianjun Yang .

Editor information

Editors and Affiliations

  1. Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany

    Christine Kranz

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Yang, N., Jiang, X. (2018). DNA Sequencing Using Carbon Nanopores. In: Kranz, C. (eds) Carbon-Based Nanosensor Technology. Springer Series on Chemical Sensors and Biosensors, vol 17. Springer, Cham. https://doi.org/10.1007/5346_2018_23

Download citation

Publish with us

Policies and ethics

Search

Navigation