Skip to main content
Log in

Integrated solid-state nanopore devices for third generation DNA sequencing

  • Review
  • Published:
Science China Technological Sciences Aims and scope Submit manuscript

Abstract

Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore. It is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial resolution. More integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event, such as transverse tunneling current, local potential change, and capacitance oriented voltage resonance. In this mini review, the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Sanger F, Nicklen S, Coulson A R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA, 1977, 74: 5463–5467

    Article  Google Scholar 

  2. Maxam A M, Gilbert W. New method for sequencing DNA. Proc Natl Acad Sci USA, 1977, 74: 560–564

    Article  Google Scholar 

  3. Sanger F, Air G M, Barrell B G, et al. Nucleotide-sequence of bacteriophage phichi174 DNA. Nature, 1977, 265: 687–695

    Article  Google Scholar 

  4. Fuller C W, Middendorf L R, Benner S A, et al. The challenges of sequencing by synthesis. Nat Biotech, 2009, 27: 1013–1023

    Article  Google Scholar 

  5. Niedringhaus T P, Milanova D, Kerby M B, et al. Landscape of next-generation sequencing technologies. Anal Chem, 2011, 83: 4327–4341

    Article  Google Scholar 

  6. Coulter W H. US Patent Specification 2656508. 1953

  7. Kasianowicz J J, Brandin E, Branton D, et al. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA, 1996, 93: 13770–13773

    Article  Google Scholar 

  8. Keyser U F. Controlling molecular transport through nanopores. J Royal Soc Interface, 2011, 8: 1369–1378

    Article  Google Scholar 

  9. Garaj S, Hubbard W, Reina A, et al. Graphene as a subnanometre trans-electrode membrane. Nature, 2010, 467: 190–193

    Article  Google Scholar 

  10. Garaj S, Liu S, Golovchenko J A, et al. Molecule-hugging graphene nanopores. Proc Natl Acad Sci USA, 2013, 110: 12192–12196

    Article  Google Scholar 

  11. Venta K, Shemer G, Puster M, et al. Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS Nano, 2013, 7: 4629–4636

    Article  Google Scholar 

  12. Schneider G F, Kowalczyk S W, Calado V E, et al. DNA translocation through graphene nanopores. Nano Letters, 2010, 10: 3163–3167

    Article  Google Scholar 

  13. Merchant C A, Healy K, Wanunu M, et al. DNA translocation through graphene nanopores. Nano Letters, 2010, 10: 2915–2921

    Article  Google Scholar 

  14. Xie P, Xiong Q H, Fang Y, et al. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nat Nanotech, 2012, 7: 119–125

    Article  Google Scholar 

  15. Traversi F, Raillon C, Benameur S M, et al. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat Nanotech, 2013, 8: 939–945

    Article  Google Scholar 

  16. Tsutsui M, Taniguchi M, Yokota K, et al. Identifying single nucleotides by tunnelling current. Nat Nanotech, 2010, 5: 286–290

    Article  Google Scholar 

  17. Fanget A, Traversi F, Khlybov S, et al. Nanopore integrated nanogaps for DNA detection. Nano Lett, 2014, 14: 244–249

    Article  Google Scholar 

  18. Menard L D, Mair C E, Woodson M E, et al. A device for performing lateral conductance measurements on individual double-stranded DNA molecules. ACS Nano, 2012, 6: 9087–9094

    Article  Google Scholar 

  19. Gracheva M E, Xiong A, Aksimentiev A, et al. Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor. Nanotechnology, 2006, 17: 622

    Article  Google Scholar 

  20. Heng J B, Aksimentiev A, Ho C, et al. Beyond the gene chip. Bell Labs Tech J, 2005, 10: 5–22

    Article  Google Scholar 

  21. Sigalov G, Comer J, Timp G, et al. Detection of DNA sequences using an alternating electric field in a nanopore capacitor. Nano Lett, 2008, 8: 56–63

    Article  Google Scholar 

  22. Deamer D W, Akeson M. Nanopores and nucleic acids: Prospects for ultrarapid sequencing. Trends Biotech, 2000, 18: 147–151

    Article  Google Scholar 

  23. Li J, Stein D, McMullan C, et al. Ion-beam sculpting at nanometre length scales. Nature, 2001, 412: 166–169

    Article  Google Scholar 

  24. Kowalczyk S W, Blosser T R, Dekker C. Biomimetic nanopores: Learning from and about nature. Trends Biotech, 2011, 29: 607–614

    Article  Google Scholar 

  25. Venkatesan B M, Bashir R. Nanopore sensors for nucleic acid analysis. Nat Nanotech, 2011, 6: 615–624

    Article  Google Scholar 

  26. Haque F, Li J, Wu H C, et al. Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA. Nano Today, 2013, 8: 56–74

    Article  Google Scholar 

  27. Dekker C. Solid-state nanopores. Nat Nanotech, 2007, 2: 209–215

    Article  Google Scholar 

  28. Derrington I M, Butler T Z, Collins M D, et al. Nanopore DNA sequencing with mspa. Proc Natl Acad Sci USA, 2010, 107: 16060–16065

    Article  Google Scholar 

  29. Bhakdi S, Tranum-Jensen J. Alpha-toxin of staphylococcus aureus. Microbiol Rev, 1991, 55: 733–751

    Google Scholar 

  30. Clarke J, Wu H C, Jayasinghe L, et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotech, 2009, 4: 265–270

    Article  Google Scholar 

  31. Kumar S, Tao C, Chien M, et al. Peg-labeled nucleotides and nanopore detection for single molecule DNA sequencing by synthesis. Sci Rep, 2012, 2: 1–8

    Google Scholar 

  32. Robertson J W, Rodrigues C G, Stanford V M, et al. Single-molecule mass spectrometry in solution using a solitary nanopore. Proc Natl Acad Sci USA, 2007, 104: 8207–8211

    Article  Google Scholar 

  33. Butler T Z, Pavlenok M, Derrington I M, et al. Single-molecule DNA detection with an engineered mspa protein nanopore. Proc Natl Acad Sci USA, 2008, 105: 20647–20652

    Article  Google Scholar 

  34. Storm A, Chen J, Ling X, et al. Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater, 2003, 2: 537–540

    Article  Google Scholar 

  35. Zhao Q, Sigalov G, Dimitrov V, et al. Detecting snps using a synthetic nanopore. Nano Lett, 2007, 7: 1680–1685

    Article  Google Scholar 

  36. White H S, Bund A. Ion current rectification at nanopores in glass membranes. Langmuir, 2008, 24: 2212–2218

    Article  Google Scholar 

  37. Prabhu A S, Freedman K J, Robertson J W, et al. Sem-induced shrinking of solid-state nanopores for single molecule detection. Nanotechnology, 2011, 22: 425302

    Article  Google Scholar 

  38. Lu N, Wang J, Floresca H C, et al. In situ studies on the shrinkage and expansion of graphene nanopores under electron beam irradiation at temperatures in the range of 400–1200°C. Carbon, 2012, 50: 2961–2965

    Article  Google Scholar 

  39. Kwok H, Briggs K, Tabard-Cossa V. Nanopore fabrication by controlled dielectric breakdown. PLoS One, 2014, 9: e92880

    Article  Google Scholar 

  40. Chang H, Kosari F, Andreadakis G, et al. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano Lett, 2004, 4: 1551–1556

    Article  Google Scholar 

  41. Venkatesan B M, Estrada D, Banerjee S, et al. Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes. ACS Nano, 2011, 6: 441–450

    Article  Google Scholar 

  42. Liu K, Feng J, Kis A, et al. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano, 2014, 8: 2504–2511

    Article  Google Scholar 

  43. Liu S, Lu B, Zhao Q, et al. Boron nitride nanopores: Highly sensitive DNA single-molecule detectors. Adv Mater, 2013, 25: 4549–4554

    Article  Google Scholar 

  44. Larkin J, Henley R, Bell D C, et al. Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano, 2013, 7: 10121–10128

    Article  Google Scholar 

  45. Coleman J N, Lotya M, O’Neill A, et al. Two-dimensional nanosheets produced by liquid exfoliation of layered materials. Science, 2011, 331: 568–571

    Article  Google Scholar 

  46. Novoselov K S, Jiang D, Schedin F, et al. Two-dimensional atomic crystals. Proc Natl Acad Sci USA, 2005, 102: 10451–10453

    Article  Google Scholar 

  47. Yao Y, Lin Z, Li Z, et al. Large-scale production of two-dimensional nanosheets. J Mater Chem, 2012, 22: 13494–13499

    Article  Google Scholar 

  48. Yu J, Huang X, Wu C, et al. Interfacial modification of boron nitride nanoplatelets for epoxy composites with improved thermal properties. Polymer, 2012, 53: 471–480

    Article  Google Scholar 

  49. Zhang Z, Guo W. Energy-gap modulation of bn ribbons by transverse electric fields: First-principles calculations. Phys Rev B, 2008, 77: 075403

    Article  Google Scholar 

  50. Sekar P, Greyson E C, Barton J E, et al. Synthesis of nanoscale nbse2 materials from molecular precursors. J Am Chem Soc, 2005, 127: 2054–2055

    Article  Google Scholar 

  51. Radisavljevic B, Radenovic A, Brivio J, et al. Single-layer MoS2 transistors. Nat Nanotech, 2011, 6: 147–150

    Article  Google Scholar 

  52. Yuan Y, Li R, Liu Z. Establishing water-soluble layered ws2 nanosheet as a platform for biosensing. Anal Chem, 2014, 86: 3610–3615

    Article  Google Scholar 

  53. Li H, Wu J, Yin Z, et al. Preparation and applications of mechanically exfoliated single-layer and multi layer MoS2 and WSe2 nanosheets. Acc Chem Res, 2014, 47: 1067–1075

    Article  Google Scholar 

  54. Hall J E. Access resistance of a small circular pore. J General Physiol, 1975, 66: 531–532

    Article  Google Scholar 

  55. Bi K, Wang J, Wang Y, et al. The thermal conductivity of sige heterostructure nanowires with different cores and shells. Phys Lett A, 2012, 376: 2668–2671

    Article  Google Scholar 

  56. Kowalczyk S W, Grosberg A Y, Rabin Y, et al. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology, 2011, 22: 315101

    Article  Google Scholar 

  57. Duan C, Majumdar A. Anomalous ion transport in 2-nm hydrophilic nanochannels. Nat Nanotech, 2010, 5: 848–852

    Article  Google Scholar 

  58. Chen Y, Ni Z, Wang G, et al. Electroosmotic flow in nanotubes with high surface charge densities. Nano Lett, 2008, 8: 42–48

    Article  Google Scholar 

  59. Tong H D, Jansen H V, Gadgil V J, et al. Silicon nitride nanosieve membrane. Nano Lett, 2004, 4: 283–287

    Article  Google Scholar 

  60. Fologea D, Uplinger J, Thomas B, et al. Slowing DNA translocation in a solid-state nanopore. Nano Lett, 2005, 5: 1734–1737

    Article  Google Scholar 

  61. Fologea D, Gershow M, Ledden B, et al. Detecting single stranded DNA with a solid state nanopore. Nano Lett, 2005, 5: 1905–1909

    Article  Google Scholar 

  62. Hyun C, Kaur H, Rollings R, et al. Threading immobilized DNA molecules through a solid-state nanopore at > 100 mu s per base rate. ACS Nano, 2013, 7: 5892–5900

    Article  Google Scholar 

  63. Si W, Sha J, Liu L, et al. Effect of nanopore size on poly(dt)30 translocation through silicon nitride membrane. Sci China Tech Sci, 2013, 56: 2398–2402

    Article  Google Scholar 

  64. Zhang Y, Liu L, Sha J, et al. Nanopore detection of DNA molecules in magnesium chloride solutions. Nanoscale Res Lett, 2013, 8: 245

    Article  Google Scholar 

  65. Geim A K, Novoselov K S. The rise of graphene. Nat Mater, 2007, 6: 183–191

    Article  Google Scholar 

  66. Fischbein M D, Drndić M. Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett, 2008, 93: 113107

    Article  Google Scholar 

  67. Reina A, Thiele S, Jia X, et al. Growth of large-area single-and bi-layer graphene by controlled carbon precipitation on polycrystalline ni surfaces. Nano Res, 2009, 2: 509–516

    Article  Google Scholar 

  68. Ni Z, Bu H, Zou M, et al. Anisotropic mechanical properties of graphene sheets from molecular dynamics. Physica B, 2010, 405: 1301–1306

    Article  Google Scholar 

  69. Bu H, Chen Y, Zou M, et al. Atomistic simulations of mechanical properties of graphene nanoribbons. Phys Lett A, 2009, 373: 3359–3362

    Article  Google Scholar 

  70. Wei Z, Bi K, Chen Y. Thermal conductivity of graphene nanoribbons simulated by molecular dynamics. J Southeast Univ Nat Sci Ed, 2010, 40: 306–310

    Google Scholar 

  71. Wei Z Y, Chen Y F, Dames C. Wave packet simulations of phonon boundary scattering at graphene edges. J Appl Phys, 2012, 112: 024328

    Article  Google Scholar 

  72. Wei Z, Ni Z, Bi K, et al. In-plane lattice thermal conductivities of multilayer graphene films. Carbon, 2011, 49: 2653–2658

    Article  Google Scholar 

  73. Gu Y, Ni Z, Chen M, et al. The phonon thermal conductivity of single-layer graphene from complete phonon dispersion relations. J Heat Transfer-Trans ASME, 2012, 134: 062401

    Article  Google Scholar 

  74. Li J, Zhang Y, Yang J, et al. Molecular dynamics study of DNA translocation through graphene nanopores. Phys Rev E, 2013, 87: 062707

    Article  Google Scholar 

  75. Qiu Y, Tan Q, Si W, et al. Ion specificity in nacl solution confined in silicon nanochannels. Sci China Tech Sci, 2014, 57: 230–238

    Article  Google Scholar 

  76. Venkatesan B M, Dorvel B, Yemenicioglu S, et al. Highly sensitive, mechanically stable nanopore sensors for DNA analysis. Adv Mater, 2009, 21: 2771–2776

    Article  Google Scholar 

  77. Shi Y, Hamsen C, Jia X, et al. Synthesis of few-layer hexagonal boron nitride thin film by chemical vapor deposition. Nano Lett, 2010, 10: 4134–4139

    Article  Google Scholar 

  78. Nielsen R H, Wilfing G. Hafnium and hafnium compounds. In: Ullmann’s Encyclopedia of Industrial Chemistry. 2000

    Google Scholar 

  79. Radisavljevic B, Whitwick M B, Kis A. Integrated circuits and logic operations based on single-layer MoS2. ACS Nano, 2011, 5: 9934–9938

    Article  Google Scholar 

  80. Wang Q H, Kalantar-Zadeh K, Kis A, et al. Electronics and optoelectronics of two-dimensional transition metal dichalcogenides. Nat Nanotech, 2012, 7: 699–712

    Article  Google Scholar 

  81. Xie P, Xiong Q, Fang Y, et al. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nat Nanotech, 2011, 7: 119–125

    Article  Google Scholar 

  82. Traversi F, Raillon C, Benameur S, et al. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat Nanotech, 2013, 8: 939–945

    Article  Google Scholar 

  83. Ivanov A P, Instuli E, McGilvery C M, et al. DNA tunneling detector embedded in a nanopore. Nano Lett, 2010, 11: 279–285

    Article  Google Scholar 

  84. Arscott P G, Lee G, Bloomfield V A, et al. Scanning tunnelling microscopy of z-DNA. Nature, 1989, 339: 484–486

    Article  Google Scholar 

  85. Dunlap D D, Bustamante C. Images of single-stranded nucleic acids by scanning tunnelling microscopy. Nature, 1989, 342: 204–206

    Article  Google Scholar 

  86. Driscoll R J, Youngquist M G, Baldeschwieler J D. Atomic-scale imaging of DNA using scanning tunnelling microscopy. Nature, 1990, 346: 294–296

    Article  Google Scholar 

  87. Heckl W, Smith D, Binnig G, et al. Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy. Proc Natl Acad Sci USA, 1991, 88: 8003–8005

    Article  Google Scholar 

  88. King G, Golovchenko J. Probing nanotube-nanopore interactions. Phys Rev Lett, 2005, 95: 216103

    Article  Google Scholar 

  89. Lagerqvist J, Zwolak M, Di Ventra M. Fast DNA sequencing via transverse electronic transport. Nano Lett, 2006, 6: 779–782

    Article  Google Scholar 

  90. Fanget A, Traversi F, Khlybov S, et al. Nanopore integrated nanogaps for DNA detection. Nano Lett, 2014, 14: 244–249

    Article  Google Scholar 

  91. Chen Y S, Lee C H, Hung M Y, et al. DNA sequencing using electrical conductance measurements of a DNA polymerase. Nat Nanotech, 2013, 8: 609–609

    Article  Google Scholar 

  92. Chen Y S, Lee C H, Hung M Y, et al. DNA sequencing using electrical conductance measurements of a DNA polymerase. Nat Nanotech, 2013, 8: 452–458

    Article  Google Scholar 

  93. Rosenstein J K, Wanunu M, Merchant C A, et al. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat Methods, 2012, 9: 487–492

    Article  Google Scholar 

  94. Uddin A, Yemenicioglu S, Chen C, et al. Integration of solid-state nanopores in a 0.5 μm cmos foundry process. Nanotechnology, 2013, 24: 155501

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to YunFei Chen.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wu, G., Zhang, Y., Si, W. et al. Integrated solid-state nanopore devices for third generation DNA sequencing. Sci. China Technol. Sci. 57, 1925–1935 (2014). https://doi.org/10.1007/s11431-014-5644-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11431-014-5644-8

Keywords

Navigation