Advertisement

Challenges of Single-Molecule DNA Sequencing with Solid-State Nanopores

  • Yusuke GotoEmail author
  • Rena Akahori
  • Itaru Yanagi
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1129)

Abstract

A powerful DNA sequencing tool with high accuracy, long read length and high-throughput would be required more and more for decoding the complicated genetic code. Solid-state nanopore has attracted many researchers for its promising future as a next-generation DNA sequencing platform due to the processability, the robustness and the large-scale integratability. While the diverse materials have been widely explored for a solid-state nanopore, silicon nitride (Si3N4) is especially preferable from the viewpoint of mass production based on semiconductor fabrication process. Here, as a nanopore sensing mechanism, we focused on the ionic blockade current method which is the most developed technique. We also highlight the main challenges of Si3N4 nanopore-based DNA sequencer that should be addressed: the fabrication of ultra-small nanopore and ultra-thin membrane, the modulation of DNA translocation speed and the detection of base-specific signals. In this chapter, we discuss the recent progress relating to solid-state nanopore DNA sequencing, which helps to provide a comprehensive information about the current technical situation.

Notes

Acknowledgments

The authors would like to express the utmost thanks to all co-workers for their dedication to Hitachi’s solid-state nanopore DNA sequencer project.

References

  1. Akahori R, Haga T, Hatano T, Yanagi I, Ohura T, Hamamura H, Iwasaki T, Yokoi T, Anazawa T. Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter. Nanotechnology. 2014;25(27):275501.CrossRefGoogle Scholar
  2. Akahori R, Yanagi I, Goto Y, Harada K, Yokoi T, Takeda K. Discrimination of three types of homopolymers in single-stranded DNA with solid-state nanopores through external control of the DNA motion. Sci Rep. 2017;7:9073.CrossRefGoogle Scholar
  3. Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26(10):1146–53.CrossRefGoogle Scholar
  4. Briggs K, Kwok H, Tabard-Cossa V. Automated fabrication of 2-nm solid-state nanopores for nucleic acid analysis. Small. 2014;10(10):2077–86.CrossRefGoogle Scholar
  5. Briggs K, Charron M, Kwok H, Le T, Chahal S, Bustamante J, Waugh M, Tabard-Cossa V. Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution. Nanotechnology. 2015;26(8):084004.CrossRefGoogle Scholar
  6. Carlsen AT, Zahid OK, Ruzicka J, Taylor EW, Hall AR. Interpreting the conductance blockades of DNA translocations through solid-state nanopores. ACS Nano. 2014;8(5):4754–60.CrossRefGoogle Scholar
  7. Carson S, Wanunu M. Challenges in DNA motion control and sequence readout using nanopore devices. Nanotechnology. 2015;26(7):074004.CrossRefGoogle Scholar
  8. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol. 2009;4(4):265–70.CrossRefGoogle Scholar
  9. Dekker C. Solid-state nanopores. Nat Nanotechnol. 2007;2(4):209–15.CrossRefGoogle Scholar
  10. Derrington IM, Butler TZ, Collins MD, Manrao E, Pavlenok M, Niederweis M, Gundlach JH. Nanopore DNA sequencing with MspA. Proc Natl Acad Sci U S A. 2010;107(37):16060–5.CrossRefGoogle Scholar
  11. Edel JB, Albrecht T. Engineered nanopores for bioanalytical applications. Amsterdam: Elsevier Science; 2013.Google Scholar
  12. Feng J, Liu K, Bulushev RD, Khlybov S, Dumcenco D, Kis A, Radenovic A. Identification of single nucleotides in MoS2 nanopores. Nat Nanotechnol. 2015;10(12):1070–6.CrossRefGoogle Scholar
  13. Fologea D, Uplinger J, Thomas B, McNabb DS, Li J. Slowing DNA translocation in a solid-state nanopore. Nano Lett. 2005;5(9):1734–7.CrossRefGoogle Scholar
  14. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333–51.CrossRefGoogle Scholar
  15. Goto Y, Haga T, Yanagi I, Yokoi T, Takeda K. Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure. Sci Rep. 2015;5:16640.CrossRefGoogle Scholar
  16. Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda K. Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Sci Rep. 2016;6:31324.CrossRefGoogle Scholar
  17. Goto Y, Akahori R, Matsui K, Yanagawa Y, Aoki M, Yanagi I, Nara Y, Yoshida M, Yokoi T, Takeda K. Solid-state nanopore DNA sequencing: single-nucleotide discrimination and bidirectional DNA translocation. In: Advances in genome biology and technology (AGBT) The General Meeting. Hollywood: The Diplomat Beach Resort; 13–16 February, 2017.Google Scholar
  18. Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda K. Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution. Nanoscale. 2018;10(44):20844–50.CrossRefGoogle Scholar
  19. Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. Nat Nanotechnol. 2016;11(2):127–36.CrossRefGoogle Scholar
  20. Howorka S, Cheley S, Bayley H. Sequence-specific detection of individual DNA strands using engineered nanopores. Nat Biotechnol. 2001;19(7):636–9.CrossRefGoogle Scholar
  21. Iqbal SM, Bashir R. Nanopores: sensing and fundamental biological interactions. Heidelberg: Springer; 2011.CrossRefGoogle Scholar
  22. Jain M, Koren S, Miga KH, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36(4):338–45.CrossRefGoogle Scholar
  23. Keyser UF, Koeleman BN, van Dorp S, Krapf D, Smeets RMM, Lemay SG, Dekker NH, Dekker C. Direct force measurements on DNA in a solid-state nanopore. Nat Phys. 2006;2(7):473–7.CrossRefGoogle Scholar
  24. Kowalczyk SW, Tuijtel MW, Donkers SP, Dekker C. Unraveling single-stranded DNA in a solid-state nanopore. Nano Lett. 2010;10(4):1414–20.CrossRefGoogle Scholar
  25. Kwok H, Briggs K, Tabard-Cossa V. Nanopore fabrication by controlled breakdown. PLoS One. 2014;9(3):e92880.CrossRefGoogle Scholar
  26. Larkin J, Henley R, Bell DC, Cohen-Karni T, Rosenstein JK, Wanunu M. Slow DNA transport through nanopores in hafnium oxide membranes. ACS Nano. 2013;7(11):10121–8.CrossRefGoogle Scholar
  27. Laszlo AH, Derrington IM, Ross BC, et al. Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol. 2014;32(8):829–33.CrossRefGoogle Scholar
  28. Lee M-H, Kumar A, Park K-B, Cho S-Y, Kim H-M, Lim M-C, Kim Y-R, Kim K-B. A low-noise solid-state nanopore platform based on a highly insulating substrate. Sci Rep. 2014;4:7448.CrossRefGoogle Scholar
  29. Lindsay S. The promises and challenges of solid-state sequencing. Nat Nanotechnol. 2016;11(2):109–11.CrossRefGoogle Scholar
  30. Liu S, Lu B, Zhao Q, et al. Boron nitride nanopores: highly sensitive DNA single-molecule detectors. Adv Mater. 2013;25(33):4549–54.CrossRefGoogle Scholar
  31. Liu K, Feng J, Kis A, Radenovic A. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano. 2014;8(3):2504–11.CrossRefGoogle Scholar
  32. Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, Pavlenok M, Niederweis M, Gundlach JH. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol. 2012;30(4):349–53.CrossRefGoogle Scholar
  33. Nelson EM, Li H, Timp G. Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography. ACS Nano. 2014;8(6):5484–93.CrossRefGoogle Scholar
  34. Pennisi E. Search for pore-fection. Science. 2012;336(6081):534–7.CrossRefGoogle Scholar
  35. Schneider GF, Kowalczyk SW, Calado VE, Pandraud G, Zandbergen HW, Vandersypen LM, Dekker C. DNA translocation through graphene nanopores. Nano Lett. 2010;10(8):3163–7.CrossRefGoogle Scholar
  36. Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature. 2017;550(7676):345–53.CrossRefGoogle Scholar
  37. Sigalov G, Comer J, Timp G, Aksimentiev A. Detection of DNA sequences using an alternating electric field in a nanopore capacitor. Nano Lett. 2008;8(1):56–63.CrossRefGoogle Scholar
  38. Squires AH, Hersey JS, Grinstaff MW, Meller A. A nanopore-nanofiber mesh biosensor to control DNA translocation. J Am Chem Soc. 2013;135(44):16304–7.CrossRefGoogle Scholar
  39. Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C. Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater. 2003;2(8):537–40.CrossRefGoogle Scholar
  40. Tsutsui M, Taniguchi M, Yokota K, Kawai T. Identifying single nucleotides by tunnelling current. Nat Nanotechnol. 2010;5(4):286–90.CrossRefGoogle Scholar
  41. Venkatesan BM, Bashir R. Nanopore sensors for nucleic acid analysis. Nat Nanotechnol. 2011;6(10):615–24.CrossRefGoogle Scholar
  42. Venta K, Shemer G, Puster M, Rodríguez-Manzo JA, Balan A, Rosenstein JK, Shepard K, Drndić M. Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS Nano. 2013;7(5):4629–36.CrossRefGoogle Scholar
  43. Wang D, Harrer S, Luan B, Stolovitzky G, Peng H, Afzali-Ardakani A. Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane. Sci Rep. 2014;4:3985.CrossRefGoogle Scholar
  44. Wanunu M. Nanopores: a journey towards DNA sequencing. Phys Life Rev. 2012;9(2):125–58.CrossRefGoogle Scholar
  45. Wanunu M, Sutin J, McNally B, Chow A, Meller A. DNA translocation governed by interactions with solid-state nanopores. Biophys J. 2008;95(10):4716–25.CrossRefGoogle Scholar
  46. Yanagi I, Akahori R, Hatano T, Takeda K. Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection. Sci Rep. 2014;4:5000.CrossRefGoogle Scholar
  47. Yanagi I, Ishida T, Fujisaki K, Takeda K. Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process. Sci Rep. 2015;5:14656.Google Scholar
  48. Yanagi I, Akahori R, Aoki M, Harada K, Takeda K. Multichannel detection of ionic currents through two nanopores fabricated on integrated Si3N4 membranes. Lab Chip. 2016;16(17):3340–50.CrossRefGoogle Scholar
  49. Yanagi I, Fujisaki K, Hamamura H, Takeda K. Thickness-dependent dielectric breakdown and nanopore creation on sub-10-nm-thick SiN membranes in solution. J Appl Phys. 2017;121(4):045301.CrossRefGoogle Scholar
  50. Yoshida H, Goto Y, Akahori R, Tada Y, Terada S, Komura M, Iyoda T. Slowing the translocation of single-stranded DNA by using nano-cylindrical passage self-assembled by amphiphilic block copolymers. Nanoscale. 2016;8(43):18270–6.CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Center for Technology Innovation – Healthcare, Research & Development GroupHitachi Ltd.Kokubunji-shiJapan

Personalised recommendations