Skip to main content
SpringerLink
Log in

Recent advances of DNA sequencing via nanopore-based technologies

  • Progress
  • Chemistry
  • Published:
Science Bulletin

Abstract

This review briefly summarizes recent progress in nanopore DNA sequencing from the beginning of 2012 to July 2014. Although partial successes have been achieved in different types of nanopores, biological pores such as α-hemolysin and MspA afford most promising results.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  1. Wen S, Zeng T, Liu L et al (2011) Highly sensitive and selective DNA-based detection of mercury(II) with α-hemolysin nanopore. J Am Chem Soc 133:18312–18317

    Article  Google Scholar 

  2. Yang C, Liu L, Zeng T et al (2013) Highly sensitive simultaneous detection of lead(II) and barium(II) with g-quadruplex DNA in α-hemolysin nanopore. Anal Chem 85:7302–7307

    Article  Google Scholar 

  3. Wu HC, Bayley H (2008) Single-molecule detection of nitrogen mustards by covalent reaction within a protein nanopore. J Am Chem Soc 130:6813–6819

    Article  Google Scholar 

  4. Steffensen MB, Rotem D, Bayley H (2014) Single-molecule analysis of chirality in a multicomponent reaction network. Nat Chem 6:603–607

    Article  Google Scholar 

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

    Article  Google Scholar 

  6. Sutherland TC, Long YT, Stefureac RI et al (2004) Structure of peptides investigated by nanopore analysis. Nano Lett 4:1273–1277

    Article  Google Scholar 

  7. Raillon C, Cousin P, Traversi F et al (2012) Nanopore detection of single molecule RNAP-DNA transcription complex. Nano Lett 12:1157–1164

    Article  Google Scholar 

  8. Rosen CB, Rodriguez-Larrea D, Bayley H (2014) Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat Biotechnol 32:179–181

    Article  Google Scholar 

  9. Branton D, Deamer DW, Marziali A et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153

    Article  Google Scholar 

  10. Song LZ, Hobaugh MR, Shustak C et al (1996) Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science 274:1859–1866

    Article  Google Scholar 

  11. Butler TZ, Pavlenok M, Derrington IM et al (2008) Single-molecule DNA detection with an engineered MspA protein nanopore. Proc Natl Acad Sci USA 105:20647–20652

    Article  Google Scholar 

  12. Wendell D, Jing P, Geng J et al (2009) Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores. Nat Nanotechnol 4:765–772

    Article  Google Scholar 

  13. Wanunu M, Dadosh T, Ray V et al (2010) Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat Nanotechnol 5:807–814

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  18. Langecker M, Arnaut V, Martin TG et al (2012) Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338:932–936

    Article  Google Scholar 

  19. Liu L, Yang C, Zhao K et al (2013) Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor. Nat Commun 4:2989

    Google Scholar 

  20. Stoddart D, Heron AJ, Mikhailova E et al (2009) Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc Natl Acad Sci USA 106:7702–7707

    Article  Google Scholar 

  21. Meller A, Nivon L, Brandin E et al (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci USA 97:1079–1084

    Article  Google Scholar 

  22. Mathe J, Aksimentiev A, Nelson DR et al (2005) Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel. Proc Natl Acad Sci USA 102:12377–12382

    Article  Google Scholar 

  23. de Zoysa RSS, Jayawardhana DA, Zhao QT et al (2009) Slowing DNA translocation through nanopores using a solution containing organic salts. J Phys Chem B 113:13332–13336

    Article  Google Scholar 

  24. Kawano R, Schibel AEP, Cauley C et al (2009) Controlling the translocation of single-stranded DNA through α-hemolysin ion channels using viscosity. Langmuir 25:1233–1237

    Article  Google Scholar 

  25. Rincon-Restrepo M, Mikhailova E, Bayley H et al (2011) Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes. Nano Lett 11:746–750

    Article  Google Scholar 

  26. Cherf GM, Lieberman KR, Rashid H et al (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat Biotechnol 30:344–348

    Article  Google Scholar 

  27. Kumar S, Tao C, Chien M et al (2012) PEG-labeled nucleotides and nanopore detection for single molecule DNA sequencing by synthesis. Sci Rep 2:684

    Google Scholar 

  28. Manrao EA, Derrington IM, Laszlo AH et al (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30:349–353

    Article  Google Scholar 

  29. Laszlo AH, Derrington IM, Ross BC et al (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32:829–833

    Article  Google Scholar 

  30. Laszlo AH, Derrington IM, Brinkerhoff H et al (2013) Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc Natl Acad Sci USA 110:18904–18909

    Article  Google Scholar 

  31. Schreiber J, Wescoe ZL, Abu-Shumays R et al (2013) Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc Natl Acad Sci USA 110:18910–18915

    Article  Google Scholar 

  32. Jing P, Haque F, Shu D et al (2010) One-way traffic of a viral motor channel for double-stranded DNA translocation. Nano Lett 10:3620–3627

    Article  Google Scholar 

  33. Geng J, Wang SY, Fang HM et al (2013) Channel size conversion of phi29 DNA-packaging nanomotor for discrimination of single- and double-stranded nucleic acids. ACS Nano 7:3315–3323

    Article  Google Scholar 

  34. Deng XL, Takami T, Son JW et al (2014) Effect of concentration gradient on ionic current rectification in polyethyleneimine modified glass nano-pipettes. Sci Rep 4:4005

    Google Scholar 

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

    Article  Google Scholar 

  36. Iqbal SM, Akin D, Bashir R (2007) Solid-state nanopore channels with DNA selectivity. Nat Nanotechnol 2:243–248

    Article  Google Scholar 

  37. Anderson BN, Muthukumar M, Meller A (2013) pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano 7:1408–1414

    Article  Google Scholar 

  38. Wang D, Harrer S, Luan B et al (2014) Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane. Sci Rep 4:3985

    Google Scholar 

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

    Article  Google Scholar 

  40. Zhang Y, Wu G, Si W et al (2014) Retarding and manipulating of DNA molecules translocation through nanopores. Chin Sci Bull 59:4908–4917

    Article  Google Scholar 

  41. Wanunu M, Cohen-Karni D, Johnson RR et al (2011) Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. J Am Chem Soc 133:486–492

    Article  Google Scholar 

  42. Shim J, Humphreys GI, Venkatesan BM et al (2013) Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep 3:1389

    Google Scholar 

  43. Merchant CA, Healy K, Wanunu M et al (2010) DNA translocation through graphene nanopores. Nano Lett 10:2915–2921

    Article  Google Scholar 

  44. Schneider GF, Kowalczyk SW, Calado VE et al (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163–3167

    Article  Google Scholar 

  45. Saha KK, Drndic M, Nikolic 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  Google Scholar 

  46. Traversi F, Raillon C, Benameur SM et al (2013) Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat Nanotechnol 8:939–945

    Article  Google Scholar 

  47. Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302

    Article  Google Scholar 

  48. Douglas SM, Dietz H, Liedl T et al (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414–418

    Article  Google Scholar 

  49. Han D, Pal S, Nangreave J et al (2011) DNA origami with complex curvatures in three-dimensional space. Science 332:342–346

    Article  Google Scholar 

  50. Wei R, Martin TG, Rant U et al (2012) DNA origami gatekeepers for solid-state nanopores. Angew Chem-Int Edit 51:4864–4867

    Article  Google Scholar 

  51. Hernandez-Ainsa S, Bell NAW, Thacker VV et al (2013) DNA origami nanopores for controlling DNA translocation. ACS Nano 7:6024–6030

    Article  Google Scholar 

  52. Liu HT, He J, Tang JY et al (2010) Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327:64–67

    Article  Google Scholar 

  53. Gao R, Ying YL, Yan BY et al (2014) An integrated current measurement system for nanopore analysis. Chin Sci Bull 59:4968–4973

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Natural Science Foundation of China (21175135, 21375130, 21205119), the National Basic Research Program of China (2010CB933600), and the 100 Talents Program of the Chinese Academy of Sciences.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China

    Bing-Yuan Guo, Tao Zeng & Hai-Chen Wu

  2. National Center for Nanoscience and Technology of China, Beijing, 100190, China

    Tao Zeng

Authors
  1. Bing-Yuan Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tao Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hai-Chen Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hai-Chen Wu.

Additional information

SPECIAL TOPIC: Nanopore for DNA Sequencing

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guo, BY., Zeng, T. & Wu, HC. Recent advances of DNA sequencing via nanopore-based technologies. Sci. Bull. 60, 287–295 (2015). https://doi.org/10.1007/s11434-014-0707-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11434-014-0707-6

Keywords

Search

Navigation