Nucleic Acid Nanotechnology pp 287-303

Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 29) | Cite as

Nucleic Acid Sequencing and Analysis with Nanopores

Chapter

Abstract

It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but they do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule.

References

  1. Akeson M, Branton D, Kasianowicz JJ et al (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. doi:10.1016/S0006-3495(99)77153-5 PubMedCrossRefGoogle Scholar
  2. Astier Y, Braha O, Bayley H (2006) Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. J Am Chem Soc 128:1705–1710. doi:10.1021/ja057123 PubMedCrossRefGoogle Scholar
  3. Chen P, Mitsui T, Farmer DB et al (2004) Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. Nano Lett 4:1333–1337. doi:10.1021/nl0494001 CrossRefGoogle Scholar
  4. 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. doi:10.1038/nbt.2147 PubMedCrossRefGoogle Scholar
  5. Deamer DW, Branton D (2002) Characterization of nucleic acids by nanopore analysis. Acc Chem Res 35:817–825. doi:10.1021/ar000138m PubMedCrossRefGoogle Scholar
  6. Derrington IM, Butler TZ, Collins MD et al (2010) Nanopore DNA sequencing with MspA. Proc Natl Acad Sci USA 107:16060–16065 doi:10.1073/pnas.1001831107 Google Scholar
  7. Fischbein MD, Drndic M (2008) Electron beam nanosculpting of suspended graphene sheets. Appl Phys Lett 93:113107. doi:10.1063/1.2980518 CrossRefGoogle Scholar
  8. Fologea D, Gershow M, Ledden B et al (2005) Detecting single stranded DNA with a solid state nanopore. Nano Lett 5:1905–1909. doi:10.1021/nl051199m PubMedCrossRefGoogle Scholar
  9. Garaj S, Hubbard W, Reina A et al (2010) Graphene as a subnanometre trans-electrode membrane. Nature 467:190–193. doi:10.1038/nature09379 PubMedCrossRefGoogle Scholar
  10. Garaj S, Liu S, Golovchenko JA, Branton D (2013) Molecule-hugging graphene nanopores. Proc Natl Acad Sci USA - July 8 Early Edition. doi:10.1073/pnas.1220012110
  11. genome.gov. DNA sequencing costs. http://www.genome.gov/sequencingcosts/. Accessed 25 Mar 2013
  12. Girit CO, Meyer JC, Erni R et al (2009) Graphene at the edge: stability and dynamics. Science 323:1705–1708. doi:10.1126/science.1166999 PubMedCrossRefGoogle Scholar
  13. Green RE, Krause J, Briggs AW et al (2010) A draft sequence of the neandertal genome. Science 328:710–722. doi:10.1126/science.1188021 PubMedCrossRefGoogle Scholar
  14. Hall AR, van Dorp S, Lemay SG, Dekker C (2009) Electrophoretic force on a protein-coated DNA molecule in a solid-state nanopore. Nano Lett 9:4441–4445. doi:10.1021/nl9027318 PubMedCrossRefGoogle Scholar
  15. Hall AR, Scott A, Rotem D et al (2010) Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores. Nat Nanotechnol 5:874–877. doi:10.1038/nnano.2010.237 PubMedCrossRefGoogle Scholar
  16. Han A, Schürmann G, Mondin G et al (2006) Sensing protein molecules using nanofabricated pores. Appl Phys Lett 88:093901. doi:10.1063/1.2180868 CrossRefGoogle Scholar
  17. Huang S, He J, Chang S et al (2010) Identifying single bases in a DNA oligomer with electron tunnelling. Nat Nanotechnol 5:868–873. doi:10.1038/nnano.2010.213 PubMedCrossRefGoogle Scholar
  18. Human Genome Sequencing Consortium I (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931–945. doi:10.1038/nature03001 CrossRefGoogle Scholar
  19. Ivanov AP, Instuli E, McGilvery CM et al (2011) DNA tunneling detector embedded in a nanopore. Nano Lett 11:279–285. doi:10.1021/nl103873a PubMedCrossRefGoogle Scholar
  20. Kasianowicz J, Brandin E, Branton D, Deamer D (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770–13773PubMedCrossRefGoogle Scholar
  21. Krause J, Fu Q, Good JM et al (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894–897. doi:10.1038/nature08976 PubMedCrossRefGoogle Scholar
  22. Li J, Stein D, McMullan C et al (2001) Ion-beam sculpting at nanometre length scales. Nature 412:166–169PubMedCrossRefGoogle Scholar
  23. Li J, Gershow M, Stein D et al (2003) DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater 2:611–615. doi:10.1038/nmat965 PubMedCrossRefGoogle Scholar
  24. Lieberman KR, Cherf GM, Doody MJ et al (2010) Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. J Am Chem Soc 132:17961–17972. doi:10.1021/ja1087612 PubMedCrossRefGoogle Scholar
  25. Lu B, Albertorio F, Hoogerheide DP, Golovchenko JA (2011) Origins and consequences of velocity fluctuations during DNA passage through a nanopore. Biophys J 101:70–79. doi:10.1016/j.bpj.2011.05.034 PubMedCrossRefGoogle Scholar
  26. Luan B, Peng H, Polonsky S et al (2010) Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 104:238103. doi:10.1103/PhysRevLett.104.238103 PubMedCrossRefGoogle Scholar
  27. Manrao EA, Derrington IM, Pavlenok M et al (2011) Nucleotide discrimination with DNA immobilized in the MspA nanopore. PLoS One 6:e25723. doi:10.1371/journal.pone.0025723 PubMedCrossRefGoogle 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. doi:10.1038/nbt.2171 PubMedCrossRefGoogle Scholar
  29. McNally B, Singer A, Yu Z et al (2010) Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett 10:2237–2244. doi:10.1021/nl1012147 PubMedCrossRefGoogle Scholar
  30. Meller A, Nivon L, Brandin E et al (2000) Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci USA 97:1079–1084. doi:10.1073/pnas.97.3.1079 PubMedCrossRefGoogle Scholar
  31. Meller A, Nivon L, Branton D (2001) Voltage-driven DNA translocations through a nanopore. Phys Rev Lett 86:3435–3438. doi:10.1103/PhysRevLett.86.3435 PubMedCrossRefGoogle Scholar
  32. Merchant CA, Healy K, Wanunu M et al (2010) DNA translocation through graphene nanopores. Nano Lett 10:2915–2921. doi:10.1021/nl101046t PubMedCrossRefGoogle Scholar
  33. 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. doi:10.1021/nl9035934 PubMedCrossRefGoogle Scholar
  34. Olasagasti F, Lieberman KR, Benner S et al (2010) Replication of individual DNA molecules under electronic control using a protein nanopore. Nat Nanotechnol 5:798–806. doi:10.1038/nnano.2010.177 PubMedCrossRefGoogle Scholar
  35. Park SR, Peng H, Ling XS (2007) Fabrication of nanopores in silicon chips using feedback chemical etching. Small 3:116–119. doi:10.1002/smll.200600268 PubMedCrossRefGoogle Scholar
  36. Postma HWC (2010) Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett 10:420–425. doi:10.1021/nl9029237 PubMedCrossRefGoogle Scholar
  37. Raillon C, Cousin P, Traversi F et al (2012) Nanopore detection of single molecule RNAP–DNA transcription complex. Nano Lett 12(3):1157–1164. doi:10.1021/nl3002827 PubMedCrossRefGoogle Scholar
  38. Russo CJ, Golovchenko JA (2012) Atom-by-atom nucleation and growth of graphene nanopores. Proc Natl Acad Sci USA 109:5953–5957. doi:10.1073/pnas.1119827109
  39. Sadki ES, Garaj S, Vlassarev D et al (2011) Embedding a carbon nanotube across the diameter of a solid state nanopore. J Vac Sci Technol B 29:053001-1–053001-4. doi:10.1116/1.3628602 CrossRefGoogle Scholar
  40. Schloss JA (2008) How to get genomes at one ten-thousandth the cost. Nat Biotechnol 26:1113–1115. doi:10.1038/nbt1008-1113 PubMedCrossRefGoogle Scholar
  41. Schneider GF, Kowalczyk SW, Calado VE et al (2010) DNA translocation through graphene nanopores. Nano Lett 10:3163–3167. doi:10.1021/nl102069z PubMedCrossRefGoogle Scholar
  42. Song B, Schneider GF, Xu Q et al (2011) Atomic-scale electron-beam sculpting of near-defect-free graphene nanostructures. Nano Lett 11:2247–2250. doi:10.1021/nl200369r PubMedCrossRefGoogle Scholar
  43. Storm A, Chen J, Ling X et al (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2:537–540. doi:10.1038/nmat941 PubMedCrossRefGoogle Scholar
  44. Storm A, Chen J, Zandbergen H, Dekker C (2005) Translocation of double-strand DNA through a silicon oxide nanopore. Phys Rev E Stat Nonlin Soft Matter Phys 71(5 Pt 1):051903. doi:10.1103/PhysRevE.71.051903 PubMedCrossRefGoogle Scholar
  45. Talaga DS, Li J (2009) Single-molecule protein unfolding in solid state nanopores. J Am Chem Soc 131:9287–9297. doi:10.1021/ja901088b PubMedCrossRefGoogle Scholar
  46. Tsutsui M, Taniguchi M, Yokota K, Kawai T (2010) Identifying single nucleotides by tunnelling current. Nat Nanotechnol 5:286–290. doi:10.1038/nnano.2010.42 PubMedCrossRefGoogle Scholar
  47. Venkatesan BM, Estrada D, Banerjee S et al (2012) Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA–protein complexes. ACS Nano 6:441–450. doi:10.1021/nn203769e PubMedCrossRefGoogle Scholar
  48. Wu H-C, Astier Y, Maglia G et al (2007) Protein nanopores with covalently attached molecular adapters. J Am Chem Soc 129:16142–16148. doi:10.1021/ja0761840 PubMedCrossRefGoogle Scholar
  49. Yusko EC, Johnson JM, Majd S et al (2011) Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat Nanotechnol 6:253–260. doi:10.1038/nnano.2011.12 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  1. 1.Department of PhysicsNational University of SingaporeSingaporeSingapore
  2. 2.Department of BioengineeringNational University of SingaporeSingaporeSingapore
  3. 3.Graphene Research CenterNational University of SingaporeSingaporeSingapore
  4. 4.Nanoscience & Nanotechnology Initiative (NUSNNI)National University of SingaporeSingaporeSingapore

Personalised recommendations