SpringerLink
Log in

Challenging Nanopores with Analyte Scope and Environment

  • Review
  • Published:
Journal of Analysis and Testing Aims and scope Submit manuscript

Abstract

Nanopores are nanofluidic channels formed through thin membranes that can deliver standout single-molecule and single-particle sensing capabilities. Analytical targets include small molecules and nanoparticles, and the DNA, protein, and glycan biopolymers underpinning genomics, proteomics, and glycomics. Detection—notably even in the simplest implementation, resistive-pulse sensing—does not inherently require sample labeling and, thus, offers the potential for general sensing utility combined with the prospective benefits of reduced sample processing requirements. A key pursuit for biopolymer sensing is the characterization of monomer sequence. This review article will provide an overview of the use of nanopores for general chemical sensing and –omics-related applications, writ-large. The broad analyte scope provides fertile ground for a discussion of principles governing nanopore sensing and considerations useful for guiding nanopore development. For nanopores to be effective in the face of broad analyte scope, stringent requirements on analytical performance must be met within the particular analyte class without sacrificing the operational flexibility necessary to be responsive across classes presenting very different physical and chemical challenges. These sample-driven challenges provide a unifying framework for discussing aspects of nanopore fabrication, properties, and integration; sensing paradigms, performance, and prospects; fundamental electrokinetic and interfacial phenomena; and practical challenges facing the use and further development of nanopore devices.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Thailand)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26(10):1146–53. https://doi.org/10.1038/nbt.1495.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wanunu M. Nanopores: a journey towards DNA sequencing. Phys Life Rev. 2012;9(2):125–58. https://doi.org/10.1016/j.plrev.2012.05.010.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, et al. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. Biomicrofluidics. 2016;10(3):032902. https://doi.org/10.1063/1.4948525.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Sexton LT, Horne LP, Martin CR. Develo** synthetic conical nanopores for biosensing applications. Mol BioSyst. 2007;3(10):667–85.

    Article  CAS  PubMed  Google Scholar 

  5. Choi Y, Baker LA, Hillebrenner H, Martin CR. Biosensing with conically shaped nanopores and nanotubes. PCCP. 2006;8(43):4976–88.

    Article  CAS  PubMed  Google Scholar 

  6. Oukhaled A, Bacri L, Pastoriza-Gallego M, Betton J-M, Pelta J. Sensing proteins through nanopores: fundamental to applications. ACS Chem Biol. 2012;7(12):1935–49. https://doi.org/10.1021/cb300449t.

    Article  CAS  PubMed  Google Scholar 

  7. Shi W, Friedman AK, Baker LA. Nanopore sensing. Anal Chem. 2017;89(1):157–88. https://doi.org/10.1021/acs.analchem.6b04260.

    Article  CAS  PubMed  Google Scholar 

  8. Haywood DG, Saha-Shah A, Baker LA, Jacobson SC. Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem. 2015;87(1):172–87. https://doi.org/10.1021/ac504180h.

    Article  CAS  PubMed  Google Scholar 

  9. Taniguchi M. Selective multidetection using nanopores. Anal Chem. 2015;87(1):188–99. https://doi.org/10.1021/ac504186m.

    Article  CAS  PubMed  Google Scholar 

  10. Mathwig K, Albrecht T, Goluch ED, Rassaei L. Challenges of biomolecular detection at the nanoscale: nanopores and microelectrodes. Anal Chem. 2015;87(11):5470–5. https://doi.org/10.1021/acs.analchem.5b01167.

    Article  CAS  PubMed  Google Scholar 

  11. Kocer A, Tauk L, Déjardin P. Nanopore sensors: from hybrid to abiotic systems. Biosens Bioelectron. 2012;38(1):1–10.

    Article  CAS  PubMed  Google Scholar 

  12. Bayley H, Martin CR. Resistive-pulse sensing-from microbes to molecules. Chem Rev. 2000;100(7):2575–94. https://doi.org/10.1021/cr980099g.

    Article  CAS  PubMed  Google Scholar 

  13. Reiner JE, Balijepalli A, Robertson JWF, Campbell J, Suehle J, Kasianowicz JJ. Disease detection and management via single nanopore-based sensors. Chem Rev. 2012;112(12):6431–51. https://doi.org/10.1021/cr300381m.

    Article  CAS  PubMed  Google Scholar 

  14. Howorka S, Siwy Z. Nanopore analytics: sensing of single molecules. Chem Soc Rev. 2009;38(8):2360–84.

    Article  CAS  PubMed  Google Scholar 

  15. Hou X, Guo W, Jiang L. Biomimetic smart nanopores and nanochannels. Chem Soc Rev. 2011;40(5):2385–401. https://doi.org/10.1039/C0CS00053A.

    Article  CAS  PubMed  Google Scholar 

  16. Miles BN, Ivanov AP, Wilson KA, Dogan F, Japrung D, Edel JB. Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. Chem Soc Rev. 2013;42(1):15–28. https://doi.org/10.1039/c2cs35286a.

    Article  CAS  PubMed  Google Scholar 

  17. Albrecht T, Edel JB, Winterhalter M. New developments in nanopore research—from fundamentals to applications. J Phys Condens Matter. 2010;22(45):450301.

    Article  PubMed  Google Scholar 

  18. Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol. 2010;21(4):439–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, et al. Fabrication of solid-state nanopores and its perspectives. Electrophoresis. 2015;36(19):2367–79. https://doi.org/10.1002/elps.201400612.

    Article  CAS  PubMed  Google Scholar 

  20. Healy K, Schiedt B, Morrison AP. Solid-state nanopore technologies for nanopore-based DNA analysis. Nanomedicine. 2007;2(6):875–97. https://doi.org/10.2217/17435889.2.6.875.

    Article  CAS  PubMed  Google Scholar 

  21. Healy K. Nanopore-based single-molecule DNA analysis. Nanomedicine. 2007;2(4):459–81. https://doi.org/10.2217/17435889.2.4.459.

    Article  CAS  PubMed  Google Scholar 

  22. Haque F, Li J, Wu H-C, Liang X-J, Guo P. Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA. Nano Today. 2013;8(1):56–74. https://doi.org/10.1016/j.nantod.2012.12.008.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lee K, Park K-B, Kim H-J, Yu J-S, Chae H, Kim H-M, et al. Recent progress in solid-state nanopores. Adv Mater. 2018;30(42):1704680. https://doi.org/10.1002/adma.201704680.

    Article  CAS  Google Scholar 

  24. Fu K, Bohn PW. Nanopore electrochemistry: a nexus for molecular control of electron transfer reactions. ACS Cent Sci. 2018;4(1):20–9. https://doi.org/10.1021/acscentsci.7b00576.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Piruska A, Gong M, Sweedler JV, Bohn PW. Nanofluidics in chemical analysis. Chem Soc Rev. 2010;39(3):1060–72. https://doi.org/10.1039/b900409m.

    Article  CAS  PubMed  Google Scholar 

  26. National Research Council. Transforming glycoscience: a roadmap for the future. Washington, DC: The National Academies Press; 2012.

    Google Scholar 

  27. Soskine M, Biesemans A, De Maeyer M, Maglia G. Tuning the size and properties of ClyA nanopores assisted by directed evolution. J Am Chem Soc. 2013;135(36):13456–63. https://doi.org/10.1021/ja4053398.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE. Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science. 1996;274(5294):1859–65. https://doi.org/10.1126/science.274.5294.1859.

    Article  CAS  PubMed  Google Scholar 

  29. Derrington IM, Butler TZ, Collins MD, Manrao E, Pavlenok M, Niederweis M, et al. Nanopore DNA sequencing with MspA. Proc Natl Acad Sci USA. 2010;107(37):16060–5. https://doi.org/10.1073/pnas.1001831107.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Ma L, Cockroft SL. Biological nanopores for single-molecule biophysics. ChemBioChem. 2010;11(1):25–34.

    Article  CAS  PubMed  Google Scholar 

  31. Sakai N, Matile S. Synthetic ion channels. Langmuir. 2013;29(29):9031–40. https://doi.org/10.1021/la400716c.

    Article  CAS  PubMed  Google Scholar 

  32. Sakai N, Mareda J, Matile S. artificial beta-barrels. Acc Chem Res. 2008;41(10):1354–65. https://doi.org/10.1021/ar700229r.

    Article  CAS  PubMed  Google Scholar 

  33. Litvinchuk S, Tanaka H, Miyatake T, Pasini D, Tanaka T, Bollot G et al. Synthetic pores with reactive signal amplifiers as artificial tongues. Nat Mater. 2007;6(8):576–80. http://www.nature.com/nmat/journal/v6/n8/suppinfo/nmat1933_S1.html.

  34. Hernández-Ainsa S, Misiunas K, Thacker VV, Hemmig EA, Keyser UF. Voltage-dependent properties of DNA origami nanopores. Nano Lett. 2014;14(3):1270–4. https://doi.org/10.1021/nl404183t.

    Article  CAS  PubMed  Google Scholar 

  35. Bell NAW, Thacker VV, Hernandez-Ainsa S, Fuentes-Perez ME, Moreno-Herrero F, Liedl T, et al. Multiplexed ionic current sensing with glass nanopores. Lab Chip. 2013;13(10):1859–62. https://doi.org/10.1039/c3lc50069a.

    Article  CAS  PubMed  Google Scholar 

  36. Hernández-Ainsa S, Bell NAW, Thacker VV, Göpfrich K, Misiunas K, Fuentes-Perez ME, et al. DNA origami nanopores for controlling DNA translocation. ACS Nano. 2013;7(7):6024–30. https://doi.org/10.1021/nn401759r.

    Article  CAS  PubMed  Google Scholar 

  37. Plesa C, Ananth AN, Linko V, Gülcher C, Katan AJ, Dietz H, et al. Ionic permeability and mechanical properties of DNA origami nanoplates on solid-state nanopores. ACS Nano. 2013;8(1):35–43. https://doi.org/10.1021/nn405045x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science. 2012;338(6109):932–6. https://doi.org/10.1126/science.1225624.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wharton JE, ** P, Sexton LT, Horne LP, Sherrill SA, Mino WK, et al. A method for reproducibly preparing synthetic nanopores for resistive-pulse biosensors. Small. 2007;3(8):1424–30. https://doi.org/10.1002/smll.200700106.

    Article  CAS  PubMed  Google Scholar 

  40. Vogel R, Willmott G, Kozak D, Roberts GS, Anderson W, Groenewegen L, et al. Quantitative sizing of nano/microparticles with a tunable elastomeric pore sensor. Anal Chem. 2011;83(9):3499–506. https://doi.org/10.1021/ac200195n.

    Article  CAS  PubMed  Google Scholar 

  41. Menon VP, Martin CR. Fabrication and evaluation of nanoelectrode ensembles. Anal Chem. 1995;67(13):1920–8. https://doi.org/10.1021/ac00109a003.

    Article  CAS  Google Scholar 

  42. Karawdeniya BI, Bandara YMNDY, Whelan JC, Dwyer JR. General strategy to make an on-demand library of structurally and functionally diverse SERS substrates. ACS Appl Nano Mater. 2018;1(2):960–8. https://doi.org/10.1021/acsanm.7b00385.

    Article  CAS  Google Scholar 

  43. Whelan JC, Karawdeniya BI, Bandara YMNDY, Velleco BD, Masterson CM, Dwyer JR. Electroless plating of thin gold films directly onto silicon nitride thin films and into micropores. ACS Appl Mater Interfaces. 2014;6(14):10952–7. https://doi.org/10.1021/am501971n.

    Article  CAS  PubMed  Google Scholar 

  44. Bandara YMNDY, Karawdeniya BI, Whelan JC, Ginsberg LDS, Dwyer JR. Solution-based photo-patterned gold film formation on silicon nitride. ACS Appl Mater Interfaces. 2016;8(51):34964–9. https://doi.org/10.1021/acsami.6b12720.

    Article  CAS  PubMed  Google Scholar 

  45. Møller P, Nielsen LP. Advanced surface technology. Denmark: Møller & Nielsen APS; 2013.

    Google Scholar 

  46. Zabetakis D, Dressick WJ. Selective electroless metallization of patterned polymeric films for lithography applications. ACS Appl Mater Interfaces. 2009;1(1):4–25. https://doi.org/10.1021/am800121d.

    Article  CAS  PubMed  Google Scholar 

  47. 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. http://www.nature.com/nmat/journal/v2/n8/suppinfo/nmat941_S1.html.

  48. Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA. Ion-beam sculpting at nanometre length scales. Nature. 2001;412(6843):166–9.

    Article  CAS  PubMed  Google Scholar 

  49. Dwyer JR, Harb M. Through a window, brightly: a review of selected nanofabricated thin-film platforms for spectroscopy, imaging, and detection. Appl Spectrosc. 2017;71(9):2051–75. https://doi.org/10.1177/0003702817715496.

    Article  CAS  PubMed  Google Scholar 

  50. Dwyer JR, Bandara Y, Whelan JC, Karawdeniya BI, Nichols JW. Silicon nitride thin films for nanofluidic device fabrication. In: Edel J, Ivanov A, Kim M, editors. Nanofluidics, vol. 41. 2nd ed. Cambridge: Royal Society for Chemistry Nanoscience & Nanotechnology; 2016.

    Google Scholar 

  51. Di Ventra M, Taniguchi M. Decoding DNA, RNA and peptides with quantum tunnelling. Nat Nano. 2016;11(2):117–26. https://doi.org/10.1038/nnano.2015.320.

    Article  CAS  Google Scholar 

  52. Joshua JM, Robert NC, Kelly BM, Jon-Paul SD, Christopher CS, Joshua DW, et al. Lift-off of large-scale ultrathin nanomembranes. J Micromech Microeng. 2015;25(1):015011.

    Article  Google Scholar 

  53. Williams KR, Muller RS. Etch rates for micromachining processing. J Microelectromech Syst. 1996;5(4):256–69. https://doi.org/10.1109/84.546406.

    Article  CAS  Google Scholar 

  54. Vlassiouk I, Apel PY, Dmitriev SN, Healy K, Siwy ZS. Versatile ultrathin nanoporous silicon nitride membranes. Proc Natl Acad Sci USA. 2009;106(50):21039–44. https://doi.org/10.1073/pnas.0911450106.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Duan C, Wang W, **e Q. Review article: fabrication of nanofluidic devices. Biomicrofluidics. 2013;7(2):026501–41.

    Article  PubMed Central  Google Scholar 

  56. Bandara Y, Karawdeniya BI, Dwyer JR. Real-time profiling of solid-state nanopores during solution-phase nanofabrication. ACS Appl Mater Interfaces. 2016;8(44):30583–9. https://doi.org/10.1021/acsami.6b10045.

    Article  CAS  PubMed  Google Scholar 

  57. Kwok H, Briggs K, Tabard-Cossa V. Nanopore fabrication by controlled dielectric breakdown. PLoS One. 2014;9(3):e92880. https://doi.org/10.1371/journal.pone.0092880.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. 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. https://doi.org/10.1002/smll.201303602.

    Article  CAS  PubMed  Google Scholar 

  59. Bandara Y, Nichols JW, Iroshika Karawdeniya B, Dwyer JR. Conductance-based profiling of nanopores: accommodating fabrication irregularities. Electrophoresis. 2018;39(4):626–34. https://doi.org/10.1002/elps.201700299.

    Article  CAS  PubMed  Google Scholar 

  60. Kuan AT, Lu B, **e P, Szalay T, Golovchenko JA. Electrical pulse fabrication of graphene nanopores in electrolyte solution. Appl Phys Lett. 2015;106(20):203109. https://doi.org/10.1063/1.4921620.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Wei R, Pedone D, Zürner A, Döblinger M, Rant U. Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing. Small. 2010;6(13):1406–14. https://doi.org/10.1002/smll.201000253.

    Article  CAS  PubMed  Google Scholar 

  62. Wanunu M, Meller A. Chemically modified solid-state nanopores. Nano Lett. 2007;7(6):1580–5. https://doi.org/10.1021/nl070462b.

    Article  CAS  PubMed  Google Scholar 

  63. Yusko EC, Johnson JM, Majd S, Prangkio P, Rollings RC, Li J, et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat Nanotechnol. 2011;6:253–60. https://doi.org/10.1038/nnano.2011.12.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Lepoitevin M, Ma T, Bechelany M, Janot J-M, Balme S. Functionalization of single solid state nanopores to mimic biological ion channels: a review. Adv Colloid Interface Sci. 2017;250:195–213. https://doi.org/10.1016/j.cis.2017.09.001.

    Article  CAS  PubMed  Google Scholar 

  65. Anderson BN, Muthukumar M, Meller A. pH tuning of DNA translocation time through organically functionalized nanopores. ACS Nano. 2012;7(2):1408–14. https://doi.org/10.1021/nn3051677.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Valentina M, Paola F, Giuseppe F, Luca R, Ugo V. Size and functional tuning of solid state nanopores by chemical functionalization. Nanotechnology. 2012;23(43):435301.

    Article  Google Scholar 

  67. Mussi V, Fanzio P, Repetto L, Firpo G, Scaruffi P, Stigliani S, et al. DNA-functionalized solid state nanopore for biosensing. Nanotechnology. 2010;21(14):145102. https://doi.org/10.1088/0957-4484/21/14/145102.

    Article  CAS  PubMed  Google Scholar 

  68. Mussi V, Fanzio P, Repetto L, Firpo G, Scaruffi P, Stigliani S, et al. Electrical characterization of DNA-functionalized solid state nanopores for bio-sensing. J Phys Condens Matter. 2010;22(45):454104.

    Article  CAS  PubMed  Google Scholar 

  69. Liebes Y, Drozdov M, Avital YY, Kauffmann Y, Rapaport H, Kaplan WD, et al. Reconstructing solid state nanopore shape from electrical measurements. Appl Phys Lett. 2010;97(22):223105.

    Article  Google Scholar 

  70. Ayub M, Ivanov A, Instuli E, Cecchini M, Chansin G, McGilvery C, et al. Nanopore/electrode structures for single-molecule biosensing. Electrochim Acta. 2010;55(27):8237–43.

    Article  CAS  Google Scholar 

  71. Stein D, Kruithof M, Dekker C. Surface-charge-governed ion transport in nanofluidic channels. Phys Rev Lett. 2004;93(3):035901.

    Article  PubMed  Google Scholar 

  72. Frament CM, Dwyer JR. Conductance-based determination of solid-state nanopore size and shape: an exploration of performance limits. J Phys Chem C. 2012;116(44):23315–21. https://doi.org/10.1021/jp305381j.

    Article  CAS  Google Scholar 

  73. Kowalczyk SW, Grosberg AY, Rabin Y, Dekker C. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology. 2011;22(31):315101.

    Article  PubMed  Google Scholar 

  74. Behrens SH, Grier DG. The charge of glass and silica surfaces. J Chem Phys. 2001;115(14):6716–21.

    Article  CAS  Google Scholar 

  75. DeBlois RW, Bean CP. Counting and sizing of submicron particles by the resistive pulse technique. Rev Sci Instrum. 1970;41(7):909–16.

    Article  Google Scholar 

  76. Lee C, Joly L, Siria A, Biance A-L, Fulcrand R, Bocquet L. Large apparent electric size of solid-state nanopores due to spatially extended surface conduction. Nano Lett. 2012;12(8):4037–44. https://doi.org/10.1021/nl301412b.

    Article  CAS  PubMed  Google Scholar 

  77. Detcheverry F, Bocquet L. Thermal fluctuations in nanofluidic transport. Phys Rev Lett. 2012;109(2):024501.

    Article  PubMed  Google Scholar 

  78. Firnkes M, Pedone D, Knezevic J, Döblinger M, Rant U. Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. Nano Lett. 2010;6(8):895–909. https://doi.org/10.1021/nl100861c.

    Article  CAS  Google Scholar 

  79. Hoogerheide DP, Garaj S, Golovchenko JA. Probing surface charge fluctuations with solid-state nanopores. Phys Rev Lett. 2009;102(25):256804.

    Article  PubMed  PubMed Central  Google Scholar 

  80. Karawdeniya BI, Bandara Y, Nichols JW, Chevalier RB, Dwyer JR. Surveying silicon nitride nanopores for glycomics and heparin quality assurance. Nat Commun. 2018;9(1):3278. https://doi.org/10.1038/s41467-018-05751-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Frament CM, Bandara N, Dwyer JR. Nanopore surface coating delivers nanopore size and shape through conductance-based sizing. ACS Appl Mater Interfaces. 2013;5(19):9330–7. https://doi.org/10.1021/am4026455.

    Article  CAS  PubMed  Google Scholar 

  82. 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. https://doi.org/10.1529/biophysj.108.140475.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Carbonaro A, Sohn LL. A resistive-pulse sensor chip for multianalyte immunoassays. Lab Chip. 2005. https://doi.org/10.1039/b504827c.

    Article  PubMed  Google Scholar 

  84. Aksimentiev A. Deciphering ionic current signatures of DNA transport through a nanopore. Nanoscale. 2010;2(4):468–83. https://doi.org/10.1039/b9nr00275h.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Smeets RMM, Keyser UF, Krapf D, Wu M-Y, Dekker NH, Dekker C. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 2006;6(1):89–95. https://doi.org/10.1021/nl052107w.

    Article  CAS  PubMed  Google Scholar 

  86. Beamish E, Kwok H, Tabard-Cossa V, Godin M. Precise control of the size and noise of solid-state nanopores using high electric fields. Nanotechnology. 2012;23(40):405301.

    Article  PubMed  Google Scholar 

  87. Tabard-Cossa V, Trivedi D, Wiggin M, Jetha NN, Marziali A. Noise analysis and reduction in solid-state nanopores. Nanotechnology. 2007. https://doi.org/10.1088/0957-4484/18/30/305505.

    Article  Google Scholar 

  88. Li J, Gershow M, Stein D, Brandin E, Golovchenko JA. DNA molecules and configurations in a solid-state nanopore microscope. Nat Mater. 2003;2:611. https://doi.org/10.1038/nmat965.

    Article  CAS  PubMed  Google Scholar 

  89. Schoch RB, Han J, Renaud P. Transport phenomena in nanofluidics. Rev Mod Phys. 2008;80(3):839–83.

    Article  CAS  Google Scholar 

  90. Reiner JE, Kasianowicz JJ, Nablo BJ, Robertson JWF. Theory for polymer analysis using nanopore-based single-molecule mass spectrometry. Proc Natl Acad Sci USA. 2010;107(27):12080–5. https://doi.org/10.1073/pnas.1002194107.

    Article  PubMed  PubMed Central  Google Scholar 

  91. Weerakoon-Ratnayake KM, O’Neil CE, Uba FI, Soper SA. Thermoplastic nanofluidic devices for biomedical applications. Lab Chip. 2017;17(3):362–81. https://doi.org/10.1039/C6LC01173J.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Uba FI, Pullagurla SR, Sirasunthorn N, Wu J, Park S, Chantiwas R, et al. Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels. Analyst. 2015;140(1):113–26. https://doi.org/10.1039/C4AN01439A.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Haywood DG, Harms ZD, Jacobson SC. Electroosmotic flow in nanofluidic channels. Anal Chem. 2014;86(22):11174–80. https://doi.org/10.1021/ac502596m.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Mabey D, Peeling RW, Ustianowski A, Perkins MD. Diagnostics for the develo** world. Nat Rev Microbiol. 2004;2:231. https://doi.org/10.1038/nrmicro841.

    Article  CAS  PubMed  Google Scholar 

  95. Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530:228. https://doi.org/10.1038/nature16996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins KH, McIntyre ABR, et al. Nanopore DNA sequencing and genome assembly on the international space station. Sci Rep UK. 2017;7(1):18022. https://doi.org/10.1038/s41598-017-18364-0.

    Article  CAS  Google Scholar 

  97. Peveler WJ, Yazdani M, Rotello VM. Selectivity and specificity: pros and cons in sensing. ACS Sens. 2016;1(11):1282–5. https://doi.org/10.1021/acssensors.6b00564.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Tabard-Cossa V, Wiggin M, Trivedi D, Jetha NN, Dwyer JR, Marziali A. Single-molecule bonds characterized by solid-state nanopore force spectroscopy. ACS Nano. 2009;3(10):3009–14. https://doi.org/10.1021/nn900713a.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Tropini C, Marziali A. Multi-nanopore force spectroscopy for DNA analysis. Biophys J. 2007;92(5):1632–7. https://doi.org/10.1529/biophysj.106.094060.

    Article  CAS  PubMed  Google Scholar 

  100. Nakane J, Wiggin M, Marziali A. A nanosensor for transmembrane capture and identification of single nucleic acid molecules. Biophys J. 2004;87(1):615–21. https://doi.org/10.1529/biophysj.104.040212.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Mathe J, Visram H, Viasnoff V, Rabin Y, Meller A. Nanopore unzip** of individual DNA hairpin molecules. Biophys J. 2004;87(5):3205–12. https://doi.org/10.1529/biophysj.104.047274.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Renner S, Geltinger S, Simmel FC. Nanopore translocation and force spectroscopy experiments in microemulsion droplets. Small. 2010;6(2):190–4. https://doi.org/10.1002/smll.200901435.

    Article  CAS  PubMed  Google Scholar 

  103. Hornblower B, Coombs A, Whitaker RD, Kolomeisky A, Picone SJ, Meller A, et al. Single-molecule analysis of DNA-protein complexes using nanopores. Nat Methods. 2007;4(4):315–7. https://doi.org/10.1038/nmeth1021.

    Article  CAS  PubMed  Google Scholar 

  104. Dudko OK, Mathe J, Szabo A, Meller A, Hummer G. Extracting kinetics from single-molecule force spectroscopy: nanopore unzip** of DNA hairpins. Biophys J. 2007;92(12):4188–95. https://doi.org/10.1529/biophysj.106.102855.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. McNally B, Wanunu M, Meller A. Electromechanical unzip** of individual DNA molecules using synthetic sub-2 nm pores. Nano Lett. 2008;8(10):3418–22. https://doi.org/10.1021/nl802218f.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Evans E. Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy. Biophys Chem. 1999;82(2–3):83–97.

    Article  CAS  PubMed  Google Scholar 

  107. Heins EA, Siwy ZS, Baker LA, Martin CR. Detecting single porphyrin molecules in a conically shaped synthetic nanopore. Nano Lett. 2005;5(9):1824–9. https://doi.org/10.1021/nl050925i.

    Article  CAS  PubMed  Google Scholar 

  108. Braha O, Gu L-Q, Zhou L, Lu X, Cheley S, Bayley H. Simultaneous stochastic sensing of divalent metal ions. Nat Biotechnol. 2000;18:1005. https://doi.org/10.1038/79275.

    Article  CAS  PubMed  Google Scholar 

  109. Boersma AJ, Brain KL, Bayley H. Real-time stochastic detection of multiple neurotransmitters with a protein nanopore. ACS Nano. 2012;6(6):5304–8. https://doi.org/10.1021/nn301125y.

    Article  CAS  PubMed  Google Scholar 

  110. Guan X, Gu L-Q, Cheley S, Braha O, Bayley H. Stochastic sensing of TNT with a genetically engineered pore. ChemBioChem. 2005;6(10):1875–81. https://doi.org/10.1002/cbic.200500064.

    Article  CAS  PubMed  Google Scholar 

  111. Boersma AJ, Bayley H. Continuous stochastic detection of amino acid enantiomers with a protein nanopore. Angew Chem Int Ed. 2012;51(38):9606–9. https://doi.org/10.1002/anie.201205687.

    Article  CAS  Google Scholar 

  112. Kang X-F, Cheley S, Guan X, Bayley H. Stochastic detection of enantiomers. J Am Chem Soc. 2006;128(33):10684–5. https://doi.org/10.1021/ja063485l.

    Article  CAS  PubMed  Google Scholar 

  113. Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE. Landscape of next-generation sequencing technologies. Anal Chem. 2011;83(12):4327–41. https://doi.org/10.1021/ac2010857.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Wang Y, Yao F, Kang X-F. Tetramethylammonium-filled protein nanopore for single-molecule analysis. Anal Chem. 2015;87(19):9991–7. https://doi.org/10.1021/acs.analchem.5b02611.

    Article  CAS  PubMed  Google Scholar 

  115. Wanunu M, Morrison W, Rabin Y, Grosberg AY, Meller A. Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. Nat Nano. 2010;5(2):160–5. http://www.nature.com/nnano/journal/v5/n2/suppinfo/nnano.2009.379_S1.html.

  116. Pitchford WH, Kim H-J, Ivanov AP, Kim H-M, Yu J-S, Leatherbarrow RJ, et al. Synchronized optical and electronic detection of biomolecules using a low noise nanopore platform. ACS Nano. 2015;9(2):1740–8. https://doi.org/10.1021/nn506572r.

    Article  CAS  PubMed  Google Scholar 

  117. Morin TJ, McKenna WL, Shropshire TD, Wride DA, Deschamps JD, Liu X, et al. A handheld platform for target protein detection and quantification using disposable nanopore strips. Sci Rep UK. 2018;8(1):14834. https://doi.org/10.1038/s41598-018-33086-7.

    Article  CAS  Google Scholar 

  118. Jayasena SD. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem. 1999;45(9):1628–50.

    CAS  PubMed  Google Scholar 

  119. O’Sullivan C. Aptasensors—the future of biosensing? Anal Bioanal Chem. 2002;372(1):44–8. https://doi.org/10.1007/s00216-001-1189-3.

    Article  CAS  PubMed  Google Scholar 

  120. Luzi E, Minunni M, Tombelli S, Mascini M. New trends in affinity sensing: aptamers for ligand binding. Trends Anal Chem. 2003;22(11):810–8.

    Article  CAS  Google Scholar 

  121. Bunka DHJ, Stockley PG. Aptamers come of age—at last. Nat Rev Microbiol. 2006;4(8):588–96.

    Article  CAS  PubMed  Google Scholar 

  122. Tennico YH, Hutanu D, Koesdjojo MT, Bartel CM, Remcho VT. On-chip aptamer-based sandwich assay for thrombin detection employing magnetic beads and quantum dots. Anal Chem. 2010;82(13):5591–7. https://doi.org/10.1021/ac101269u.

    Article  CAS  PubMed  Google Scholar 

  123. Lubin AA, Plaxco KW. Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Acc Chem Res. 2010;43(4):496–505. https://doi.org/10.1021/ar900165x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Takemura K, Wang P, Vorberg I, Surewicz W, Priola SA, Kanthasamy A, et al. DNA aptamers that bind to PrPC and not PrPSc show sequence and structure specificity. Exp Biol Med. 2006;231(2):204–14.

    Article  CAS  Google Scholar 

  125. Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science. 2008;319(5863):630–3. https://doi.org/10.1126/science.1151298.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Lin L, Wang H, Liu Y, Yan H, Lindsay S. Recognition imaging with a DNA aptamer. Biophys J. 2006;90(11):4236–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Bock LC, Griffin LC, Latham JA, Vermaas EH, Toole JJ. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature. 1992;355(6360):564–6.

    Article  CAS  PubMed  Google Scholar 

  128. Tasset DM, Kubik MF, Steiner W. Oligonucleotide inhibitors of human thrombin that bind distinct epitopes. J Mol Biol. 1997;272(5):688–98.

    Article  CAS  PubMed  Google Scholar 

  129. Shim JW, Gu L-Q. Encapsulating a single G-quadruplex aptamer in a protein nanocavity. J Phys Chem B. 2008;112(28):8354–60. https://doi.org/10.1021/jp0775911.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Wiggin M, Tropini C, Tabard-Cossa V, Jetha NN, Marziali A. Nonexponential kinetics of DNA escape from alpha-hemolysin nanopores. Biophys J. 2008;95(11):5317–23. https://doi.org/10.1529/biophysj.108.137760.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Ding S, Gao C, Gu L-Q. Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. Anal Chem. 2009;81(16):6649–55. https://doi.org/10.1021/ac9006705.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Abelow AE, Schepelina O, White RJ, Vallee-Belisle A, Plaxco KW, Zharov I. Biomimetic glass nanopores employing aptamer gates responsive to a small molecule. Chem Commun. 2010;46(42):7984–6.

    Article  CAS  Google Scholar 

  133. Kawano R, Osaki T, Sasaki H, Takinoue M, Yoshizawa S, Takeuchi S. Rapid detection of a cocaine-binding aptamer using biological nanopores on a chip. J Am Chem Soc. 2011;133(22):8474–7. https://doi.org/10.1021/ja2026085.

    Article  CAS  PubMed  Google Scholar 

  134. Ying Y-L, Wang H-Y, Sutherland TC, Long Y-T. Monitoring of an ATP-binding aptamer and its conformational changes using an α-hemolysin nanopore. Small. 2011;7(1):87–94. https://doi.org/10.1002/smll.201001428.

    Article  CAS  PubMed  Google Scholar 

  135. Kong J, Zhu J, Chen K, Keyser UF. Specific biosensing using DNA aptamers and nanopores. Adv Funct Mater. 2018. https://doi.org/10.1002/adfm.201807555.

    Article  Google Scholar 

  136. Winters-Hilt S. The α-hemolysin nanopore transduction detector—single-molecule binding studies and immunological screening of antibodies and aptamers. BMC Bioinform. 2007;8(7):S9. https://doi.org/10.1186/1471-2105-8-s7-s9.

    Article  Google Scholar 

  137. Harms ZD, Haywood DG, Kneller AR, Jacobson SC. Conductivity-based detection techniques in nanofluidic devices. Analyst. 2015;140(14):4779–91. https://doi.org/10.1039/C5AN00075K.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Freedman KJ, Haq SR, Edel JB, Jemth P, Kim MJ. Single molecule unfolding and stretching of protein domains inside a solid-state nanopore by electric field. Sci Rep. 2013. https://doi.org/10.1038/srep01638.

    Article  PubMed  PubMed Central  Google Scholar 

  139. Pastoriza-Gallego M, Breton M-F, Discala F, Auvray L, Betton J-M, Pelta J. Evidence of unfolded protein translocation through a protein nanopore. ACS Nano. 2014;8(11):11350–60. https://doi.org/10.1021/nn5042398.

    Article  CAS  PubMed  Google Scholar 

  140. Payet L, Martinho M, Pastoriza-Gallego M, Betton J-M, Auvray L, Pelta J, et al. Thermal unfolding of proteins probed at the single molecule level using nanopores. Anal Chem. 2012;84(9):4071–6. https://doi.org/10.1021/ac300129e.

    Article  CAS  PubMed  Google Scholar 

  141. Merstorf C, Cressiot B, Pastoriza-Gallego M, Oukhaled A, Betton J-M, Auvray L, et al. Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording. ACS Chem Biol. 2012;7(4):652–8. https://doi.org/10.1021/cb2004737.

    Article  CAS  PubMed  Google Scholar 

  142. Cressiot B, Oukhaled A, Patriarche G, Pastoriza-Gallego M, Betton J-M, Auvray L, et al. Protein transport through a narrow solid-state nanopore at high voltage: experiments and theory. ACS Nano. 2012;6(7):6236–43. https://doi.org/10.1021/nn301672g.

    Article  CAS  PubMed  Google Scholar 

  143. Singh PR, Bárcena-Uribarri I, Modi N, Kleinekathöfer U, Benz R, Winterhalter M, et al. Pulling peptides across nanochannels: resolving peptide binding and translocation through the hetero-oligomeric channel from nocardia farcinica. ACS Nano. 2012;6(12):10699–707. https://doi.org/10.1021/nn303900y.

    Article  CAS  PubMed  Google Scholar 

  144. Jetha NN, Semenchenko V, Wishart DS, Cashman NR, Marziali A. Nanopore analysis of wild-type and mutant prion protein (PrPC): single molecule discrimination and PrPC kinetics. PLoS One. 2013;8(2):e54982.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Radu IS, Dhruti T, Andre M, Jeremy SL. Evidence that small proteins translocate through silicon nitride pores in a folded conformation. J Phys Condens Matter. 2010;22(45):454133.

    Article  Google Scholar 

  146. Yusko EC, Bruhn BR, Eggenberger OM, Houghtaling J, Rollings RC, Walsh NC et al. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat Nanotechnol. 2016;12:360. https://doi.org/10.1038/nnano.2016.267. https://www.nature.com/articles/nnano.2016.267#supplementary-information.

  147. Sexton LT, Horne LP, Sherrill SA, Bishop GW, Baker LA, Martin CR. Resistive-pulse studies of proteins and protein/antibody complexes using a conical nanotube sensor. J Am Chem Soc. 2007;129(43):13144–52. https://doi.org/10.1021/ja0739943.

    Article  CAS  PubMed  Google Scholar 

  148. Movileanu L, Schmittschmitt JP, Martin Scholtz J, Bayley H. Interactions of peptides with a protein pore. Biophys J. 2005;89(2):1030–45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Siwy Z, Trofin L, Kohli P, Baker LA, Trautmann C, Martin CR. Protein biosensors based on biofunctionalized conical gold nanotubes. J Am Chem Soc. 2005;127(14):5000–1. https://doi.org/10.1021/ja043910f.

    Article  CAS  PubMed  Google Scholar 

  150. Sha J, Si W, Xu B, Zhang S, Li K, Lin K, et al. Identification of spherical and nonspherical proteins by a solid-state nanopore. Anal Chem. 2018;90(23):13826–31. https://doi.org/10.1021/acs.analchem.8b04136.

    Article  CAS  PubMed  Google Scholar 

  151. Restrepo-Pérez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. Nat Nanotechnol. 2018;13(9):786–96. https://doi.org/10.1038/s41565-018-0236-6.

    Article  CAS  PubMed  Google Scholar 

  152. Dong X, Zhou S, Mechref Y. LC-MS/MS analysis of permethylated free oligosaccharides and N-glycans derived from human, bovine, and goat milk samples. Electrophoresis. 2016;37(11):1532–48. https://doi.org/10.1002/elps.201500561.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Imberty A, Pérez S. Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev. 2000;100(12):4567–88. https://doi.org/10.1021/cr990343j.

    Article  CAS  PubMed  Google Scholar 

  154. DeMarco ML, Woods RJ. Structural glycobiology: a game of snakes and ladders. Glycobiology. 2008;18(6):426–40. https://doi.org/10.1093/glycob/cwn026.

    Article  CAS  PubMed  Google Scholar 

  155. Dove A. The bittersweet promise of glycobiology. Nat Biotechnol. 2001;19:913–7. https://doi.org/10.1038/nbt1001-913.

    Article  CAS  PubMed  Google Scholar 

  156. Ernst B, Magnani JL. From carbohydrate leads to glycomimetic drugs. Nat Rev Drug Discov. 2009;8(8):661–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Helenius A, Aebi M. Intracellular functions of N-linked glycans. Science. 2001;291(5512):2364–9. https://doi.org/10.1126/science.291.5512.2364.

    Article  CAS  PubMed  Google Scholar 

  158. Rudd PM, Elliott T, Cresswell P, Wilson IA, Dwek RA. Glycosylation and the immune system. Science. 2001;291(5512):2370–6. https://doi.org/10.1126/science.291.5512.2370.

    Article  CAS  PubMed  Google Scholar 

  159. Pinho SS, Reis CA. Glycosylation in cancer: mechanisms and clinical implications. Nat Rev Cancer. 2015;15(9):540–55. https://doi.org/10.1038/nrc3982.

    Article  CAS  PubMed  Google Scholar 

  160. Seeberger PH. Chemical glycobiology: why now? Nat Chem Biol. 2009;5(6):368–72.

    Article  CAS  PubMed  Google Scholar 

  161. Lichtenstein RG, Rabinovich GA. Glycobiology of cell death: when glycans and lectins govern cell fate. Cell Death Differ. 2013;20(8):976–86. https://doi.org/10.1038/cdd.2013.50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Dalziel M, Crispin M, Scanlan CN, Zitzmann N, Dwek RA. Emerging principles for the therapeutic exploitation of glycosylation. Science. 2014. https://doi.org/10.1126/science.1235681.

    Article  PubMed  Google Scholar 

  163. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME, editors. Essentials of glycobiology. 2nd ed. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009.

    Google Scholar 

  164. Czjzek M. Biochemistry: a wine-induced breakdown. Nature. 2017;544(7648):45–6. https://doi.org/10.1038/nature21901.

    Article  CAS  PubMed  Google Scholar 

  165. Lester J, Chandler T, Gemene KL. Reversible electrochemical sensor for detection of high-charge density polyanion contaminants in heparin. Anal Chem. 2015;87(22):11537–43. https://doi.org/10.1021/acs.analchem.5b03347.

    Article  CAS  PubMed  Google Scholar 

  166. Kim D-H, Park YJ, Jung KH, Lee K-H. Ratiometric detection of nanomolar concentrations of heparin in serum and plasma samples using a fluorescent chemosensor based on peptides. Anal Chem. 2014;86(13):6580–6. https://doi.org/10.1021/ac501089m.

    Article  CAS  PubMed  Google Scholar 

  167. Liu H, Zhang Z, Linhardt RJ. Lessons learned from the contamination of heparin. Nat Prod Rep. 2009;26(3):313–21. https://doi.org/10.1039/B819896A.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Korir A, Larive C. Advances in the separation, sensitive detection, and characterization of heparin and heparan sulfate. Anal Bioanal Chem. 2009;393(1):155–69. https://doi.org/10.1007/s00216-008-2412-2.

    Article  CAS  PubMed  Google Scholar 

  169. Kishimoto TK, Viswanathan K, Ganguly T, Elankumaran S, Smith S, Pelzer K, et al. Contaminated heparin associated with adverse clinical events and activation of the contact system. New Engl J Med. 2008;358(23):2457–67. https://doi.org/10.1056/NEJMoa0803200.

    Article  CAS  PubMed  Google Scholar 

  170. Guerrini M, Beccati D, Shriver Z, Naggi A, Viswanathan K, Bisio A, et al. Oversulfated chondroitin sulfate is a contaminant in heparin associated with adverse clinical events. Nat Biotech. 2008;26(6):669–75. https://doi.org/10.1038/nbt1407.

    Article  CAS  Google Scholar 

  171. Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem. 2014;86(1):196–212. https://doi.org/10.1021/ac403969n.

    Article  CAS  PubMed  Google Scholar 

  172. Kasianowicz JJ, Brandin E, Branton D, Deamer DW. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA. 1996;93(24):13770–3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Bacri L, Oukhaled A, Hémon E, Bassafoula FB, Auvray L, Daniel R. Discrimination of neutral oligosaccharides through a nanopore. Biochem Biophys Res Commun. 2011;412(4):561–4. https://doi.org/10.1016/j.bbrc.2011.07.121.

    Article  CAS  PubMed  Google Scholar 

  174. Fennouri A, Przybylski C, Pastoriza-Gallego M, Bacri L, Auvray L, Daniel R. Single molecule detection of glycosaminoglycan hyaluronic acid oligosaccharides and depolymerization enzyme activity using a protein nanopore. ACS Nano. 2012;6(11):9672–8. https://doi.org/10.1021/nn3031047.

    Article  CAS  PubMed  Google Scholar 

  175. Fennouri A, Daniel R, Pastoriza-Gallego M, Auvray L, Pelta J, Bacri L. Kinetics of enzymatic degradation of high molecular weight polysaccharides through a nanopore: experiments and data-modeling. Anal Chem. 2013;85(18):8488–92. https://doi.org/10.1021/ac4020929.

    Article  CAS  PubMed  Google Scholar 

  176. Kullman L, Winterhalter M, Bezrukov SM. Transport of maltodextrins through maltoporin: a single-channel study. Biophys J. 2002;82(2):803–12. https://doi.org/10.1016/S0006-3495(02)75442-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Zhao S, Zheng Y-B, Cai S-L, Weng Y-H, Cao S-H, Yang J-L, et al. Sugar-stimulated robust nanodevice: 4-carboxyphenylboronic acid modified single glass conical nanopores. Electrochem Commun. 2013;36:71–4. https://doi.org/10.1016/j.elecom.2013.09.009.

    Article  CAS  Google Scholar 

  178. Zheng Y-B, Zhao S, Cao S-H, Cai S-L, Cai X-H, Li Y-Q. A temperature, pH and sugar triple-stimuli-responsive nanofluidic diode. Nanoscale. 2017;9(1):433–9. https://doi.org/10.1039/C6NR07339E.

    Article  CAS  PubMed  Google Scholar 

  179. Nguyen QH, Ali M, Neumann R, Ensinger W. Saccharide/glycoprotein recognition inside synthetic ion channels modified with boronic acid. Sens Actuators B Chem. 2012;162(1):216–22. https://doi.org/10.1016/j.snb.2011.12.070.

    Article  CAS  Google Scholar 

  180. Vilozny B, Wollenberg AL, Actis P, Hwang D, Singaram B, Pourmand N. Carbohydrate-actuated nanofluidic diode: switchable current rectification in a nanopipette. Nanoscale. 2013;5(19):9214–21. https://doi.org/10.1039/C3NR02105J.

    Article  CAS  PubMed  Google Scholar 

  181. Sun Z, Han C, Wen L, Tian D, Li H, Jiang L. pH gated glucose responsive biomimetic single nanochannels. Chem Commun. 2012;48(27):3282–4. https://doi.org/10.1039/C2CC17277A.

    Article  CAS  Google Scholar 

  182. Oukhaled G, Bacri L, Mathé J, Pelta J, Auvray L. Effect of screening on the transport of polyelectrolytes through nanopores. Europhys Lett. 2008;82(4):48003.

    Article  Google Scholar 

  183. Rivas F, Zahid OK, Reesink HL, Peal BT, Nixon AJ, DeAngelis PL, et al. Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor. Nat Commun. 2018;9(1):1037. https://doi.org/10.1038/s41467-018-03439-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Ali M, Ramirez P, Tahir MN, Mafe S, Siwy Z, Neumann R, et al. Biomolecular conjugation inside synthetic polymer nanopores via glycoprotein-lectin interactions. Nanoscale. 2011;3(4):1894–903. https://doi.org/10.1039/C1NR00003A.

    Article  CAS  PubMed  Google Scholar 

  185. Linhardt RJ. 2003 Claude S. Hudson award address in carbohydrate chemistry. Heparin: structure and activity. J Med Chem. 2003;46(13):2551–64. https://doi.org/10.1021/jm030176m.

    Article  CAS  PubMed  Google Scholar 

  186. Solá RJ, Griebenow K. Glycosylation of therapeutic proteins. BioDrugs. 2010;24(1):9–21. https://doi.org/10.2165/11530550-000000000-00000.

    Article  PubMed  PubMed Central  Google Scholar 

  187. Seeberger PH, Cummings RD. Glycans in biotechnology. In: Varki A, Cummings RD, Esko JD, et al., editors. Essentials of glycobiology. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2017 (Internet).

    Google Scholar 

Download references

Acknowledgements

This material is based on work supported by the National Science Foundation under 1808344 and 1150085.

Author information

Author notes

  1. Buddini I. Karawdeniya & Y. M. Nuwan D. Y. Bandara

    Present address: Department of Mechanical Engineering, Lyle School of Engineering, Southern Methodist University, Dallas, TX, 75275, USA

  2. Jonathan W. Nichols

    Present address: Nova Biomedical, 200 Prospect Street, Waltham, MA, 02454-9141, USA

Authors and Affiliations

  1. Department of Chemistry, University of Rhode Island, Richard E. Beaupre Center for Chemical and Forensic Sciences, 140 Flagg Rd., Kingston, RI, 02881, USA

    Robert B. Chevalier, James T. Hagan & Jason R. Dwyer

Authors
  1. Buddini I. Karawdeniya
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Y. M. Nuwan D. Y. Bandara
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jonathan W. Nichols
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Robert B. Chevalier
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. James T. Hagan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jason R. Dwyer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jason R. Dwyer.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Karawdeniya, B.I., Bandara, Y.M.N.D.Y., Nichols, J.W. et al. Challenging Nanopores with Analyte Scope and Environment. J. Anal. Test. 3, 61–79 (2019). https://doi.org/10.1007/s41664-019-00092-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s41664-019-00092-1

Keywords

Search

Navigation