Skip to main content

Single-Molecule Ionic and Optical Sensing with Nanoapertures

  • Chapter
  • First Online:
Single Molecule Sensing Beyond Fluorescence

Part of the book series: Nanostructure Science and Technology ((NST))

Abstract

Solid-state nanoapertures (nanometer sized holes within a membrane) allow for the interrogation of single molecules by probing them within their nanoscale volume through which molecules pass in a single-file manner. Molecules are probed using two main techniques: ionic sensing where a salt solution and applied voltage is used to produce an ionic current through the nanopore, and optical sensing through a shift in the resonance wavelength of the plasmonic nanoaperture. Here, we briefly review the basic principles, applications, and challenges in sensing with solid-state nanoapertures, as well as some strategies for further improvements. We compare the complimentary features of the two approaches and highlight recent attempts to combine them into new sensing platforms.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Daniel Branton, David W. Deamer, Andre Marziali, Hagan Bayley, Steven A. Benner, Thomas Butler, Massimiliano Di Ventra, Slaven Garaj, Andrew Hibbs, Xiaohua Huang, Stevan B. Jovanovich, Predrag S. Krstic, Stuart Lindsay, Xinsheng Sean Ling, Carlos H. Mastrangelo, Amit Meller, John S. Oliver, Yuriy V. Pershin, J. Michael Ramsey, Robert Riehn, Gautam V. Soni, Vincent Tabard-Cossa, Meni Wanunu, Matthew Wiggin, and Jeffery A. Schloss. The potential and challenges of nanopore sequencing. 26(10):1146–1153, 2008.

    Google Scholar 

  2. Laura Restrepo-Pérez, Chirlmin Joo, and Cees Dekker. Paving the way to single-molecule protein sequencing. Nature nanotechnology, 13(9):786–796, 2018.

    Article  Google Scholar 

  3. John J Kasianowicz and Sergey M Bezrukov. On ’three decades of nanopore sequencing’. Nature Biotechnology, 34(5), 2016.

    Google Scholar 

  4. Jordanka Zlatanova and Kensal van Holde. Single-Molecule Biology: What Is It and How Does It Work? Molecular cell, 24(3):317–329, 2006.

    Article  CAS  Google Scholar 

  5. Taekjip Ha, Alexander G. Kozlov, and Timothy M. Lohman. Single-molecule views of protein movement on single-stranded DNA. Annual Review of Biophysics, 2012.

    Google Scholar 

  6. Weichun Zhang, Martín Caldarola, Xuxing Lu, Biswajit Pradhan, and Michel Orrit. Single-molecule fluorescence enhancement of a near-infrared dye by gold nanorods using DNA transient binding. Physical Chemistry Chemical Physics, 20(31):20468–20475, 2018.

    Article  CAS  Google Scholar 

  7. K Ravi Acharya and Matthew D Lloyd. The advantages and limitations of protein crystal structures. Trends in pharmacological sciences, 26(1):10–14, 2005.

    Google Scholar 

  8. Xavier Michalet, Shimon Weiss, and Marcus Jäger. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chemical reviews, 106(5):1785–1813, 2006.

    Article  CAS  PubMed Central  Google Scholar 

  9. Eugene Kim, Martin D. Baaske, Isabel Schuldes, Peter S. Wilsch, and Frank Vollmer. Label-free optical detection of single enzyme-reactant reactions and associated conformational changes. Science Advances, 3(3):e1603044, 2017.

    Article  PubMed Central  Google Scholar 

  10. J Kong, J Zhu, and U F Keyser. Single molecule based SNP detection using designed DNA carriers and solid-state nanopores. Chemical Communications, 53(2):436–439, 2017.

    Article  CAS  Google Scholar 

  11. Q. Zhao, G. Sigalov, V. Dimitrov, B. Dorvel, U. Mirsaidov, S. Sligar, A. Aksimentiev, and G. Timp. Detecting SNPs using a synthetic nanopore. Nano Letters, 7(6):1680–1685, 2007.

    Article  CAS  PubMed Central  Google Scholar 

  12. Andrea M. Armani, Rajan P. Kulkarni, Scott E. Fraser, Richard C. Flagan, and Kerry J. Vahala. Label-free, single-molecule detection with optical microcavities. Science, 317(5839):783–787, 2007.

    Article  CAS  Google Scholar 

  13. D Cibran Perez-Gonzalez and J Carlos Penedo. Single-molecule strategies for DNA and RNA diagnostics. RNA and DNA Diagnostics, Springer: 297-312, 2015.

    Google Scholar 

  14. David R. Walt. Optical methods for single molecule detection and analysis. Analytical Chemistry, 85(3):1258–1263, 2013.

    Article  CAS  Google Scholar 

  15. Eugene Kim, Martin D. Baaske, and Frank Vollmer. Towards next-generation label-free biosensors: recent advances in whispering gallery mode sensors. Lab on a Chip 17(7):1190–1205, 2017.

    Article  CAS  Google Scholar 

  16. Murugappan Muthukumar, Calin Plesa, and Cees Dekker. Single-molecule sensing with nanopores. Physics Today, 68(8):40–46, 2015.

    Article  CAS  Google Scholar 

  17. Nitinun Varongchayakul, Jiaxi Song, Amit Meller, and Mark W. Grinstaff. Single-molecule protein sensing in a nanopore: a tutorial. Chemical Society reviews, 47(23):8512–8524, 2018.

    Article  CAS  PubMed Central  Google Scholar 

  18. Yanxiao Feng, Yuechuan Zhang, Cuifeng Ying, Deqiang Wang, and Chunlei Du. Nanopore-based Fourth-generation DNA Sequencing Technology. Genomics, Proteomics & Bioinformatics, 13(1):4–16, 2015.

    Article  CAS  Google Scholar 

  19. Qi Chen and Zewen Liu. Fabrication and applications of solid-state nanopores. Sensors, 19(8):1886, 2019.

    Article  CAS  PubMed Central  Google Scholar 

  20. S. Garaj, W. Hubbard, A. Reina, J. Kong, D. Branton, and J. A. Golovchenko. Graphene as a subnanometre trans-electrode membrane. Nature, 467(7312):190–193, 2010.

    Article  CAS  PubMed Central  Google Scholar 

  21. Ke Liu, Martina Lihter, Aditya Sarathy, Sabina Caneva, Hu Qiu, Davide Deiana, Vasiliki Tileli, Duncan T. L. Alexander, Stephan Hofmann, Dumitru Dumcenco, Andras Kis, Jean-Pierre Leburton, and Aleksandra Radenovic. Geometrical effect in 2d nanopores. Nano Letters, 17(7):4223–4230, 07 2017.

    Google Scholar 

  22. Christopher A Merchant, Ken Healy, Meni Wanunu, Vishva Ray, Neil Peterman, John Bartel, Michael D Fischbein, Kimberly Venta, Zhengtang Luo, AT Charlie Johnson, et al. Dna translocation through graphene nanopores. Nano letters, 10(8):2915–2921, 2010.

    Google Scholar 

  23. John J. Kasianowicz, Eric Brandin, Daniel Branton, and David W. Deamer. Characterization of individual polynucleotide molecules using a membrane channel. Proceedings of the National Academy of Sciences of the United States of America, 93(24):13770–13773, 1996.

    Article  CAS  PubMed Central  Google Scholar 

  24. Yi Xu, Ping Bai, Xiaodong Zhou, Yuriy Akimov, Ching Eng Png, Lay-Kee Ang, Wolfgang Knoll, and Lin Wu. Optical Refractive Index Sensors with Plasmonic and Photonic Structures: Promising and Inconvenient Truth. Advanced Optical Materials, 7(9):1801433, 2019.

    Google Scholar 

  25. Helen Miller, Zhaokun Zhou, Jack Shepherd, Adam J.M. Wollman, and Mark C. Leake. Single-molecule techniques in biophysics: a review of the progress in methods and applications. Reports on Progress in Physics, 81(2):024601, 2017.

    Google Scholar 

  26. Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, et al. Precision and accuracy of single-molecule fret measurements—a multi-laboratory benchmark study. Nature methods, 15(9):669–676, 2018.

    Google Scholar 

  27. M. Götz, P. Wortmann, S. Schmid, and T. Hugel. A Multicolor Single-Molecule FRET Approach to Study Protein Dynamics and Interactions Simultaneously. Methods in enzymology 581:487–516, 2016.

    Article  Google Scholar 

  28. Wallace H Coulter. Means for counting particles suspended in a fluid. US Patent 2,656,508, 1953.

    Google Scholar 

  29. Hagan Bayley and Charles R Martin. Resistive-pulse sensing from microbes to molecules. Chemical reviews, 100(7):2575–2594, 2000.

    Google Scholar 

  30. Meni Wanunu. Nanopores: A journey towards DNA sequencing. Physics of Life Reviews, 9(2):125–158, 2012.

    Article  PubMed Central  Google Scholar 

  31. Tim Albrecht. Single-Molecule Analysis with Solid-State Nanopores. Annual Review of Analytical Chemistry, 12(1):371–387, 2019.

    Article  Google Scholar 

  32. A. J. Storm, J. H. Chen, X. S. Ling, H. W. Zandbergen, and C. Dekker. Fabrication of solid-state nanopores with single-nanometre precision. Nature Materials, 2(8):537–540, 2003.

    Article  CAS  Google Scholar 

  33. Daniel V. Verschueren, Wayne Yang, and Cees Dekker. Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes. Nanotechnology, 29(14):145302, 2018.

    Article  PubMed Central  Google Scholar 

  34. Harold Kwok, Kyle Briggs, and Vincent Tabard-Cossa. Nanopore fabrication by controlled dielectric breakdown. PloS one, 9(3):92880, 2014.

    Article  Google Scholar 

  35. Benjamin N. Miles, Aleksandar P. Ivanov, Kerry A. Wilson, Fatma Dogan, Deanpen Japrung, and Joshua B. Edel. Single molecule sensing with solid-state nanopores: Novel materials, methods, and applications. Chemical Society Reviews, 42(1):15–28, 2013.

    Article  CAS  Google Scholar 

  36. Stefan W Kowalczyk, Alexander Y Grosberg, Yitzhak Rabin, and Cees Dekker. Modeling the conductance and DNA blockade of solid-state nanopores. Nanotechnology, 22:315101–315106, 2011.

    Google Scholar 

  37. Ralph M.M. Smeets, Ulrich F. Keyser, Diego Krapf, Meng Yue Wu, Nynke H. Dekker, and Cees Dekker. Salt dependence of ion transport and DMA translocation through solid-state nanopores. Nano Letters, 6(1):89–95, 2006.

    Google Scholar 

  38. Daniel Fologea, James Uplinger, Brian Thomas, David S. McNabb, and Jiali Li. Slowing DNA translocation in a solid-state nanopore. Nano Letters, 5(9):1734-1737, 2005.

    Article  CAS  PubMed Central  Google Scholar 

  39. Jiali Li, Derek Stein, Ciaran McMullan, Daniel Branton, Michael J. Aziz, and Jene A. Golovchenko. Ion-beam sculpting at nanometre length scales. Nature, 412(6843):166–169, 2001.

    Article  CAS  Google Scholar 

  40. Laurent D. Menard and J. Michael Ramsey. Fabrication of Sub-5 nm Nanochannels in Insulating Substrates Using Focused Ion Beam Milling. Nano Letters, 11(2):512–517, 2011.

    Google Scholar 

  41. Sergii Pud, Daniel Verschueren, Nikola Vukovic, Calin Plesa, Magnus P. Jonsson, and Cees Dekker. Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown. Nano Letters, 15(10), 2015.

    Google Scholar 

  42. Kyle Briggs, Martin Charron, Harold Kwok, Timothea Le, Sanmeet Chahal, José Bustamante, Matthew Waugh, and Vincent Tabard-Cossa. Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution. Nanotechnology, 26(8), 2015.

    Google Scholar 

  43. Yuning Zhang, Yoichi Miyahara, Nassim Derriche, Wayne Yang, Khadija Yazda, Xavier Capaldi, Zezhou Liu, Peter Grutter, and Walter Reisner. Nanopore Formation via Tip-Controlled Local Breakdown Using an Atomic Force Microscope. Small Methods, 3(7):1900147, 2019.

    Article  Google Scholar 

  44. Jothi Priyanka Thiruraman, Paul Masih Das, and Marija Drndic. Stochastic Ionic Transport in Single Atomic Zero-D Pores. ACS Nano, 14(9):11831-11845, 2020.

    Google Scholar 

  45. Jiali Li, Marc Gershow, Derek Stein, Eric Brandin, and Jene Andrew Golovchenko. Dna molecules and configurations in a solid-state nanopore microscope. Nature materials, 2(9):611–615, 2003.

    Google Scholar 

  46. Mirna Mihovilovic, Nicholas Hagerty, and Derek Stein. Statistics of dna capture by a solid-state nanopore. Physical Review Letters, 110(2):028102, 2013.

    Article  Google Scholar 

  47. A. J. Storm, J. H. Chen, H. W. Zandbergen, and C. Dekker. Translocation of double-strand DNA through a silicon oxide nanopore. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 71(5):051903, 2005.

    Article  CAS  Google Scholar 

  48. Rajesh Kumar Sharma, Ishita Agrawal, Liang Dai, Patrick S. Doyle, and Slaven Garaj. Complex DNA knots detected with a nanopore sensor. Nature Communications, 10(1):4473, 2019.

    Google Scholar 

  49. C Plesa, D Verschueren, S Pud, J Van Der Torre, J W Ruitenberg, M J Witteveen, M P Jonsson, A Y Grosberg, Y Rabin, and C Dekker. Direct observation of DNA knots using a solid-state nanopore. Nature Nanotechnology, 11(12):1093–1097, 2016.

    Article  CAS  Google Scholar 

  50. Calin Plesa, Stefan W Kowalczyk, Ruben Zinsmeester, Alexander Y Grosberg, Yitzhak Rabin, and Cees Dekker. Fast translocation of proteins through solid state nanopores. Nano letters, 13(2):658–663, 2013.

    Google Scholar 

  51. Roman D Bulushev, Sanjin Marion, Ekaterina Petrova, Sebastian J Davis, Sebastian J Maerkl, and Aleksandra Radenovic. Single molecule localization and discrimination of dna–protein complexes by controlled translocation through nanocapillaries. Nano letters, 16(12):7882–7890, 2016.

    Google Scholar 

  52. Erik C. Yusko, Brandon R. Bruhn, Olivia M. Eggenberger, Jared Houghtaling, Ryan C. Rollings, Nathan C. Walsh, Santoshi Nandivada, Mariya Pindrus, Adam R. Hall, David Sept, Jiali Li, Devendra S. Kalonia, and Michael Mayer. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nature Nanotechnology, 12(4), 2017.

    Google Scholar 

  53. Alessio Fragasso, Hendrik W De Vries, John Andersson, Eli O Van Der Sluis, Erik Van Der Giessen, Andreas Dahlin, Patrick R Onck, and Cees Dekker. A designer fg-nup that reconstitutes the selective transport barrier of the nuclear pore complex. Nature communications, 12(1):1–15, 2021.

    Google Scholar 

  54. Philip Ketterer, Adithya N Ananth, Diederik S Laman Trip, Ankur Mishra, Eva Bertosin, Mahipal Ganji, Jaco van der Torre, Patrick Onck, Hendrik Dietz, and Cees Dekker. Dna origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex. Nature communications, 9(1):1–8, 2018.

    Google Scholar 

  55. Stefan W Kowalczyk, Timothy R Blosser, and Cees Dekker. Biomimetic nanopores: learning from and about nature. Trends in biotechnology, 29(12):607–614, 2011.

    Google Scholar 

  56. Nicole E. Weckman, Niklas Ermann, Richard Gutierrez, Kaikai Chen, James Graham, Ran Tivony, Andrew Heron, and Ulrich F. Keyser. Multiplexed DNA Identification Using Site Specific dCas9 Barcodes and Nanopore Sensing. ACS Sensors, 4(8):2065–2072, 2019.

    Article  CAS  Google Scholar 

  57. J Y Y Sze, A P Ivanov, A E G Cass, and J B Edel. Single molecule multiplexed nanopore protein screening in human serum using aptamer modified DNA carriers. Nature Communications, 8(1):1-10, 2017.

    Article  CAS  Google Scholar 

  58. RMM Smeets, Stefan W Kowalczyk, AR Hall, NH Dekker, and C Dekker. Translocation of reca-coated double-stranded dna through solid-state nanopores. Nano letters, 9(9):3089–3095, 2009.

    Google Scholar 

  59. Kaikai Chen, Matyas Juhasz, Felix Gularek, Elmar Weinhold, Yu Tian, Ulrich F Keyser, and Nicholas AW Bell. Ionic current-based mapping of short sequence motifs in single dna molecules using solid-state nanopores. Nano letters, 17(9):5199–5205, 2017.

    Google Scholar 

  60. Aleksandre Japaridze, Wayne Yang, Cees Dekker, William Nasser, and Georgi Muskhelishvili. Dna sequence-directed cooperation between nucleoid-associated proteins. iScience, 24(5):102408, 2021.

    Google Scholar 

  61. Wayne Yang, Laura Restrepo-Pérez, Michel Bengtson, Stephanie J. Heerema, Anthony Birnie, Jaco van der Torre, and Cees Dekker. Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores. Nano Letters, 18(10):6469–6474, 2018.

    Article  CAS  PubMed Central  Google Scholar 

  62. Stefan W Kowalczyk, David B Wells, Aleksei Aksimentiev, and Cees Dekker. Slowing down dna translocation through a nanopore in lithium chloride. Nano letters, 12(2):1038–1044, 2012.

    Google Scholar 

  63. Stephen E Halford and John F Marko. How do site-specific dna-binding proteins find their targets? Nucleic acids research, 32(10):3040–3052, 2004.

    Google Scholar 

  64. Alessio Fragasso, Sonja Schmid, and Cees Dekker. Comparing current noise in biological and solid-state nanopores. ACS nano, 14(2):1338–1349, 2020.

    Article  CAS  PubMed Central  Google Scholar 

  65. Alessio Fragasso, Sergii Pud, and Cees Dekker. 1/f noise in solid-state nanopores is governed by access and surface regions. Nanotechnology, 30(39):395202, 2019.

    Article  CAS  Google Scholar 

  66. Chenyu Wen, Shuangshuang Zeng, Kai Arstila, Timo Sajavaara, Yu Zhu, Zhen Zhang, and Shi Li Zhang. Generalized Noise Study of Solid-State Nanopores at Low Frequencies. ACS Sensors, 2(2):300–307, 2017.

    Google Scholar 

  67. Ralph MM Smeets, Ulrich F Keyser, Nynke H Dekker, and Cees Dekker. Noise in solid-state nanopores. Proceedings of the National Academy of Sciences, 105(2):417–421, 2008.

    Google Scholar 

  68. Calin Plesa, Justus W. Ruitenberg, Menno J. Witteveen, and Cees Dekker. Detection of individual proteins bound along DNA using solid-state nanopores. Nano Letters, 15(5):3153-3158, 2015.

    Article  CAS  Google Scholar 

  69. Calin Plesa, Nick Van Loo, Philip Ketterer, Hendrik Dietz, and Cees Dekker. Velocity of dna during translocation through a solid-state nanopore. Nano letters, 15(1):732–737, 2015.

    Article  CAS  Google Scholar 

  70. Jacob K Rosenstein, Meni Wanunu, Christopher A Merchant, Marija Drndic, and Kenneth L Shepard. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nature methods, 9(5):487, 2012.

    Google Scholar 

  71. Adrian Balan, Chen-Chi Chien, Rebecca Engelke, and Marija Drndić. Suspended solid-state membranes on glass chips with sub 1-pf capacitance for biomolecule sensing applications. Scientific reports, 5(1):1–8, 2015.

    Google Scholar 

  72. Min-Hyun Lee, Ashvani Kumar, Kyeong-Beom Park, Seong-Yong Cho, Hyun-Mi Kim, Min-Cheol Lim, Young-Rok Kim, and Ki-Bum Kim. A low-noise solid-state nanopore platform based on a highly insulating substrate. Scientific reports, 4(1):1–7, 2014.

    CAS  Google Scholar 

  73. Sonja Schmid, Pierre Stömmer, Hendrik Dietz, and Cees Dekker. Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations. bioRxiv, 2021.

    Google Scholar 

  74. Sonja Schmid and Cees Dekker. Nanopores: a versatile tool to study protein dynamics. Essays in Biochemistry, 65(1):93–107, 2021.

    Article  CAS  Google Scholar 

  75. Grégory F. Schneider, Qiang Xu, Susanne Hage, Stephanie Luik, Johannes N. H. Spoor, Sairam Malladi, Henny Zandbergen, and Cees Dekker. Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation. Nature Communications, 4(1):2619, 2013.

    Google Scholar 

  76. Stephanie J. Heerema and Cees Dekker. Graphene nanodevices for DNA sequencing. Nature Nanotechnology, 11(2):127–136, 2016.

    Article  CAS  Google Scholar 

  77. Michael Graf, Martina Lihter, Damir Altus, Sanjin Marion, and Aleksandra Radenovic. Transverse Detection of DNA Using a MoS2 Nanopore. Nano Letters, 19(12):9075–9083, 2019.

    Article  CAS  Google Scholar 

  78. Mingye Xiong, Michael Graf, Nagendra Athreya, Aleksandra Radenovic, and Jean-Pierre Leburton. Microscopic detection analysis of single molecules in mos2 membrane nanopores. ACS nano, 14(11):16131–16139, 2020.

    Article  Google Scholar 

  79. Wayne Yang, Boya Radha, Adnan Choudhary, Yi You, Gangaiah Mettela, Andre K Geim, Aleksei Aksimentiev, Ashok Keerthi, and Cees Dekker. Translocation of dna through ultrathin nanoslits. Advanced Materials, 33(11):2007682, 2021.

    Google Scholar 

  80. B Radha, Ali Esfandiar, FC Wang, AP Rooney, K Gopinadhan, Ashok Keerthi, Artem Mishchenko, Amritha Janardanan, Peter Blake, Laura Fumagalli, et al. Molecular transport through capillaries made with atomic-scale precision. Nature, 538(7624):222–225, 2016.

    Google Scholar 

  81. C. Genet and T. W. Ebbesen. Light in tiny holes. Nature, 445(7123):39–46, 2007.

    Article  CAS  Google Scholar 

  82. Thomas W Ebbesen, Henri J Lezec, HF Ghaemi, Tineke Thio, and Peter A Wolff. Extraordinary optical transmission through sub-wavelength hole arrays. Nature, 391(6668):667–669, 1998.

    Google Scholar 

  83. Daniel V. Verschueren, Sergii Pud, Xin Shi, Lorenzo De Angelis, L. Kuipers, and Cees Dekker. Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores. ACS Nano, 13(1):61–70, 2019.

    Google Scholar 

  84. Mathieu L. Juan, Reuven Gordon, Yuanjie Pang, Fatima Eftekhari, and Romain Quidant. Self-induced back-action optical trapping of dielectric nanoparticles. Nature Physics, 5(12):915–919, 2009.

    Article  CAS  Google Scholar 

  85. Avijit Barik, Lauren M Otto, Daehan Yoo, Jincy Jose, Timothy W Johnson, and Sang-Hyun Oh. Dielectrophoresis-Enhanced Plasmonic Sensing with Gold Nanohole Arrays. Nano Letters, 14:2020, 2014.

    Google Scholar 

  86. Seung Ju Yoon, Jungmin Lee, Sangyoon Han, Chang Kyu Kim, Chi Won Ahn, Myung Ki Kim, and Yong Hee Lee. Non-fluorescent nanoscopic monitoring of a single trapped nanoparticle via nonlinear point sources. Nature Communications, 9(1):341401, 2018.

    Google Scholar 

  87. James V Coe, Joseph M Heer, Shannon Teeters-Kennedy, Hong Tian, and Kenneth R Rodriguez. Extraordinary transmission of metal films with arrays of subwavelength holes. Annu. Rev. Phys. Chem., 59:179–202, 2008.

    Google Scholar 

  88. Reuven Gordon. Biosensing with nanoaperture optical tweezers. Optics & Laser Technology, 109:328–335, 2019.

    Article  CAS  Google Scholar 

  89. Pau Mestres, Johann Berthelot, Srdjan S Aćimović, and Romain Quidant. Unraveling the optomechanical nature of plasmonic trapping. Light: Science & Applications, 5(7):16092–16092, 2016.

    Google Scholar 

  90. Serap Aksu, Ahmet A. Yanik, Ronen Adato, Alp Artar, Min Huang, and Hatice Altug. High-throughput nanofabrication of infrared plasmonic nanoantenna arrays for vibrational nanospectroscopy. Nano Letters, 10(7):2511–2518, 2010.

    Article  CAS  Google Scholar 

  91. Xin Shi, Daniel Verschueren, Sergii Pud, and Cees Dekker. Integrating Sub-3 nm Plasmonic Gaps into Solid-State Nanopores. Small, 14(18):1703307, 2018.

    Article  Google Scholar 

  92. Myung Ki Kim, Hongchul Sim, Seung Ju Yoon, Su Hyun Gong, Chi Won Ahn, Yong Hoon Cho, and Yong Hee Lee. Squeezing Photons into a Point-Like Space. Nano Letters, 15(6):4102–4107, 2015.

    Google Scholar 

  93. Alemayehu Nana Koya, Joao Cunha, Tian-Long Guo, Andrea Toma, Denis Garoli, Tao Wang, Saulius Juodkazis, Dan Cojoc, and Remo Proietti Zaccaria. Novel plasmonic nanocavities for optical trapping-assisted biosensing applications. Advanced Optical Materials, 8(7):1901481, 2020.

    Google Scholar 

  94. Mathieu L Juan, Maurizio Righini, and Romain Quidant. Plasmon nano-optical tweezers. Nature photonics, 5(6):349, 2011.

    Google Scholar 

  95. Abhay Kotnala and Reuven Gordon. Double nanohole optical tweezers visualize protein p53 suppressing unzipping of single dna-hairpins. Biomedical optics express, 5(6):1886–1894, 2014.

    Article  PubMed Central  Google Scholar 

  96. M Righini, P Ghenuche, S Cherukulappurath, Viktor Myroshnychenko, Francisco Javier Garcia de Abajo, and Romain Quidant. Nano-optical trapping of rayleigh particles and escherichia coli bacteria with resonant optical antennas. Nano letters, 9(10):3387–3391, 2009.

    Google Scholar 

  97. Yuanjie Pang and Reuven Gordon. Optical trapping of a single protein. Nano Letters, 12(1):402–406, 2012.

    Article  CAS  Google Scholar 

  98. Daniel Verschueren, Xin Shi, and Cees Dekker. Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores. Small Methods, 3(5):1800465, 2019.

    Article  Google Scholar 

  99. Ana Zehtabi-Oskuie, Hao Jiang, Bryce R. Cyr, Douglas W. Rennehan, Ahmed A. Al-Balushi, and Reuven Gordon. Double nanohole optical trapping: Dynamics and protein-antibody co-trapping. Lab on a Chip, 13(13):2563–2568, 2013.

    Article  CAS  Google Scholar 

  100. Xin Shi, Daniel V. Verschueren, and Cees Dekker. Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing. Nano Letters, 18(12):8003–8010, 2018.

    Article  CAS  PubMed Central  Google Scholar 

  101. Noa Hacohen, Candice JX Ip, and Reuven Gordon. Analysis of egg white protein composition with double nanohole optical tweezers. ACS omega, 3(5):5266–5272, 2018.

    Google Scholar 

  102. Quanbo Jiang, Benoit Rogez, Jean-Benoît Claude, Guillaume Baffou, and Jérôme Wenger. Temperature measurement in plasmonic nanoapertures used for optical trapping. ACS photonics, 6(7):1763–1773, 2019.

    Article  CAS  Google Scholar 

  103. Liselotte Jauffred, Akbar Samadi, Henrik Klingberg, Poul Martin Bendix, and Lene B Oddershede. Plasmonic heating of nanostructures. Chemical reviews, 119(13):8087–8130, 2019.

    CAS  Google Scholar 

  104. Colin R Crick, Pablo Albella, Hyung-Jun Kim, Aleksandar P Ivanov, Ki-Bum Kim, Stefan A Maier, and Joshua B Edel. Low-noise plasmonic nanopore biosensors for single molecule detection at elevated temperatures. ACS Photonics, 4(11):2835–2842, 2017.

    Google Scholar 

  105. Ulrich F Keyser, Diego Krapf, Bernard N Koeleman, Ralph MM Smeets, Nynke H Dekker, and Cees Dekker. Nanopore tomography of a laser focus. Nano letters, 5(11):2253–2256, 2005.

    Google Scholar 

  106. Francesca Nicoli, Daniel Verschueren, Misha Klein, Cees Dekker, and Magnus P Jonsson. Dna translocations through solid-state plasmonic nanopores. Nano letters, 14(12):6917–6925, 2014.

    Google Scholar 

  107. Brian J Roxworthy, Abdul M Bhuiya, Surya P Vanka, and Kimani C Toussaint. Understanding and controlling plasmon-induced convection. Nature communications, 5(1):1–8, 2014.

    Google Scholar 

  108. Erik Schäffer, Simon F Nørrelykke, and Jonathon Howard. Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers. Langmuir, 23(7):3654–3665, 2007.

    Google Scholar 

  109. Bita Malekian, Kunli Xiong, Evan SH Kang, John Andersson, Gustav Emilsson, Marcus Rommel, Takumi Sannomiya, Magnus P Jonsson, and Andreas Dahlin. Optical properties of plasmonic nanopore arrays prepared by electron beam and colloidal lithography. Nanoscale Advances, 1(11):4282–4289, 2019.

    Google Scholar 

  110. Liang Pan, Yongshik Park, Yi Xiong, Erick Ulin-Avila, Yuan Wang, Li Zeng, Shaomin Xiong, Junsuk Rho, Cheng Sun, David B Bogy, and Xiang Zhang. Maskless plasmonic lithography at 22 nm resolution. Scientific reports, 1(1):1–6, 2011.

    Google Scholar 

  111. Quanbo Jiang, Benoît Rogez, Jean-Benoît Claude, Antonin Moreau, Julien Lumeau, Guillaume Baffou, and Jérôme Wenger. Adhesion layer influence on controlling the local temperature in plasmonic gold nanoholes. Nanoscale, 12(4):2524–2531, 2020.

    Article  CAS  Google Scholar 

  112. Kai Wang, Ethan Schonbrun, Paul Steinvurzel, and Kenneth B. Crozier. Trapping and rotating nanoparticles using a plasmonic nano-tweezer with an integrated heat sink. Nature Communications, 2(1):1–6, 2011.

    Article  Google Scholar 

  113. H. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, and W. W. Webb. Zero-mode waveguides for single-molecule analysis at high concentrations. Science, 299(5607):682–686, 2003.

    Article  CAS  Google Scholar 

  114. Ossama N. Assad, Tal Gilboa, Joshua Spitzberg, Matyas Juhasz, Elmar Weinhold, and Amit Meller. Light-Enhancing Plasmonic-Nanopore Biosensor for Superior Single-Molecule Detection. Advanced Materials, 29(9):1605442, 2017.

    Article  Google Scholar 

  115. Joseph Larkin, Robert Y Henley, Vivek Jadhav, Jonas Korlach, and Meni Wanunu. Length-independent dna packing into nanopore zero-mode waveguides for low-input dna sequencing. Nature nanotechnology, 12(12):1169–1175, 2017.

    Google Scholar 

  116. Joshua D Spitzberg, Adam Zrehen, Xander F van Kooten, and Amit Meller. Plasmonic-nanopore biosensors for superior single-molecule detection. Advanced Materials, 31(23):1900422, 2019.

    Google Scholar 

  117. Justus C Ndukaife, Alexander V Kildishev, Agbai George, Agwu Nnanna, Vladimir M Shalaev, Steven T Wereley, and Alexandra Boltasseva. Long-range and rapid transport of individual nano-objects by a hybrid electrothermoplasmonic nanotweezer. Natue Nanotechnology, 11, 2016.

    Google Scholar 

  118. Ben McNally, Alon Singer, Zhiliang Yu, Yingjie Sun, Zhiping Weng, and Amit Meller. Optical recognition of converted dna nucleotides for single-molecule dna sequencing using nanopore arrays. Nano letters, 10(6):2237–2244, 2010.

    Article  CAS  PubMed Central  Google Scholar 

  119. Brett N Anderson, Ossama N Assad, Tal Gilboa, Allison H Squires, Daniel Bar, and Amit Meller. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS nano, 8(11):11836–11845, 2014.

    Google Scholar 

  120. Tal Gilboa and Amit Meller. Optical sensing and analyte manipulation in solid-state nanopores. Analyst, 140(14):4733–4747, 2015.

    Article  CAS  Google Scholar 

  121. Tal Gilboa, Adam Zrehen, Arik Girsault, and Amit Meller. Optically-monitored nanopore fabrication using a focused laser beam. Scientific reports, 8(1):1–10, 2018.

    Article  CAS  Google Scholar 

  122. Tal Gilboa, Eran Zvuloni, Adam Zrehen, Allison H. Squires, and Amit Meller. Automated, Ultra-Fast Laser-Drilling of Nanometer Scale Pores and Nanopore Arrays in Aqueous Solutions. Advanced Functional Materials, 30(18):1900642, 2020.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Alessio Fragasso, Xin Shi and Sonja Schmid for fruitful discussions. C.D would like to acknowledge funding from ERC grant SynDiv 669598 and the Netherlands Organization for Scientific Research (NWO/OCW) as part of the Frontiers of Nanoscience and Basyc programs.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Cees Dekker .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Yang, W., Dekker, C. (2022). Single-Molecule Ionic and Optical Sensing with Nanoapertures. In: Bowen, W., Vollmer, F., Gordon, R. (eds) Single Molecule Sensing Beyond Fluorescence . Nanostructure Science and Technology. Springer, Cham. https://doi.org/10.1007/978-3-030-90339-8_12

Download citation

Publish with us

Policies and ethics