Nanoelectronics for DNA Sensing

  • Predrag S. Krstić
Part of the Nanostructure Science and Technology book series (NST)


The human genome sequencing is the fastest developing field of the contemporary science, possibly offering significant contribution to the personalized medicine–a cheap and fast tabletop single molecule reading device on a chip. This can be achieved with physical methods, based on the reading of an electrical response while a segment of a DNA molecule is passing through a synthetic nanopore. The challenges, and possible solutions to the problems of sensitivity of the electrical reading as well as to the control of a DNA localization and motion are considered.


Tunneling Current Resonant Tunneling Paul Trap Quadrupole Trap Linear Paul Trap 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the U.S. National Human Genome Research Institute of the National Institutes of Health under grant no. 1R21HG004764-01. The author acknowledges support by U.S. Department of Energy (DOE) at ORNL managed by a UT-Battelle for the U.S. DOE under contract no. DEAC05-00OR22725, by the U.S. DOE, and U.S. NHGRI under grant no. 1 R21 HG003578-01. A portion of this research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at ORNL by the Division of Scientific User Facilities, U.S. DOE.


  1. 1.
    Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., Jovanovich, S.B., Krstic, P.S., Lindsay, S., Ling, X.S., Mastrangelo, C.H., Meller, A., Oliver, J.S., Pershin, Y.V., Ramsey, J.M., Riehn, R., Soni, G.V., Tabard-Cossa, V., Wanunu, M., Wiggin, M., Schloss, J.A.: The Potential and Challenges of Nanopore Sequencing. Nature Biotechnol. 26, 1146 (2008)CrossRefGoogle Scholar
  2. 2.
    S. Joseph, W. Guan, M.A. Reed, and P.S. Krstic: A long DNA segment in a linear nanoscale Paul trap. Nanotechnol. 21, 015103 (2010)Google Scholar
  3. 3.
    Haitao Liu, Jin He, Jinyao Tang, Hao Liu, Pei Pang, Di Cao, Predrag Krstic, Sony Joseph, Stuart Lindsay, Colin Nuckolls: Translocation of Single-Stranded DNA Through Single-Walled Carbon Nanotubes. Science 327, 64 (2010)CrossRefGoogle Scholar
  4. 4.
    Chan, E.Y.: Advances in sequencing technology. Mutat. Res. Fund. Mol. Mech. Mut. 573 13–40 (2005)CrossRefGoogle Scholar
  5. 5.
    Fredlake, C. P., Hert, D. G., Mardis, E. R., Barron, A. E.: What is the future of electrophoresis in large-scale genomic sequencing? Electrophoresis 27, 3689–702 (2006)CrossRefGoogle Scholar
  6. 6.
    Healy, K.: Nanopore-based single-molecule DNA analysis. Nanomedicine 2, 459–81 (2007)CrossRefGoogle Scholar
  7. 7.
    Kricka, L. J., Park, J. Y., Li, S. F. Y. Fortina, P.: Miniaturized detection technology in molecular diagnostics. Exp. Rev. Mol. Diagn. 5, 549–59 (2005)CrossRefGoogle Scholar
  8. 8.
    Nakane, J. J., Akeson, M., Marziali, A.: Nanopore sensors for nucleic acid analysis. J. Phys.: Condens. Matter 15, R1365–R1393 (2003)CrossRefGoogle Scholar
  9. 9.
    Rhee, M., Burns, M. A.: Nanopore sequencing technology: Research trends and applications. Trends Biotechnol. 24, 580–6 (2006)CrossRefGoogle Scholar
  10. 10.
    Rhee, M., Burns, M. A.: Nanopore sequencing technology: Nanopore preparations. Trends. Biotechnol. 25, 174–81 (2007)CrossRefGoogle Scholar
  11. 11.
    Ryan, D., Rahimi, M., Lund, J., Mehta, R., Parviz, B. A.: Toward nanoscale genome sequencing. Trends Biotechnol. 25, 385–9 (2007)CrossRefGoogle Scholar
  12. 12.
    Lagerqvist, J., Zwolak, M., Di Ventra, M.: Comment on Characterization of the tunneling conductance across DNA bases. Phys. Rev. E 76, 013901 (2007)CrossRefGoogle Scholar
  13. 13.
    Tabard-Cossa, V., Trivedi, D., Wiggin, M., Jetha, N. N., Marziali, A.: Noise analysis and reduction in solid-state nanopores. Nanotechnology 18 305505 (2007)CrossRefGoogle Scholar
  14. 14.
    Zhang, X.-G., Krstic, P.S., Zikic, R., Wells, J. C., Fuentes-Cabrera, M.: First-principles transversal DNA conductance deconstructed. Biophys. J. 91, L04 (2006)CrossRefGoogle Scholar
  15. 15.
    Zikic, R., Krstic, P.S., Zhang, X.-G., Fuentes-Cabrera, M., Wells, J., Zhao, X.C.: Characterization of the tunneling conductance across DNA bases. Phys. Rev. E 74, 011919 (2006)CrossRefGoogle Scholar
  16. 16.
    Trepagnier, E. H., Radenovic, A., Sivak, D., Geissler, P., Liphardt, J.: Controlling DNA capture and propagation through artificial nanopores. Nano Lett. 7, 2824–30 (2007)CrossRefGoogle Scholar
  17. 17.
    Tsai, Y.S., Chen, C.M.: Driven polymer transport through a nanopore controlled by a rotating electric field: off-lattice computer simulations. J. Chem. Phys. 126, 144910 (2007)CrossRefGoogle Scholar
  18. 18.
    Chen, C.M., Peng, E.H.: Nanopore sequencing of polynucleotides assisted by a rotating electric field. Appl. Phys. Lett. 82 1308–10 (2003)CrossRefGoogle Scholar
  19. 19.
    Paul, W.: Electromagnetic traps for charged and neutral particles. Rev. Mod. Phys. 62, 531 (1990)CrossRefGoogle Scholar
  20. 20.
    Zhao, X., Krstic, P.S.: A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap. Nanotechnology 19, 195702(2008)CrossRefGoogle Scholar
  21. 21.
    Arnott, D., Henzel, W.J., Stults, J.T.: Rapid identification of comigrating gel-isolated proteins by ion trap mass spectrometry. Electrophoresis 19, 968–80 (1998)CrossRefGoogle Scholar
  22. 22.
    Zikic, R., Krstic, P.S., Zhang, X.-G., Fuentes-Cabrera, M., Wells, J., Zhao, X.C.: Comment on Characterization of the tunneling conductance across DNA bases. Reply, Phys. Rev. E 76, 013902 (2007)CrossRefGoogle Scholar
  23. 23.
    Meunier, V., Krstic, P.S.: Enhancement of the Transverse Conductance in DNA nucleotides. J. Chem. Phys. 128, 041103 (2008)CrossRefGoogle Scholar
  24. 24.
    Zhao, X.C., Payne, C.M., Cummings, P.T., Lee, J.W.: Single stranded DNA molecules translocation through nanoelectrode gaps. Nanotechnology 18, 424018 (2007)CrossRefGoogle Scholar
  25. 25.
    Zhao, X.C., Payne, C.M., Cummings, P.T.: Controlled translocation of DNA segments through nanoelectrode gaps from molecular dynamics. J. Phys. Chem. C 112, 8 (2008)Google Scholar
  26. 26.
    Payne, C.M., Zhao, X.C., Vlcek, L., Cummings, P.T.: Molecular dynamics simulation of ss-DNA translocation through a copper nanoelectrode gap. J. Phys. Chem. B112, 1712 (2008)Google Scholar
  27. 27.
    Payne, C.M., Zhao, X.C., Cummings, P.T.: Molecular simulation of DNA transport in solution. Mol. Simulat. 33, 399 (2007)CrossRefGoogle Scholar
  28. 28.
    Predrag Krstic, Erica Forzani, Nongjian Tao, Anatoli Korkin, Design and function of molecular and bioelectronics devices. Editorial Nanotechnol 18, 420201 (2007)Google Scholar
  29. 29.
    Miguel Fuentes-Cabrera, Vincent Meunier, Bobby G Sumpter, Benzo homologated nucleobases in a nanotube-electrode set-up for DNA sequencing. Nanotechnology 18, 424019 (2007)CrossRefGoogle Scholar
  30. 30.
    Krstic, P.S., Wells, J.C., Miguel Fuentes-Cabrera, Dong Hu, Lee, J.W.: Toward Electronic Conductance Characterization of DNA Nucleotide Bases. Solid State Phenomena 121–123, 1387 (2007)CrossRefGoogle Scholar
  31. 31.
    Krstic, P.S., Meunier, V.: Sensing Single Molecules Between Doped Carbon Nanotubes, Invention disclosure, Docket #: 1300001981, DOE S#: S-111, 599 (August 2007)Google Scholar
  32. 32.
    Lee, J.W., Thundat, T.G., Greenbaum, E.: DNA and RNA sequencing by nanoscale reading through programmable electrophoresis and nanoelectrode-gated tunneling and dielectric detection, US Patent No. 6905586 (2005)Google Scholar
  33. 33.
    Cui, X.D., Primak, A., Zarate, X., Tomfohr, J., Sankey, O.F., Moore, A.L., Moore, T.A., Gust, D., Harris, G., Lindsay, S.M.: Reproducible measurement of single-molecule conductivity. Science 294, 571 (2001)CrossRefGoogle Scholar
  34. 34.
    Reed, M.A., Zhao, C., Muller, C.J., Burgin, T.P., Tour, J.M.: Conductance of a molecular junction. Science 278, 252 (1997)CrossRefGoogle Scholar
  35. 35.
    Roy, S., Vedala, H., Datta Roy, A., Do-h Kim, Doud, M., Mathee, K., Shin, H-k, Shimamoto, N., Prasad, V., Choi, W.: Direct Electrical Measurements on Single-Molecule Genomic DNA Using Single-Walled Carbon Nanotubes. Nano Letter 8, 26 (2008)CrossRefGoogle Scholar
  36. 36.
    Tao, N.J.: Electron transport in molecular junctions. Nature Nanotechnol. 1, 173 (2006)CrossRefGoogle Scholar
  37. 37.
    Leibfried, D., Blatt, R., Monroe, C., Wineland, D.: Quantum dynamics of single trapped ions. Rev. Mod. Phys. 75, 281–324 (2003)CrossRefGoogle Scholar
  38. 38.
    Vant, K., Chiaverini, J., Lybarger, W., Berkeland, D.J.: Photoionization of strontium for trapped-ion quantum information processing arXiv:quant-ph 0607055 (2006)Google Scholar
  39. 39.
    Seidelin, S., Chiaverini, J., Reichle, R., Bollinger, J.J., Leibfried, D., Britton, J., Wesenberg, J.H., Blakestad, R.B., Epstein, R.J., Hume, D.B., Itano, W.M., Jost, J.D., Langer, C., Ozeri, R., Shiga, N., Wineland, D.J.: Microfabricated surface-electrode ion trap for scalable quantum information processing. Phys. Rev. Lett. 96, 253003 (2006)CrossRefGoogle Scholar
  40. 40.
    Wineland, D.J., Monroe, C., Itano, W.M., Leibfried, D., King, B.E., Meekhof, D.M.: Experimental issues in coherent quantum-state manipulation of trapped atomic ions J. Res Natl. Inst. Stand. Technol 103, 259–328 (1998)Google Scholar
  41. 41.
    Abich, K., Keil, A., Reiss, D., Wunderlich, C., Neuhauser, W., Toschek, P.E.: Thermally activated hopping of two ions trapped in a bistable potential well. J. Optics B-Quant Semiclassical Optics 6, S18–S23 (2004)CrossRefGoogle Scholar
  42. 42.
    Schiffer, J.P.: Order in confined ions. J. Phys. B-Atomic Mol. Optical Phys. 36, 511–23 (2003)CrossRefGoogle Scholar
  43. 43.
    Shi, L., Zhu, X.W., Feng, M., Fang, X.M.: Ordered structures of a few ions. Paul trap Commun. Theor. Phys. 31, 491–6 (1999)Google Scholar
  44. 44.
    Itano, W.M., Bergquist, J.C., Bollinger, J.J., Wineland, D.J.: Cooling methods in ion traps. Phys. Scripta T59, 106–20 (1995)CrossRefGoogle Scholar
  45. 45.
    Walther, H.: From a single-ion to a mesoscopic system—crystallization of ions. Paul traps Physica Scripta T59, 360–8 (1995)CrossRefGoogle Scholar
  46. 46.
    Edwards, C.S., Gill, P., Klein, H.A., Levick, A.P., Rowley, W.R.C.: Laser-cooling effects in few-ion clouds of YB+. Appl. Phys. B-Lasers Optics 59, 179–85 (1994)CrossRefGoogle Scholar
  47. 47.
    Hasegawa, T., Uekara, K.: Appl. Phys. B 1995, 61, 159–163Google Scholar
  48. 48.
    Chicone, C.: Ordinary Differential Equations with Applications, 2nd edn, Texts in Applied Mathematics, NewYork: Springer Verlag (2006)Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Physics DivisionOak Ridge National LaboratoryOak RidgeUSA

Personalised recommendations