SPICE-Circuit Simulation of the Electrical Response of a Semiconductor Membrane to a Single-Stranded DNA Translocating Through a Nanopore

Leroux, Amandine; Destiné, Jacques; Vanderheyden, Benoît; Gracheva, Maria; Leburton, Jean-Pierre

doi:10.1109/TNANO.2010.2043957

Article (Scientific journals)

SPICE-Circuit Simulation of the Electrical Response of a Semiconductor Membrane to a Single-Stranded DNA Translocating Through a Nanopore

Leroux, Amandine; Destiné, Jacques; Vanderheyden, Benoît et al.

2010 • In IEEE Transactions on Nanotechnology, 9 (3), p. 322-329

Peer reviewed

Permalink
https://hdl.handle.net/2268/74015

DOI
10.1109/TNANO.2010.2043957

Files (1)Send to Details Statistics Bibliography Similar publications

Files

Full Text

Abstract.pdf

Author postprint (18.5 kB)

Download

All documents in ORBi are protected by a user license.

Send to

RIS BibTex APA Chicago Permalink X Linkedin

Details

Keywords :

Circuit modeling; DNA sequencing; Solid-state nanopore; Spice simulation

Abstract :

[en] In this paper, we describe a circuit-element model for the electric detection of biomolecules in translocation through a nanopore in a semiconductor-oxide-semiconductor (SOS) membrane. The biomolecules are simulated as a superposition of individual charges moving through the nanopore and inducing a charge variation on the membrane electrodes that is modeled as a current source. The SOS membrane is discretized into interconnected elementary circuit elements. The model is tested on the translocation of 11 base single-stranded C3AC7 DNA molecule, for which the electric signal shows good qualitative agreement with the multiscale device approach of Gracheva et al., while quantifying the low-pass filtering in the membrane. Overall, the model confirms the possibility of identifying the sequence of the DNA bases electrically.

Disciplines :

Electrical & electronics engineering

Author, co-author :

Leroux, Amandine ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Dép. d'électric., électron. et informat. (Inst.Montefiore)

Destiné, Jacques ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Electronique, microsystèmes, mesures et instrumentation

Vanderheyden, Benoît ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Electronique et microsystèmes

Gracheva, Maria; Clarkson University > Department of Physics

Leburton, Jean-Pierre; University of Illinois at Urbana-Champaign > Beckman Institute for Advanced Science and Technology and Department of Electrical Engineering

Language :

English

Title :

SPICE-Circuit Simulation of the Electrical Response of a Semiconductor Membrane to a Single-Stranded DNA Translocating Through a Nanopore

Publication date :

May 2010

Journal title :

IEEE Transactions on Nanotechnology

Volume :

Issue :

Pages :

322-329

Peer reviewed :

Peer reviewed

Available on ORBi :

since 17 October 2010

Statistics

Number of views

258 (32 by ULiège)

Number of downloads

269 (18 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

OpenAlex citations

Bibliography

J. C. Skou, "The influence of some cations on an adenosine triphosphatase from peripheral nerves, " Biochim. Biophys. Acta., vol. 23, pp. 394-401, Feb. 1957.
B. Alberts, D. Bray, A. Jonhson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Essential Cell Biology. New York: Garland, 1998.
J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, "Characterization of individual polynucleotide molecules using a membrane channel, " Proc. Nat. Acad. Sci., vol. 93, pp. 13770-13773, Nov. 1996.
M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, and D. W. Deamer, "Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homoplymers or as segments within single RNA molecules, " Biophys., vol. 77, pp. 3227-3233, Dec. 1999.
D. Fologea, E. Brandin, J. Uplinger, D. Branton, and J. Li, "DNA conformation and base number simultaneously determined in nanopore, " Electrophoresis, vol. 28, pp. 3186-3192, Sep. 2007.
J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. Grinkova, S. Sligar, K. Schulten, and G. Timp, "Sizing DNA using a nanometer-diameter pore, " Biophys. J., vol. 87, pp. 2905-2911, Oct. 2004.
M. E. Gracheva, A. Xiong, J.-P. Leburton, A. Aksimentiev, K. Schulten, and G. Timp, "Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor, " Nanotechnology, vol. 17, pp. 622-633, Feb. 2006.
J. B. Heng, V. Dimitrov, Y. V. Grinkova, C. Ho, T. Kim, D. Muller, S. Sligar, T. Sorsch, R. Twesten, R. Timp, and G. Timp, "The detection of DNA using a silicon nanopore, " IEDM Tech. Dig., vol. 8, pp. 767-770, Sep. 2003.
J. Vidal, M. E. Gracheva, and J.-P. Leburton, "Electrically tunable solidstate silicon nanopore ion filter, " Nanoscale Res. Lett., vol. 2, pp. 61-68, Feb. 2007.
A. J. Storm, J. H. Chen, X. S. Ling, H. W. Zandbergen, and C. Dekker, "Fabrication of solid-state nanopores with single-nanometre precision, " Nat. Mater., vol. 2, pp. 537-540, Jul. 2003.
L. Petrossian, S. J. Wilk, P. Joshi, S. Hihath, S. M. Goodnick, and T. J. Thornton, "Fabrication of cylindrical nanopores and nanopore arrays in silicon-on-insulator substrates, " Microelectromech. Syst., vol. 16, pp. 1419-1428, Dec. 2007. (Pubitemid 350239135)
M. E. Gracheva, A. Aksimentiev, and J.-P. Leburton, "Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor, " Nanotechnology, vol. 17, pp. 3160-3165, Jul. 2006.
A. Aksimentiev, J. B. Heng, G. Timp, and K. Schulten, "Microscopic kinetics of DNA translocation through synthetic nanopores, " Biophys. J., vol. 87, pp. 2086-2097, Sep. 2004.
S. Tryka, "A method for calculating the average solid angle subtended by a circular disk from uniformly distributed points within a coaxial circular plane, " Rev. Sci. Instrum., vol. 70, pp. 3915-3920, Oct. 1999.
L. A. Geddes and L. E. Bake, Principles of Applied Biomedical Instrumentation, 3rd ed. New York: Willey-Interscience, 1989.
A. J. Bard and L. R. Faulkner, Electrochemical Methods. New York: Wiley-Interscience, 1980.
S. Martinoia and G. Massobrio, "A behaviorial macromodel of the ISFET in spice, " Sens. Actuators, vol. 62, pp. 182-189, 2000.