0
SPECIAL SECTION: SIMULATION AND EXPERIMENTAL STUDIES AND APPLICATIONS OF CARBON NANOTUBES AND GRAPHENES IN ENGINEERING AND MEDICINE: Guest Editorial

Gene Detection With Carbon Nanotubes

[+] Author and Article Information
Q. Wang

e-mail: q.wang@ad.umanitoba.ca

N. Wu

Department of Mechanical
and Manufacturing Engineering,
University of Manitoba,
Winnipeg, MB, R3T 5V6, Canada

1Corresponding author.

Manuscript received April 26, 2012; final manuscript received July 11, 2012; published online September 24, 2012. Assoc. Editor: Henry Hess.

J. Nanotechnol. Eng. Med 3(2), 020902 (Sep 24, 2012) (4 pages) doi:10.1115/1.4007388 History: Received April 26, 2012; Revised July 11, 2012

The potential of carbon nanotubes (CNTs) as nanosensors in detection of genes through a vibration analysis is investigated with molecular dynamics. The carbon nanotube based nanosensor under investigation is wrapped by a gene whose structure includes a single strand deoxyribose nucleic acid (DNA) with a certain number of distinct nucleobases. Different genes are differentiated or detected by identifying a differentiable sensitivity index that is defined to be the shifts of the resonant frequency of the nanotube. Simulation results indicate that the nanosensor is able to differentiate distinct genes, i.e., small proline-rich protein 2 A, small proline-rich protein 2B, small proline-rich protein 2D, and small proline-rich protein 2E, with a recognizable sensitivity. The research provides a rapid, effective, and practical method for detection of genes.

FIGURES IN THIS ARTICLE
<>
Copyright © 2012 by ASME
Your Session has timed out. Please sign back in to continue.

References

Homola, J., 2003, “Present and Future of Surface Plasmon Resonance Biosensors,” Anal. Bioanal. Chem., 377(3), pp. 528–539. [CrossRef] [PubMed]
Lud, S. Q., Nikolaides, M. G., Haase, I., Fischer, M., and BauschA. R., 2006, “Field Effect of Screened Charges: Electrical Detection of Peptides and Proteins by a Thin-Film Resistor,” Chem. Phys. Chem., 7(2), pp. 379–384. [CrossRef]
Haron, S., and Ray, A. K., 2006, “Optical Biodetection of Cadmium and Lead Ions in Water,” Med. Eng. Phys., 28(10), pp. 978–981. [CrossRef] [PubMed]
Pohanka, M., Skladal, P., and Kroca, M., 2007, “Biosensors for Biological Warfare Agent Detection,” Def. Sci. J., 57(3), pp. 185–193.
Wang, J., Jiang, M., Nilsen, T., and Getts, R., 1998, “Dendritic Nucleic Acid Probes for DNA Biosensors,” J. Am. Chem. Soc., 120(32), pp. 8281–8282. [CrossRef]
Cattrall, R. W., 1997, Chemical Sensors (Chemistry Primers), Oxford University Press, Oxford, UK.
Piunno, P., Krull, U., Hudson, R., Damha, M., and Cohen, H., 1995, “Fiber-Optic DNA Sensor for Fluorometric Nucleic Acid Determination,” Anal. Chem., 67(15), pp. 2635–2643. [CrossRef] [PubMed]
Mikkelsen, S. R., 1996, “Electrochecmical Biosensors for DNA Sequence Detection,” Electroanalysis, 8(1), pp. 15–19. [CrossRef]
Palecek, E., Fojta, M., Tomschick, M., and Wang, J., 1998, “Electrochemical Biosensors for DNA Hybridization and DNA Damage,” Biosens. Bioelectron., 13(6), pp. 621–628. [CrossRef] [PubMed]
Geim, A. K., 2009, “Graphene: Status and Prospects,” Science, 324(5934), pp. 1530–1534. [CrossRef] [PubMed]
Arash, B., Wang, Q., and Varadan, V. K., 2011, “Carbon Nanotube-Based Sensors for Detection of Gas Atoms,” ASME J. Nanotechnol. Eng. Med., 2(2), p. 021010. [CrossRef]
Chaste, J., Eichler, A., Moser, J., Ceballos, G., Rurali, R., and Bachtold, A., 2012, “A Nanomechanical Mass Sensor With Yoctogram Resolution,” Nat. Nanotechnol., 7, pp. 301–304. [CrossRef] [PubMed]
Arash, B., Wang, Q., and Duan, W. H., 2011, “Detection of Gas Atoms via Vibration of Graphenes,” Phys. Lett. A, 375(24), pp. 2411–2415. [CrossRef]
Xu, Y., Mi, X., and Aluru, N. R., 2009, “Detection of Defective DNA in Carbon Nanotubes by Combined Molecular Dynamics/Tight-Binding Technique,” Appl. Phys. Lett., 95(11), p. 113116. [CrossRef]
Li, J., Ng, H. T., Cassell, A., Fan, W., Chen, H., Ye, Q., Koehne, J., Han, J., and Meyyappan, M., 2003, “Carbon Nanotube Nanoelectrode Array for Ultrasensitive DNA Detection,” Nano Lett., 3(5), pp. 597–602. [CrossRef]
Pacios, M., Yilmaz, N., Martín-Fernández, I., Villa, R., Godignon, P., Valle, M. D., Bartrolí, J., and Esplandiu, M. J., 2012, “A Simple Approach for DNA Detection on Carbon Nanotube Microelectrode Arrays,” Sens. Actuators B, 162(1), pp. 120–127. [CrossRef]
Merchant, C. A., Healy, K., Wanunu, M., Ray, V., Peterman, N., Bartel, J., Fischbein, M. D., Venta, K., Luo, Z., Johnson, A. T. C., and Drndic, M., 2010, “DNA Translocation Through Graphene Nanopores,” Nano Lett., 10(8), pp. 2915–2921. [CrossRef] [PubMed]
Sathe, C., Zou, X., Leburton, J. P., and Schulten, K., 2011, “Computational Investigation of DNA Detection Using Graphene Nanopores,” ACS Nano, 5(11), pp. 8842–8851. [CrossRef] [PubMed]
Saha, K. K., Drndic, M., and Nikolic, B. K., 2012, “DNA Base-Specific Modulation of Microampere Transverse Edge Currents Through a Metallic Graphene Nanoribbon With a Nanopore,” Nano Lett., 12(1), pp. 50–55. [CrossRef] [PubMed]
Min, S. K., Kim, W. Y., Cho, Y., and Kim, K. S., 2011, “Fast DNA Sequencing With a Graphene-Based Nanochannel Device,” Nat. Nanotechnol., 6(3), pp. 162–165. [CrossRef] [PubMed]
Rappi, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., and Skid, W. M., 1992, “UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations,” J. Am. Chem. Soc., 114(25), pp. 10024–10035. [CrossRef]
Rappe, A. K., and Goddard, W. A., 1991, “Charge Equilibration for Molecular Dnamics Simulations,” J. Phys. Chem., 95(8), pp. 3358–3363. [CrossRef]
Kessler, C., and Manta, V., 1990, “Specificity of Restriction Endonucleases and DNA Modification Methyltransferases—A Review (Edition 3),” Gene, 92(1-2), pp. 1–240. [CrossRef] [PubMed]
Li, T., Huang, S., Jiang, W. Z., Wright, D., Spalding, M. H., Weeks, D. P., and Yang, B., 2011, “TAL Nucleases (TALNs): Hybrid Proteins Composed of TAL Effectors and FokI DNA-Cleavage Domain,” Nucl. Acids Res., 39(1), pp. 359–372. [CrossRef]
Andersen, H. C., 1980, “Molecular Dynamics Simulations at Constant Pressure and/or Temperature,” J. Chem. Phys., 72(4), pp. 2384–2393. [CrossRef]
Johnson, R. R., Kohlmeyer, A., Johnson, A. T. C., and Klein, M. L., 2009, “Free Energy Landscape of a DNA-Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics,” Nano Lett., 9(2), pp. 537–541. [CrossRef] [PubMed]
Johnson, R. R., Johnson, A. T. C., and Klein, M. L., 2008, “Probing the Structure of DNA-Carbon Nanotube Hybrids With Molecular Dynamics,” Nano Lett., 8(1), pp. 69–75. [CrossRef] [PubMed]

Figures

Grahic Jump Location
Fig. 1

An ssDNA of the first ten bases of SPR-2 A (AAGAAAAAAT) gene wrapped on a (5, 5) CNT with a length of 15 nm: (a) initial configuration; and (b) helical-stacked conformation after 10 ns of the simulation

Grahic Jump Location
Fig. 2

Snapshots of a (5, 5) CNT with a length of 15 nm wrapped by a ten-base ssDNA (AAGAAAAAAT) of the first ten bases SPR-2A gene

Grahic Jump Location
Fig. 3

Vibration of a (5, 5) CNT with a length of 15 nm: (a) pristine nanotube; and (b) nanotube wrapped by a ten-base ssDNA (AAGAAAAAAT) of the first ten bases of SPR-2A gene

Grahic Jump Location
Fig. 4

Resonant frequency of a pristine (5, 5) CNT with a length of 15 nm versus resonant frequency of the CNT wrapped by a ten-base ssDNA (AAGAAAAAAT) of the first ten bases of SPR-2A gene

Tables

Errata

Discussions

Some tools below are only available to our subscribers or users with an online account.

Related Content

Customize your page view by dragging and repositioning the boxes below.

Related Journal Articles
Related eBook Content
Topic Collections

Sorry! You do not have access to this content. For assistance or to subscribe, please contact us:

  • TELEPHONE: 1-800-843-2763 (Toll-free in the USA)
  • EMAIL: asmedigitalcollection@asme.org
Sign In