Advertisement

Biomedical Microdevices

, 18:7 | Cite as

Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids

  • Rahim Esfandyarpour
  • Lu Yang
  • Zahra koochak
  • James S. Harris
  • Ronald W. Davis
Article

Abstract

The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.

Keywords

Nanotips array Nanoelectric biosensor Label-free Single point mutations DNA sequencing Nanofabrication 

Notes

Acknowledgments

The authors like to thank Weihong Xu, Bob St.Onge, Richard W. Hyman and Raeka Aiyar for useful comments and discussions. This work was supported by the National Institutes of Health Grant No. P01HG000205.

References

  1. M. D. Adams et al., Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013), 1651–1656 (1991)CrossRefGoogle Scholar
  2. A. Ahmadian, et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280(1), 103–110 (2000)CrossRefGoogle Scholar
  3. W. Ansorge et al., Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Research 15(11), 4593–4602 (1987)CrossRefGoogle Scholar
  4. Y. Cui et al., Nanowire Nanosensors for highly sensitive and selective detection of biological and chemical species. Science 293(5533), 1289–1292 (2001)CrossRefGoogle Scholar
  5. M. L. Drumm, M. W. Konstan, M. D. Schluchter, A. Handler, R. Pace, F. Zou, M. Zariwala, D. Fargo, A. R. Xu, J. M. Dunn, R. J. Darrah, R. Dorfman, A. J. Sandford, M. Corey, J. Zielenski, P. Durie, K. Goddard, J. R. Yankaskas, F. A. Wright, M. R. Knowles, G. Gene Modifier, Study. N. Engl. J. Med. 353, 1443 (2005)CrossRefGoogle Scholar
  6. R. Esfandyarpour et al., Microneedle biosensor: A method for direct label-free real time protein detection. Sensors and Actuators B: Chemical 177, 848–855 (2013)CrossRefGoogle Scholar
  7. Z. Gao, et al. Silicon nanowire arrays for label-free detection of DNA. Anal. Chem. 79(9), 3291–3297 (2007)CrossRefGoogle Scholar
  8. S.M. Hashemi Rafsanjani, T. Cheng, S. Mittler, C. Rangan (2010) Theoretical proposal for a biosensing approach based on a linear array of immobilized gold nanoparticles. J Appl Phys 107, 094303Google Scholar
  9. S. M. Huse, et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8(7), R143 (2007)CrossRefGoogle Scholar
  10. B. Kannan, et al. High-sensitivity, label-free DNA sensors using electrochemically active conducting polymers. Anal. Chem. 83(9), 3415–3421 (2011)CrossRefGoogle Scholar
  11. L. J. Kricka, Stains, labels and detection strategies for nucleic acids assays. Annals of Clinical Biochemistry 39(2), 114–129 (2002)CrossRefGoogle Scholar
  12. Z. Li et al., Sequence-Specific label-Free DNA Sensors Based on Silicon Nanowires. Nano Letters 4(2), 245–247 (2004)Google Scholar
  13. Z. Li et al., Silicon nanowires for sequence-specific DNA sensing: device fabrication and simulation. Applied Physics A 80(6), 1257–1263 (2005)CrossRefGoogle Scholar
  14. L. J. McBride et al., Automated DNA sequencing methods involving polymerase chain reaction. Clin. Chem. 35(11), 2196–2201 (1989)Google Scholar
  15. M. L. Metzker, Emerging technologies in DNA sequencing. Genome Research 15(12), 1767–1776 (2005)CrossRefGoogle Scholar
  16. M. L. Metzker, J. Lu, R. A. Gibbs, Electrophoretically uniform fluorescent dyes for automated DNA sequencing. Science 271(5254), 1420–1422 (1996)CrossRefGoogle Scholar
  17. S.-J. Park, T. A. Taton, C. A. Mirkin, Array-based electrical detection of DNA with Nanoparticle probes. Science 295(5559), 1503–1506 (2002)Google Scholar
  18. C. Quince, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6(9), 639–641 (2009a)CrossRefGoogle Scholar
  19. C. Quince, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6(9), 639–641 (2009b)CrossRefGoogle Scholar
  20. M. Ronaghi, et al. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242(1), 84–89 (1996)CrossRefGoogle Scholar
  21. M. Ronaghi, Pyrosequencing sheds light on DNA sequencing. Genome Res. 11(1), 3–11 (2001)CrossRefGoogle Scholar
  22. M. Ronaghi, M. Uhlén, P. Nyrén, A sequencing method based on real-time pyrophosphate. Science 281(5375), 363–365 (1998)CrossRefGoogle Scholar
  23. M. D. Roses, D. Allen, Apolipoprotein E alleles as risk factors in Alzheimer’s disease. Annu. Rev. Med. 47(1), 387–400 (1996)CrossRefGoogle Scholar
  24. F. Sanger, et al. The nucleotide sequence of bacteriophage φX174. J. Mol. Biol. 125(2), 225–246 (1978)CrossRefGoogle Scholar
  25. F. Sanger, S. Nicklen, A. R. Coulson, DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. 74(12), 5463–5467 (1977)CrossRefGoogle Scholar
  26. L. M. Smith et al., Fluorescence detection in automated DNA sequence analysis. Nature 321, 674–679 (1986)CrossRefGoogle Scholar
  27. V. E. Velculescu et al., Serial analysis of gene expression. Science 270(5235), 484–487 (1995)CrossRefGoogle Scholar
  28. J. Wang, et al. Peptide nucleic acid probes for sequence-specific DNA biosensors. J. Am. Chem. Soc. 118(33), 7667–7670 (1996)CrossRefGoogle Scholar
  29. P. Xie, et al. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nat. Nanotechnol. 7(2), 119–125 (2012)CrossRefGoogle Scholar
  30. N. Zhang, D. H. Apella, Advantages of peptide nucleic acids as diagnostic platforms for detection of nucleic acids in resource-limited settings. Journal of Infectious Diseases 201(Supplement 1), S42–S45 (2010)CrossRefGoogle Scholar
  31. G.-J. Zhang et al., Highly sensitive measurements of PNA-DNA hybridization using oxide-etched silicon Nanowire biosensors. Biosensors and Bioelectronics 23(11), 1701–1707 (2008)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Rahim Esfandyarpour
    • 2
  • Lu Yang
    • 3
  • Zahra koochak
    • 1
    • 2
  • James S. Harris
    • 1
  • Ronald W. Davis
    • 2
  1. 1.Department of Electrical EngineeringStanford UniversityStanfordUSA
  2. 2.Stanford Genome Technology CenterPalo AltoUSA
  3. 3.Department of BioengineeringStanford UniversityStanfordUSA

Personalised recommendations