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

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• 作者：Rahim Esfandyarpour ; Lu Yang ; Zahra koochak ; James S. Harris…
• 关键词：Nanotips array ; Nanoelectric biosensor ; Label ; free ; Single point mutations ; DNA sequencing ; Nanofabrication
• 刊名：Biomedical Microdevices
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：18
• 期：1
• 全文大小：1,203 KB
• 参考文献：M. D. Adams et al., Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013), 1651–1656 (1991)CrossRef
  A. Ahmadian, et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280(1), 103–110 (2000)CrossRef
  W. Ansorge et al., Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Research 15(11), 4593–4602 (1987)CrossRef
  Y. Cui et al., Nanowire Nanosensors for highly sensitive and selective detection of biological and chemical species. Science 293(5533), 1289–1292 (2001)CrossRef
  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)CrossRef
  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)CrossRef
  Z. Gao, et al. Silicon nanowire arrays for label-free detection of DNA. Anal. Chem. 79(9), 3291–3297 (2007)CrossRef
  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, 094303
  S. M. Huse, et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8(7), R143 (2007)CrossRef
  B. Kannan, et al. High-sensitivity, label-free DNA sensors using electrochemically active conducting polymers. Anal. Chem. 83(9), 3415–3421 (2011)CrossRef
  L. J. Kricka, Stains, labels and detection strategies for nucleic acids assays. Annals of Clinical Biochemistry 39(2), 114–129 (2002)CrossRef
  Z. Li et al., Sequence-Specific label-Free DNA Sensors Based on Silicon Nanowires. Nano Letters 4(2), 245–247 (2004)
  Z. Li et al., Silicon nanowires for sequence-specific DNA sensing: device fabrication and simulation. Applied Physics A 80(6), 1257–1263 (2005)CrossRef
  L. J. McBride et al., Automated DNA sequencing methods involving polymerase chain reaction. Clin. Chem. 35(11), 2196–2201 (1989)
  M. L. Metzker, Emerging technologies in DNA sequencing. Genome Research 15(12), 1767–1776 (2005)CrossRef
  M. L. Metzker, J. Lu, R. A. Gibbs, Electrophoretically uniform fluorescent dyes for automated DNA sequencing. Science 271(5254), 1420–1422 (1996)CrossRef
  S.-J. Park, T. A. Taton, C. A. Mirkin, Array-based electrical detection of DNA with Nanoparticle probes. Science 295(5559), 1503–1506 (2002)
  C. Quince, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6(9), 639–641 (2009a)CrossRef
  C. Quince, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6(9), 639–641 (2009b)CrossRef
  M. Ronaghi, et al. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242(1), 84–89 (1996)CrossRef
  M. Ronaghi, Pyrosequencing sheds light on DNA sequencing. Genome Res. 11(1), 3–11 (2001)CrossRef
  M. Ronaghi, M. Uhlén, P. Nyrén, A sequencing method based on real-time pyrophosphate. Science 281(5375), 363–365 (1998)CrossRef
  M. D. Roses, D. Allen, Apolipoprotein E alleles as risk factors in Alzheimer’s disease. Annu. Rev. Med. 47(1), 387–400 (1996)CrossRef
  F. Sanger, et al. The nucleotide sequence of bacteriophage φX174. J. Mol. Biol. 125(2), 225–246 (1978)CrossRef
  F. Sanger, S. Nicklen, A. R. Coulson, DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. 74(12), 5463–5467 (1977)CrossRef
  L. M. Smith et al., Fluorescence detection in automated DNA sequence analysis. Nature 321, 674–679 (1986)CrossRef
  V. E. Velculescu et al., Serial analysis of gene expression. Science 270(5235), 484–487 (1995)CrossRef
  J. Wang, et al. Peptide nucleic acid probes for sequence-specific DNA biosensors. J. Am. Chem. Soc. 118(33), 7667–7670 (1996)CrossRef
  P. Xie, et al. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nat. Nanotechnol. 7(2), 119–125 (2012)CrossRef
  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)CrossRef
  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)CrossRef
  
• 作者单位：Rahim Esfandyarpour (2)
  Lu Yang (3)
  Zahra koochak (1) (2)
  James S. Harris (1)
  Ronald W. Davis (2)
  
  2. Stanford Genome Technology Center, 3165 Porter Dr., Palo Alto, CA, 94304, USA
  3. Department of Bioengineering, Stanford University, Stanford, CA, USA
  1. Department of Electrical Engineering, Stanford University, Stanford, CA, USA
  
• 刊物类别：Engineering
• 刊物主题：Biomedical Engineering
  Biophysics and Biomedical Physics
  Nanotechnology
  Engineering Fluid Dynamics
  
• 出版者：Springer Netherlands
• ISSN：1572-8781

文摘

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.