Nanopore with transverse nanoelectrodes for electrical characterization and sequencing of DNA

Gierhart, Brian C.; Howitt, D. G.; Chen, Shiahn J.; Zhu, Zhineng; Kotecki, David E.; Smith, Robert L.; Collins, S.D.

doi:10.1016/j.snb.2007.11.054

Cited by 61 publications

(52 citation statements)

References 32 publications

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“…To address these limitations, a number of ideas have been proposed, which supplement electrical measurements with other techniques, such as transverse electron tunneling 20,21 or nanopore electrical capacitance fluctuations. 22,23 Here we present a method that complements electrical measurements with high-sensitivity wide-field optical detection.…”

Section: Introductionmentioning

confidence: 99%

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores

Soni

Singer

et al. 2010

Review of Scientific Instruments

101

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We present a novel method for integrating two single-molecule measurement modalities, namely, total internal reflection microscopy and electrical detection of biomolecules using nanopores. Demonstrated here is the electrical measurement of nanopore based biosensing performed simultaneously and in-sync with optical detection of analytes. This method makes it possible, for the first time, to visualize DNA and DNA-protein complexes translocating through a nanopore with high temporal resolution ͑1000 frames/s͒ and good signal to background. This paper describes a detailed experimental design of custom optics and data acquisition hardware to achieve simultaneous high resolution electrical and optical measurements on labeled biomolecules as they traverse through a ϳ4 nm synthetic pore. In conclusion, we discuss new directions and measurements, which this technique opens up.

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Section: Introductionmentioning

confidence: 99%

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores

Soni

Singer

et al. 2010

Review of Scientific Instruments

101

View full text Add to dashboard Cite

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“…[11][12][13][14][15] These have been realized experimentally by high-resolution milling-based methods for a number of metal electrodes, but it has been speculated that similar techniques could be used for CNTs with possibly higher resolution. 13 On the theoretical front, the transverse tunneling conductance across nucleobases placed between two gold electrodes has been actively investigated and debated.…”

Section: Introductionmentioning

confidence: 99%

First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

et al. 2012

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Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results, we propose a DNA sequencing protocol combining three possible data analysis strategies.

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“…The fabrication of solid state nano-micro pores is a topic of intense interest for the sensing of biomolecules such as DNA (Fologea et al 2007a;Gierhart et al 2008;Kim et al 2007;Storm et al 2005), proteins (Fologea et al 2007b), and nanoparticles (Lan et al 2011). Silicon nanopores are one of the most studied solid state nanopores.…”

Section: Introductionmentioning

confidence: 99%

“…Nanopores have shown to allow linear translocations of DNA molecules in buffer conditions (Fologea et al 2005a;Heng et al 2004;Li et al 2003) when a bias voltage is applied, allowing with these devices the detection and characterization of DNA molecules, although the highspeed passage of DNA through pores with this method still remains a problem (Chen et al 2010;Fologea et al 2005b;Gierhart et al 2008;Keyser 2011;Lagerqvist et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Laser fabrication of micropores and their integration to microfluidic platforms for DNA electrophoresis

et al. 2012

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The work presents an alternative method for the manufacture of micropores by using the combination of laser ablation and wet etching. The process of laser ablation was done on silicon (Si) wafers with silicon nitride (Si 3 N 4 ) used as a sacrificial layer. The size of the pores was carefully controlled by following an optical technique. The method exhibits a series of advantages in relation micromachining techniques previously used. The fabricated pores were then integrated to polydimethylsiloxane (PDMS) microchannels, which constitutes a novel setup to be considered for microfluidic applications. Furthermore, as the system is addressed to study the electrically-driven transport of macromolecules, deoxyribonucleic acid (DNA) electrophoresis was performed in the fabricated microsystems to prove the principle. Also for these purposes, the electric field throughout the microchannel and pore region was studied in details by using numerical simulations.

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Nanopore with transverse nanoelectrodes for electrical characterization and sequencing of DNA

Cited by 61 publications

References 32 publications

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores

First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes

Laser fabrication of micropores and their integration to microfluidic platforms for DNA electrophoresis

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