Nanopore Integrated Nanogaps for DNA Detection

Fanget, Axel; Traversi, Floriano; Khlybov, S. V.; Granjon, Pierre; Magrez, Arnaud; Forró, Lászlø; Radenović, Aleksandra

doi:10.1021/nl403849g

Cited by 70 publications

(49 citation statements)

References 27 publications

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“…EBL resist thickness, thickness of electrode metallic film) and very high reproducibility was obtained. Eighty‐five percent ( n = 72) of chips had nanogap thinner than 10 nm . Ivanov et al.…”

Section: Advanced Detection Methodsmentioning

confidence: 98%

Fabrication of solid‐state nanopores and its perspectives

et al. 2015

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Fabrication of solid-state nanopores and its perspectivesNanofluidics is becoming an extensively developing technique in the field of bioanalytical chemistry. Nanoscale hole embed in an insulating membrane is employed in a vast variety of sensing platforms and applications. Although, biological nanopores have several attractive characteristics, in this paper, we focused on the solid-state nanopores due to their advantages as high stability, possibility of diameter control, and ease of surface functionalizing. A detection method, based on the translocation of analyzed molecules through nanochannels under applied voltage bias and resistive pulse sensing, is well established. Nevertheless, it seems that the new detection methods like measuring of transverse electron tunneling using nanogap electrodes or optical detection can offer significant additional advantages. The aim of this review is not to cite all related articles, but highlight the steps, which in our opinion, meant important progresses in solid-state nanopore analysis. Keywords:Fabrication / Nanofluidics / Selectivity / Sensors / Solid-state nanopores / Surface charge DOI 10.1002/elps.201400612 IntroductionNanopore analysis is a young and rapidly developing discipline with incredibly versatile applications (Fig. 1A). Undoubtedly, it has the potential to considerably change the way we think about many fields of science-medicine, chemistry, and biology. It took inspiration from biological processes of molecular transport through nanoscale pores (nanopores) and utilizes this phenomenon as analytical tool. Nucleus and surface of living cells are covered with distinct types of pore-forming proteins. They mediate the transport in order to maintain cell functions. In late 70s, Sakmann and Neher patch-clamped single ion channel, one type of pore-forming membrane proteins, and for the first time they observed single channel conductance [1]. Although, their aim was to investigate cell physiology, two decades later these measurements created the basis of nanopore sensing. Second distinct group of pore-forming proteins is some bacterial exotoxins, which represents an extremely effective tool to lyse the cells. They are able to oligomerize in lipid membranes and create there a nongating permeable pore.Correspondence: Professor Rene Kizek, Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic E-Mail: kizek@sci.muni.cz Fax: +420-545-212-044Abbreviations: ALD, atomic layer deposition; EBID, electron beam-induced deposition; EBL, electron beam lithography; FIB, focused ion beam; SAM, self-assembled monolayer; SiNx, silicon-rich nitride; STM, scanning tunneling microscopy; TEM, transmission electron microscope Kasianowicz and coworkers were the first who used nanopores as a sensor [2]. They embedded a single ␣-hemolysin protein, secreted by Staphylococcus aureus (Fig. 1Ba), to a lipid bilayer and suggested that the individual nucleotides in polynucleotide chain passing through pore in electri...

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Section: Advanced Detection Methodsmentioning

confidence: 98%

Fabrication of solid‐state nanopores and its perspectives

et al. 2015

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“…Tremendous efforts have been undertaken to realize applications of the tunneling current approach for practical uses by incorporating nanopore technologies to the quantum mechanical approach, which enables the active drawing of single-polynucleotides in the gap by means of an electrophoretic control of the translocation dynamics [11,12,13,14,15]. In contrast to the progress, however, little efforts have been made to evaluate and enhance the temporal resolution of the tunneling current measurements, which is an important issue in respect to the nanopore sequencing wherein the constituent nucleobase molecules in DNA move through the electrode gap swiftly within microseconds [12,13].…”

Section: Introductionmentioning

confidence: 99%

Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution

Morikawa

Yokota

Tanimoto

et al. 2017

Sensors

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Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO2-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.

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“…The longlasting problem of DNA conductance (Livshits et al, 2014) has been the subject of discussion, since some experiments demonstrated that DNA can carry electric current (Fanget et al, 2014), while others showed no such conductance in DNA (Porath et al, 2004). The longlasting problem of DNA conductance (Livshits et al, 2014) has been the subject of discussion, since some experiments demonstrated that DNA can carry electric current (Fanget et al, 2014), while others showed no such conductance in DNA (Porath et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Structural and computational analysis of intermolecular interactions in a new 2-thiouracil polymorph

et al. 2017

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The crystallization and characterization of a new polymorph of 2-thiouracil by single-crystal X-ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (A) crystallizes in the triclinic space group P\overline{1}, while that described herein (B) crystallizes in the monoclinic space group P2/c. Periodic DFT calculations showed that the energies of polymorphs A and B, compared to the gas-phase geometry, were -108.8 and -29.4 kJ mol, respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O...H and S...H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N-H...O and N-H...S types were found in polymorph A, whereas in polymorph B, only those of the N-H...O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak-to-medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4-10.2 and 4.9-9.2 kJ mol for polymorphs A and B, respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5-4.1 and 3.1-5.5 kJ mol for polymorphs A and B, respectively, as shown by QTAIM analysis.

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Nanopore Integrated Nanogaps for DNA Detection

Cited by 70 publications

References 27 publications

Fabrication of solid‐state nanopores and its perspectives

Fabrication of solid‐state nanopores and its perspectives

Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution

Structural and computational analysis of intermolecular interactions in a new 2-thiouracil polymorph

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