1
|
Yue S, Hou Y, Wang R, Liu S, Li M, Zhang Z, Hou M, Wang Y, Zhang Z. CMOS-compatible plasmonic hydrogen sensors with a detection limit of 40 ppm. OPTICS EXPRESS 2019; 27:19331-19347. [PMID: 31503694 DOI: 10.1364/oe.27.019331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
Sensing of leakage at an early stage is crucial for the safe utilization of hydrogen. Optical hydrogen sensors eliminate the potential hazard of ignition caused by electrical sparks but achieve a detection limit far higher than their electrical counterparts so far. To essentially improve the performance of optical hydrogen sensors in terms of detection limit, we demonstrate in this work a plasmonic hydrogen sensor based on aluminum-palladium (Al-Pd) hybrid nanorods. Arranged into high-density regular arrays, the hybrid nanorods are capable of sensing hydrogen at a concentration down to 40 ppm, i.e., one thousandth of the lower flammability limit of hydrogen in air. Different sensing behaviors are found for two sensor configurations, where Pd-Al nanorods provide larger spectral shift and Al-Pd ones exhibit shorter response time. In addition, the plasmonic hydrogen sensors here utilize exclusively CMOS-compatible materials, holding the potential for real-world, large-scale applications.
Collapse
|
2
|
Im J, Sen S, Lindsay S, Zhang P. Recognition Tunneling of Canonical and Modified RNA Nucleotides for Their Identification with the Aid of Machine Learning. ACS NANO 2018; 12:7067-7075. [PMID: 29932668 DOI: 10.1021/acsnano.8b02819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In the present study, we demonstrate a tunneling nanogap technique to identify individual RNA nucleotides, which can be used as a mechanism to read the nucleobases for direct sequencing of RNA in a solid-state nanopore. The tunneling nanogap is composed of two electrodes separated by a distance of <3 nm and functionalized with a recognition molecule. When a chemical entity is captured in the gap, it generates electron tunneling currents, a process we call recognition tunneling (RT). Using RT nanogaps created in a scanning tunneling microscope (STM), we acquired the electron tunneling signals for the canonical and two modified RNA nucleotides. To call the individual RNA nucleotides from the RT data, we adopted a machine learning algorithm, support vector machine (SVM), for the data analysis. Through the SVM, we were able to identify the individual RNA nucleotides and distinguish them from their DNA counterparts with reasonably high accuracy. Since each RNA nucleoside contains a hydroxyl group at the 2'-position of its sugar ring in an RNA strand, it allows for the formation of a tunneling junction at a larger nanogap compared to the DNA nucleoside in a DNA strand, which lacks the 2' hydroxyl group. It also proves advantageous for the manufacture of RT devices. This study is a proof-of-principle demonstration for the development of an RT nanopore device for directly sequencing single RNA molecules, including those bearing modifications.
Collapse
|
3
|
Zhang B, Song W, Pang P, Zhao Y, Zhang P, Csabai I, Vattay G, Lindsay S. Observation of Giant Conductance Fluctuations in a Protein. NANO FUTURES 2017; 1:035002. [PMID: 29552645 PMCID: PMC5851656 DOI: 10.1088/2399-1984/aa8f91] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteins are insulating molecular solids, yet even those containing easily reduced or oxidized centers can have single-molecule electronic conductances that are too large to account for with conventional transport theories. Here, we report the observation of remarkably high electronic conductance states in an electrochemically-inactive protein, the ~200 kD αVβ3 extracelluar domain of human integrin. Large current pulses (up to nA) were observed for long durations (many ms, corresponding to many pC of charge transfer) at large gap (>5nm) distances in an STM when the protein was bound specifically by a small peptide ligand attached to the electrodes. The effect is greatly reduced when a homologous, weakly-binding protein (α4β1) is used as a control. In order to overcome the limitations of the STM, the time- and voltage-dependence of the conductance were further explored using a fixed-gap (5 nm) tunneling junction device that was small enough to trap a single protein molecule at any one time. Transitions to a high conductance (~ nS) state were observed, the protein being "on" for times from ms to tenths of a second. The high-conductance states only occur above ~ 100mV applied bias, and thus are not an equilibrium property of the protein. Nanoamp two-level signals indicate the specific capture of a single molecule in an electrode gap functionalized with the ligand. This offers a new approach to label-free electronic detection of single protein molecules. Electronic structure calculations yield a distribution of energy level spacings that is consistent with a recently proposed quantum-critical state for proteins, in which small fluctuations can drive transitions between localized and band-like electronic states.
Collapse
Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Pei Pang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yanan Zhao
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Gábor Vattay
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Pázmány P. s. 1/A, Hungary
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- To whom correspondence should be addressed:
| |
Collapse
|
4
|
Biswas S, Sen S, Im J, Biswas S, Krstic P, Ashcroft B, Borges C, Zhao Y, Lindsay S, Zhang P. Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions. ACS NANO 2016; 10:11304-11316. [PMID: 28024337 DOI: 10.1021/acsnano.6b06466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.
Collapse
Affiliation(s)
| | | | | | | | - Predrag Krstic
- Institute for Advanced Computational Science, Stony Brook University , Stony Brook, New York 11794-5250, United States
| | | | | | | | | | | |
Collapse
|
5
|
Xiang D, Wang X, Jia C, Lee T, Guo X. Molecular-Scale Electronics: From Concept to Function. Chem Rev 2016; 116:4318-440. [DOI: 10.1021/acs.chemrev.5b00680] [Citation(s) in RCA: 816] [Impact Index Per Article: 102.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Dong Xiang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Key
Laboratory of Optical Information Science and Technology, Institute
of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuancheng Jia
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Takhee Lee
- Department
of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
| | - Xuefeng Guo
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Department
of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
6
|
Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
Collapse
Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| |
Collapse
|
7
|
Zhao Y, Ashcroft B, Zhang P, Liu H, Sen S, Song W, Im J, Gyarfas B, Manna S, Biswas S, Borges C, Lindsay S. Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling. NATURE NANOTECHNOLOGY 2014; 9:466-73. [PMID: 24705512 PMCID: PMC4047173 DOI: 10.1038/nnano.2014.54] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 02/18/2014] [Indexed: 05/18/2023]
Abstract
The human proteome has millions of protein variants due to alternative RNA splicing and post-translational modifications, and variants that are related to diseases are frequently present in minute concentrations. For DNA and RNA, low concentrations can be amplified using the polymerase chain reaction, but there is no such reaction for proteins. Therefore, the development of single-molecule protein sequencing is a critical step in the search for protein biomarkers. Here, we show that single amino acids can be identified by trapping the molecules between two electrodes that are coated with a layer of recognition molecules, then measuring the electron tunnelling current across the junction. A given molecule can bind in more than one way in the junction, and we therefore use a machine-learning algorithm to distinguish between the sets of electronic 'fingerprints' associated with each binding motif. With this recognition tunnelling technique, we are able to identify D and L enantiomers, a methylated amino acid, isobaric isomers and short peptides. The results suggest that direct electronic sequencing of single proteins could be possible by sequentially measuring the products of processive exopeptidase digestion, or by using a molecular motor to pull proteins through a tunnel junction integrated with a nanopore.
Collapse
Affiliation(s)
- Yanan Zhao
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3]
| | - Brian Ashcroft
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2]
| | - Peiming Zhang
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Hao Liu
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Suman Sen
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Weisi Song
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - JongOne Im
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA
| | - Saikat Manna
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Sovan Biswas
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Chad Borges
- 1] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- 1] Department of Physics, Arizona State University, PO Box 871504 Tempe, Arizona 85287, USA [2] Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, USA [3] Department of Chemistry and Biochemistry, Arizona State University, PO Box 871604, Tempe, Arizona 85287, USA
| |
Collapse
|
8
|
Krishnakumar P, Gyarfas B, Song W, Sen S, Zhang P, Krstić P, Lindsay S. Slowing DNA translocation through a nanopore using a functionalized electrode. ACS NANO 2013; 7:10319-26. [PMID: 24161197 PMCID: PMC3875158 DOI: 10.1021/nn404743f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopores were fabricated with an integrated microscale Pd electrode coated with either a hydrogen-bonding or hydrophobic monolayer. Bare pores, or those coated with octanethiol, translocated single-stranded DNA with times of a few microseconds per base. Pores functionalized with 4(5)-(2-mercaptoethyl)-1H-imidazole-2-carboxamide slowed average translocation times, calculated as the duration of the event divided by the number of bases translocated, to about 100 μs per base at biases in the range of 50 to 80 mV.
Collapse
Affiliation(s)
- Padmini Krishnakumar
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Brett Gyarfas
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Weisi Song
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Suman Sen
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Peiming Zhang
- Department of Physics, Arizona State University, Tempe, AZ 85287
| | - Predrag Krstić
- Joint Institute of Computational Science, University of Tennessee, Oak Ridge, TN 37831
- TheoretiK, Knoxville, TN 37921, USA
| | - Stuart Lindsay
- Department of Physics, Arizona State University, Tempe, AZ 85287
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| |
Collapse
|
9
|
Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|