1
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Guo J, Chen PK, Chang S. Molecular-Scale Electronics: From Individual Molecule Detection to the Application of Recognition Sensing. Anal Chem 2024; 96:9303-9316. [PMID: 38809941 DOI: 10.1021/acs.analchem.3c04656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
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2
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Aminiranjbar Z, Gultakti CA, Alangari MN, Wang Y, Demir B, Koker Z, Das AK, Anantram MP, Oren EE, Hihath J. Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements. ACS Sens 2024. [PMID: 38773960 DOI: 10.1021/acssensors.3c02734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.
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Affiliation(s)
- Zahra Aminiranjbar
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Mashari Nasser Alangari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Department of Electrical Engineering, University of Hail, Hail 2240, Saudi Arabia
| | - Yiren Wang
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Zeynep Koker
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Arindam K Das
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
- Department of Computer Science and Electrical Engineering, Eastern Washington University, Cheney, Washington 99004,United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, Davis, California 95616, United States
- Center for Bioelectronics and Biosensors, School of Electrical, Computer, and Energy Engineering, Arizona State University, Phoenix, Arizona 85287, United States
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3
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Demir B, Akin Gultakti C, Koker Z, Anantram MP, Oren EE. Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations. J Phys Chem B 2024; 128:4646-4654. [PMID: 38712954 PMCID: PMC11103695 DOI: 10.1021/acs.jpcb.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
DNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations. We use four separate single strand DNAs, each having 8 bases (4 × G4C4 and 4 × A4T4), to form two different DNA nanostructures, each having two helices bundled together with one crossover. We also generated double-stranded DNAs to compare electronic properties to decipher the effects of crossovers and bundle formations. We demonstrate that density of states and band gap of DNA origami depend on its sequence and structure. The crossover regions could reduce the conductance due to a lack of available states near the HOMO level. Furthermore, we reveal that, despite having the same sequence, the two helices in the DNA origami structure could exhibit different electronic properties, and electrode position can affect the resulting conductance values. Our study provides better understanding of the electronic properties of DNA origamis and enables us to tune these properties for electronic applications such as nanowires, switches, and logic gates.
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Affiliation(s)
- Busra Demir
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Caglanaz Akin Gultakti
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - Zeynep Koker
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - M. P. Anantram
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
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4
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Liu B, Demir B, Gultakti CA, Marrs J, Gong Y, Li R, Oren EE, Hihath J. Self-Aligning Nanojunctions for Integrated Single-Molecule Circuits. ACS NANO 2024; 18:4972-4980. [PMID: 38214957 DOI: 10.1021/acsnano.3c10844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Robust, high-yield integration of nanoscale components such as graphene nanoribbons, nanoparticles, or single-molecules with conventional electronic circuits has proven to be challenging. This difficulty arises because the contacts to these nanoscale devices must be precisely fabricated with angstrom-level resolution to make reliable connections, and at manufacturing scales this cannot be achieved with even the highest-resolution lithographic tools. Here we introduce an approach that circumvents this issue by precisely creating nanometer-scale gaps between metallic carbon electrodes by using a self-aligning, solution-phase process, which allows facile integration with conventional electronic systems with yields approaching 50%. The electrode separation is controlled by covalently binding metallic single-walled carbon nanotube (mCNT) electrodes to individual DNA duplexes to create mCNT-DNA-mCNT nanojunctions, where the gap is precisely matched to the DNA length. These junctions are then integrated with top-down lithographic techniques to create single-molecule circuits that have electronic properties dominated by the DNA in the junction, have reproducible conductance values with low dispersion, and are stable and robust enough to be utilized as active, high-specificity electronic biosensors for dynamic single-molecule detection of specific oligonucleotides, such as those related to the SARS-CoV-2 genome. This scalable approach for high-yield integration of nanometer-scale devices will enable opportunities for manufacturing of hybrid electronic systems for a wide range of applications.
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Affiliation(s)
- Bo Liu
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Jonathan Marrs
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
| | - Yichen Gong
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Ruihao Li
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Tureky
| | - Joshua Hihath
- Biodesign Center for Bioelectronics and Biosensors at Arizona State University, Tempe, Arizona 85287, United States
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
- School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
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5
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Chandra S, Williams A, Maksudov F, Kliuchnikov E, Pattiya Arachchillage KGG, Piscitelli P, Castillo A, Marx KA, Barsegov V, Artes Vivancos JM. Charge transport in individual short base stacked single-stranded RNA molecules. Sci Rep 2023; 13:19858. [PMID: 37963922 PMCID: PMC10645971 DOI: 10.1038/s41598-023-46263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around [Formula: see text] ([Formula: see text]), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | | | | | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Aderlyn Castillo
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854, USA.
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6
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Gunasinghe Pattiya Arachchillage KG, Chandra S, Williams A, Rangan S, Piscitelli P, Florence L, Ghosal Gupta S, Artes Vivancos JM. A single-molecule RNA electrical biosensor for COVID-19. Biosens Bioelectron 2023; 239:115624. [PMID: 37639885 DOI: 10.1016/j.bios.2023.115624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
The COVID-19 pandemic shows a critical need for rapid, inexpensive, and ultrasensitive early detection methods based on biomarker analysis to reduce mortality rates by containing the spread of epidemics. This can be achieved through the electrical detection of nucleic acids at the single-molecule level. In particular, the scanning tunneling microscopic-assisted break junction (STM-BJ) method can be utilized to detect individual nucleic acid molecules with high specificity and sensitivity in liquid samples. Here, we demonstrate single-molecule electrical detection of RNA coronavirus biomarkers, including those of SARS-CoV-2 as well as those of different variants and subvariants. Our target sequences include a conserved sequence in the human coronavirus family, a conserved target specific for the SARS-CoV-2 family, and specific targets at the variant and subvariant levels. Our results demonstrate that it is possible to distinguish between different variants of the COVID-19 virus using electrical conductance signals, as recently suggested by theoretical approaches. Our results pave the way for future miniaturized single-molecule electrical biosensors that could be game changers for infectious diseases and other public health applications.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Srijith Rangan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Lily Florence
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | | | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA.
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7
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Mohammad H, Anantram MP. Charge transport through DNA with energy-dependent decoherence. Phys Rev E 2023; 108:044403. [PMID: 37978586 DOI: 10.1103/physreve.108.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, USA
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8
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Zhou P, Fu Y, Wang M, Qiu R, Wang Y, Stoddart JF, Wang Y, Chen H. Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions. J Am Chem Soc 2023; 145:18800-18811. [PMID: 37590178 DOI: 10.1021/jacs.3c03282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.
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Affiliation(s)
- Ping Zhou
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yanjun Fu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Maolin Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Renhui Qiu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yuwei Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - J Fraser Stoddart
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yuping Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Hongliang Chen
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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9
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Sun R, Lv J, Xue X, Yu S, Tan Z. Chemical Sensors using Single-Molecule Electrical Measurements. Chem Asian J 2023; 18:e202300181. [PMID: 37080926 DOI: 10.1002/asia.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.
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Affiliation(s)
- Ruiqin Sun
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jieyao Lv
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xinyi Xue
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Shiyong Yu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Zhibing Tan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
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10
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Pattiya Arachchillage KGG, Chandra S, Williams A, Piscitelli P, Pham J, Castillo A, Florence L, Rangan S, Artes Vivancos JM. Electrical detection of RNA cancer biomarkers at the single-molecule level. Sci Rep 2023; 13:12428. [PMID: 37528139 PMCID: PMC10393997 DOI: 10.1038/s41598-023-39450-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Cancer is a significant healthcare issue, and early screening methods based on biomarker analysis in liquid biopsies are promising avenues to reduce mortality rates. Electrical detection of nucleic acids at the single molecule level could enable these applications. We examine the electrical detection of RNA cancer biomarkers (KRAS mutants G12C and G12V) as a single-molecule proof-of-concept electrical biosensor for cancer screening applications. We show that the electrical conductance is highly sensitive to the sequence, allowing discrimination of the mutants from a wild-type KRAS sequence differing in just one base. In addition to this high specificity, our results also show that these biosensors are sensitive down to an individual molecule with a high signal-to-noise ratio. These results pave the way for future miniaturized single-molecule electrical biosensors that could be groundbreaking for cancer screening and other applications.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Jennifer Pham
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Aderlyn Castillo
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Lily Florence
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Srijith Rangan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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11
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Gao D, Tang Z, Chen X, Wu R, Tian Y, Min Q, Zhang JR, Chen Z, Zhu JJ. Reversible Regulation of Long-Distance Charge Transport in DNA Nanowires by Dynamically Controlling Steric Conformation. NANO LETTERS 2023; 23:4201-4208. [PMID: 37188354 DOI: 10.1021/acs.nanolett.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.
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Affiliation(s)
- Di Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhuodong Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, People's Republic of China
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12
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Dief EM, Low PJ, Díez-Pérez I, Darwish N. Advances in single-molecule junctions as tools for chemical and biochemical analysis. Nat Chem 2023; 15:600-614. [PMID: 37106094 DOI: 10.1038/s41557-023-01178-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 03/02/2023] [Indexed: 04/29/2023]
Abstract
The development of miniaturized electronics has led to the design and construction of powerful experimental platforms capable of measuring electronic properties to the level of single molecules, along with new theoretical concepts to aid in the interpretation of the data. A new area of activity is now emerging concerned with repurposing the tools of molecular electronics for applications in chemical and biological analysis. Single-molecule junction techniques, such as the scanning tunnelling microscope break junction and related single-molecule circuit approaches have a remarkable capacity to transduce chemical information from individual molecules, sampled in real time, to electrical signals. In this Review, we discuss single-molecule junction approaches as emerging analytical tools for the chemical and biological sciences. We demonstrate how these analytical techniques are being extended to systems capable of probing chemical reaction mechanisms. We also examine how molecular junctions enable the detection of RNA, DNA, and traces of proteins in solution with limits of detection at the zeptomole level.
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Affiliation(s)
- Essam M Dief
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, London, UK
| | - Nadim Darwish
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
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13
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Wang Y, Demir B, Mohammad H, Oren EE, Anantram MP. Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA. Phys Rev E 2023; 107:044404. [PMID: 37198817 DOI: 10.1103/physreve.107.044404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/01/2023] [Indexed: 05/19/2023]
Abstract
DNA naturally exists in a solvent environment, comprising water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the sodium ion (Na^{+}), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment in charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.
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Affiliation(s)
- Yiren Wang
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06510, Turkey
| | - M P Anantram
- Deparment of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98105, USA
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14
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Li X, Ge W, Guo S, Bai J, Hong W. Characterization and Application of Supramolecular Junctions. Angew Chem Int Ed Engl 2023; 62:e202216819. [PMID: 36585932 DOI: 10.1002/anie.202216819] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
The convergence of supramolecular chemistry and single-molecule electronics offers a new perspective on supramolecular electronics, and provides a new avenue toward understanding and application of intermolecular charge transport at the molecular level. In this review, we will provide an overview of the advances in the characterization technique for the investigation of intermolecular charge transport, and summarize the experimental investigation of several non-covalent interactions, including π-π stacking interactions, hydrogen bonding, host-guest interactions and σ-σ interactions at the single-molecule level. We will also provide a perspective on supramolecular electronics and discuss the potential applications and future challenges.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenhui Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Shuhan Guo
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
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15
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He L, Xie Z, Long X, Zhang C, Ma K, She L. Potential differentiation of successive SARS-CoV-2 mutations by RNA: DNA hybrid analyses. Biophys Chem 2023; 297:107013. [PMID: 37030215 PMCID: PMC10065053 DOI: 10.1016/j.bpc.2023.107013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
The constant mutation of SARS-CoV-2 has triggered a new round of public health crises and has had a huge impact on existing vaccines and diagnostic tools. It is essential to develop a new flexible method to distinguish mutations to prevent the spread of the virus. In this work, we used the combination of density functional theory (DFT) and non-equilibrium Green's function formulation with decoherence, to theoretically study the effect of viral mutation on charge transport properties of viral nucleic acid molecules. We found that all mutation of SARS-CoV-2 on spike protein was accompanied by the change of gene sequence conductance, this is attributed to the change of nucleic acid molecular energy level caused by mutation. Among them, the mutations L18F, P26S, and T1027I caused the largest conductance change after mutation. This provides a theoretical possibility for detecting virus mutation based on the change of molecular conductance of virus nucleic acid.
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16
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Charge Transport across Proteins inside Proteins: Tunneling across Encapsulin Protein Cages and the Effect of Cargo Proteins. Biomolecules 2023; 13:biom13010174. [PMID: 36671559 PMCID: PMC9855946 DOI: 10.3390/biom13010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Charge transport across proteins can be surprisingly efficient over long distances-so-called long-range tunneling-but it is still unclear as to why and under which conditions (e.g., presence of co-factors, type of cargo) the long-range tunneling regime can be accessed. This paper describes molecular tunneling junctions based on an encapsulin (Enc), which is a large protein cage with a diameter of 24 nm that can be loaded with various types of (small) proteins, also referred to as "cargo". We demonstrate with dynamic light scattering, transmission electron microscopy, and atomic force microscopy that Enc, with and without cargo, can be made stable in solution and immobilized on metal electrodes without aggregation. We investigated the electronic properties of Enc in EGaIn-based tunnel junctions (EGaIn = eutectic alloy of Ga and In that is widely used to contact (bio)molecular monolayers) by measuring the current density for a large range of applied bias of ±2.5 V. The encapsulated cargo has an important effect on the electrical properties of the junctions. The measured current densities are higher for junctions with Enc loaded with redox-active cargo (ferritin-like protein) than those junctions without cargo or redox-inactive cargo (green fluorescent protein). These findings open the door to charge transport studies across complex biomolecular hierarchical structures.
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17
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Alangari M, Demir B, Gultakti CA, Oren EE, Hihath J. Mapping DNA Conformations Using Single-Molecule Conductance Measurements. Biomolecules 2023; 13:129. [PMID: 36671514 PMCID: PMC9855376 DOI: 10.3390/biom13010129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
DNA is an attractive material for a range of applications in nanoscience and nanotechnology, and it has recently been demonstrated that the electronic properties of DNA are uniquely sensitive to its sequence and structure, opening new opportunities for the development of electronic DNA biosensors. In this report, we examine the origin of multiple conductance peaks that can occur during single-molecule break-junction (SMBJ)-based conductance measurements on DNA. We demonstrate that these peaks originate from the presence of multiple DNA conformations within the solutions, in particular, double-stranded B-form DNA (dsDNA) and G-quadruplex structures. Using a combination of circular dichroism (CD) spectroscopy, computational approaches, sequence and environmental controls, and single-molecule conductance measurements, we disentangle the conductance information and demonstrate that specific conductance values come from specific conformations of the DNA and that the occurrence of these peaks can be controlled by controlling the local environment. In addition, we demonstrate that conductance measurements are uniquely sensitive to identifying these conformations in solutions and that multiple configurations can be detected in solutions over an extremely large concentration range, opening new possibilities for examining low-probability DNA conformations in solutions.
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Affiliation(s)
- Mashari Alangari
- Department of Electrical Engineering, Engineering College, University of Ha’il, Ha’il 55476, Saudi Arabia
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA 95616, USA
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Caglanaz Akin Gultakti
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
- Department of Materials Science and Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Turkey
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA 95616, USA
- Biodesign Center for Bioelectronics, School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
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18
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Charge transport properties of SARS-CoV-2 Delta variant (B.1.617.2). Process Biochem 2022; 121:656-660. [PMID: 35965635 PMCID: PMC9364919 DOI: 10.1016/j.procbio.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022]
Abstract
The B.1.617.2 (Delta) variant of concern is causing a new wave of infections in many countries. In order to better understand the changes of the SARS-CoV-2 mutation at the genetic level, we selected six mutations in the S region of the Delta variant compared with the native SARS-CoV-2 and get the conductance information of these six short RNA oligonucleotides groups by construct RNA: DNA hybrids. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. We found that conductance is very sensitive to small changes in virus sequence. Among the 6 mutations in the Delta S region, D950N shows the largest change in relative conductance, reaching a surprising 4104.75%. These results provide new insights into the Delta variant from the perspective of its electrical properties. This may be a new method to distinguish virus variation and possess great research prospects.
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19
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Yu P, Chen L, Zhang Y, Zhao S, Chen Z, Hu Y, Liu J, Yang Y, Shi J, Yao Z, Hong W. Single-Molecule Tunneling Sensors for Nitrobenzene Explosives. Anal Chem 2022; 94:12042-12050. [PMID: 35971273 DOI: 10.1021/acs.analchem.2c01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tunneling current through the single-molecule junctions principally offers the ultimate solution for chemical and biochemical sensing via the interactions between probes and target analytes at the single-molecule level. However, it remains unexplored to achieve the sensitive and selective detection of targeted analytes using single-molecule junction techniques due to the challenge in quantitative evaluation of sensing sensitivity and selectivity. Herein, we demonstrate a single-molecule tunneling sensor for the highly sensitive and selective detection of nitrobenzene explosives using scanning tunneling microscope break junction (STM-BJ). Taking advantage of π-π stacking interactions between the molecular probes and nitrobenzene explosives, we use a spectral clustering algorithm to assign the signal of probes and π-stacked probes for sensitively detecting the targeted analytes and the distinguishable conductance change of probes when interacting with different nitroaromatic explosive compounds for selective detection. We find that pronounced conductance changes up to 0.8 orders of magnitude when the probes interact with TNT. Also, we obtain a sensitivity of up to ∼10 pM for TNT and high sensitivity for eight TNT analogues. Combined with theoretical calculations, we discover that the harness of the destructive quantum interference of the probe M1OH after interacting with TNT leads to high selectivity in sensing with TNT. Our work demonstrates the great potential of the single-molecule tunneling current for environmental sensing molecules with high selectivity and sensitivity.
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Affiliation(s)
- Peikai Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Lichuan Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yanxi Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Zhixin Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yong Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Zhiyi Yao
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083 Beijing, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
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20
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Lv SL, Zeng C, Yu Z, Zheng JF, Wang YH, Shao Y, Zhou XS. Recent Advances in Single-Molecule Sensors Based on STM Break Junction Measurements. BIOSENSORS 2022; 12:bios12080565. [PMID: 35892462 PMCID: PMC9329744 DOI: 10.3390/bios12080565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022]
Abstract
Single-molecule recognition and detection with the highest resolution measurement has been one of the ultimate goals in science and engineering. Break junction techniques, originally developed to measure single-molecule conductance, recently have also been proven to have the capacity for the label-free exploration of single-molecule physics and chemistry, which paves a new way for single-molecule detection with high temporal resolution. In this review, we outline the primary advances and potential of the STM break junction technique for qualitative identification and quantitative detection at a single-molecule level. The principles of operation of these single-molecule electrical sensing mainly in three regimes, ion, environmental pH and genetic material detection, are summarized. It clearly proves that the single-molecule electrical measurements with break junction techniques show a promising perspective for designing a simple, label-free and nondestructive electrical sensor with ultrahigh sensitivity and excellent selectivity.
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21
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Aggarwal A, Naskar S, Maiti PK. Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA. J Phys Chem B 2022; 126:4636-4646. [PMID: 35729785 DOI: 10.1021/acs.jpcb.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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22
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Xiao B, He S, Sun M, Zhou J, Wang Z, Li Y, Liu S, Nau WM, Chang S. Dynamic Interconversions of Single Molecules Probed by Recognition Tunneling at Cucurbit[7]uril-Functionalized Supramolecular Junctions. Angew Chem Int Ed Engl 2022; 61:e202203830. [PMID: 35417083 PMCID: PMC9324061 DOI: 10.1002/anie.202203830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/29/2022]
Abstract
We introduce a versatile recognition tunneling technique using doubly cucurbit[7]uril‐functionalized electrodes to form supramolecular junctions that capture analytes dynamically by host–guest complexation. This results in characteristic changes in their single‐molecule conductance. For structurally related drug molecules (camptothecin, sanguinarine, chelerythrine, and berberine) and mixtures thereof, we observed distinct current switching signals related to their intrinsic conductance properties as well as pH‐dependent effects which can be traced back to their different states (protonated versus neutral). The conductance variation of a single molecule with pH shows a sigmoidal distribution, allowing us to extract a pKa value for reversible protonation, which is consistent with the reported macroscopic results. The new electronic method allows the characterization of unmodified drug molecules and showcases the transfer of dynamic supramolecular chemistry principles to single molecules.
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Affiliation(s)
- Bohuai Xiao
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Suhang He
- School of Science, Jacobs University Bremen, 28759, Bremen, Germany
| | - Mingjun Sun
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Jianghao Zhou
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Zhiye Wang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Yunchuan Li
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Simin Liu
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
| | - Werner M Nau
- School of Science, Jacobs University Bremen, 28759, Bremen, Germany
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy Wuhan University of Science and Technology, Wuhan, Hubei, 430081, China
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23
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Aiello CD, Abendroth JM, Abbas M, Afanasev A, Agarwal S, Banerjee AS, Beratan DN, Belling JN, Berche B, Botana A, Caram JR, Celardo GL, Cuniberti G, Garcia-Etxarri A, Dianat A, Diez-Perez I, Guo Y, Gutierrez R, Herrmann C, Hihath J, Kale S, Kurian P, Lai YC, Liu T, Lopez A, Medina E, Mujica V, Naaman R, Noormandipour M, Palma JL, Paltiel Y, Petuskey W, Ribeiro-Silva JC, Saenz JJ, Santos EJG, Solyanik-Gorgone M, Sorger VJ, Stemer DM, Ugalde JM, Valdes-Curiel A, Varela S, Waldeck DH, Wasielewski MR, Weiss PS, Zacharias H, Wang QH. A Chirality-Based Quantum Leap. ACS NANO 2022; 16:4989-5035. [PMID: 35318848 PMCID: PMC9278663 DOI: 10.1021/acsnano.1c01347] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
There is increasing interest in the study of chiral degrees of freedom occurring in matter and in electromagnetic fields. Opportunities in quantum sciences will likely exploit two main areas that are the focus of this Review: (1) recent observations of the chiral-induced spin selectivity (CISS) effect in chiral molecules and engineered nanomaterials and (2) rapidly evolving nanophotonic strategies designed to amplify chiral light-matter interactions. On the one hand, the CISS effect underpins the observation that charge transport through nanoscopic chiral structures favors a particular electronic spin orientation, resulting in large room-temperature spin polarizations. Observations of the CISS effect suggest opportunities for spin control and for the design and fabrication of room-temperature quantum devices from the bottom up, with atomic-scale precision and molecular modularity. On the other hand, chiral-optical effects that depend on both spin- and orbital-angular momentum of photons could offer key advantages in all-optical and quantum information technologies. In particular, amplification of these chiral light-matter interactions using rationally designed plasmonic and dielectric nanomaterials provide approaches to manipulate light intensity, polarization, and phase in confined nanoscale geometries. Any technology that relies on optimal charge transport, or optical control and readout, including quantum devices for logic, sensing, and storage, may benefit from chiral quantum properties. These properties can be theoretically and experimentally investigated from a quantum information perspective, which has not yet been fully developed. There are uncharted implications for the quantum sciences once chiral couplings can be engineered to control the storage, transduction, and manipulation of quantum information. This forward-looking Review provides a survey of the experimental and theoretical fundamentals of chiral-influenced quantum effects and presents a vision for their possible future roles in enabling room-temperature quantum technologies.
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Affiliation(s)
- Clarice D. Aiello
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John M. Abendroth
- Laboratory
for Solid State Physics, ETH Zürich, Zürich 8093, Switzerland
| | - Muneer Abbas
- Department
of Microbiology, Howard University, Washington, D.C. 20059, United States
| | - Andrei Afanasev
- Department
of Physics, George Washington University, Washington, D.C. 20052, United States
| | - Shivang Agarwal
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Amartya S. Banerjee
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - David N. Beratan
- Departments
of Chemistry, Biochemistry, and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Jason N. Belling
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Bertrand Berche
- Laboratoire
de Physique et Chimie Théoriques, UMR Université de Lorraine-CNRS, 7019 54506 Vandœuvre les
Nancy, France
| | - Antia Botana
- Department
of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Justin R. Caram
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Giuseppe Luca Celardo
- Institute
of Physics, Benemerita Universidad Autonoma
de Puebla, Apartado Postal J-48, 72570, Mexico
- Department
of Physics and Astronomy, University of
Florence, 50019 Sesto Fiorentino, Italy
| | - Gianaurelio Cuniberti
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Aitzol Garcia-Etxarri
- Donostia
International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Arezoo Dianat
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Ismael Diez-Perez
- Department
of Chemistry, Faculty of Natural and Mathematical Sciences, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Yuqi Guo
- School
for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Rafael Gutierrez
- Institute
for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany
| | - Carmen Herrmann
- Department
of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Joshua Hihath
- Department
of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
| | - Suneet Kale
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Philip Kurian
- Quantum
Biology Laboratory, Graduate School, Howard
University, Washington, D.C. 20059, United States
| | - Ying-Cheng Lai
- School
of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Tianhan Liu
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Alexander Lopez
- Escuela
Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil 090902, Ecuador
| | - Ernesto Medina
- Departamento
de Física, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Av. Diego de Robles
y Vía Interoceánica, Quito 170901, Ecuador
| | - Vladimiro Mujica
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea, 20080 Donostia, Euskadi, Spain
| | - Ron Naaman
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Mohammadreza Noormandipour
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- TCM Group,
Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Julio L. Palma
- Department
of Chemistry, Pennsylvania State University, Lemont Furnace, Pennsylvania 15456, United States
| | - Yossi Paltiel
- Applied
Physics Department and the Center for Nano-Science and Nano-Technology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - William Petuskey
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - João Carlos Ribeiro-Silva
- Laboratory
of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, 05508-900 São
Paulo, Brazil
| | - Juan José Saenz
- Donostia
International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Elton J. G. Santos
- Institute
for Condensed Matter Physics and Complex Systems, School of Physics
and Astronomy, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- Higgs Centre
for Theoretical Physics, The University
of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
| | - Maria Solyanik-Gorgone
- Department
of Electrical and Computer Engineering, George Washington University, Washington, D.C. 20052, United States
| | - Volker J. Sorger
- Department
of Electrical and Computer Engineering, George Washington University, Washington, D.C. 20052, United States
| | - Dominik M. Stemer
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jesus M. Ugalde
- Kimika
Fakultatea, Euskal Herriko Unibertsitatea, 20080 Donostia, Euskadi, Spain
| | - Ana Valdes-Curiel
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Solmar Varela
- School
of Chemical Sciences and Engineering, Yachay
Tech University, 100119 Urcuquí, Ecuador
| | - David H. Waldeck
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, Center for Molecular Quantum Transduction, and Institute
for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Paul S. Weiss
- California
NanoSystems Institute, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Materials Science and Engineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California, 90095, United States
| | - Helmut Zacharias
- Center
for Soft Nanoscience, University of Münster, 48149 Münster, Germany
| | - Qing Hua Wang
- School
for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
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24
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Xiao B, He S, Sun M, Zhou J, Wang Z, Li Y, Liu S, Nau WM, Chang S. Dynamic Interconversions of Single Molecules Probed by Recognition Tunneling at Cucurbit[7]uril‐Functionalized Supramolecular Junctions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bohuai Xiao
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
| | - Suhang He
- Jacobs University Bremen gGmbH Department of Life Sciences and Chemistry Campus Ring 1 28759 Bremen GERMANY
| | - Mingjun Sun
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
| | - Jianghao Zhou
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
| | - Zhiye Wang
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
| | - Yunchuan Li
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
| | - Simin Liu
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering CHINA
| | - Werner M. Nau
- Jacobs University Bremen Department of Chemistry Campus Ring 1School of Engineering and Science 28759 Bremen GERMANY
| | - Shuai Chang
- Wuhan University of Science and Technology The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, College of Materials and Metallurgy CHINA
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25
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Zhang M, Li Z, Jia Y, Wang F, Tian J, Zhang C, Han T, Xing R, Ye W, Wang C. Observing Mesoscopic Nucleic Acid Capacitance Effect and Mismatch Impact via Graphene Transistors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105890. [PMID: 35072345 DOI: 10.1002/smll.202105890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/05/2021] [Indexed: 06/14/2023]
Abstract
This work reports a molecular-scale capacitance effect of the double helical nucleic acid duplex structure for the first time. By quantitatively conducting large sample measurements of the electrostatic field effect using a type of high-accuracy graphene transistor biosensor, an unusual charge-transport behavior is observed in which the end-immobilized nucleic acid duplexes can store a part of ionization electrons like molecular capacitors, other than electric conductors. To elucidate this discovery, a cascaded capacitive network model is proposed as a novel equivalent circuit of nucleic acid duplexes, expanding the point-charge approximation model, by which the partial charge-transport observation is reasonably attributed to an electron-redistribution behavior within the capacitive network. Furthermore, it is experimentally confirmed that base-pair mismatches hinder the charge transport in double helical duplexes, and lead to directly identifiable alterations in electrostatic field effects. The bioelectronic principle of mismatch impact is also self-consistently explained by the newly proposed capacitive network model. The mesoscopic nucleic acid capacitance effect may enable a new kind of label-free nucleic acid analysis tool based on electronic transistor devices. The in situ and real-time nucleic acid detections for virus biomarkers, somatic mutations, and genome editing off-target may thus be predictable.
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Affiliation(s)
- Mingfeng Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Zhibo Li
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Yuan Jia
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Fuquan Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Jinpeng Tian
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Cuiping Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Tingting Han
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Ruiqing Xing
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Weixiang Ye
- Department of Physics, School of Science, Hainan University, Haikou, 570228, China
- Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, School of Science, Hainan University, Haikou, 570228, China
| | - Cheng Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
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26
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Chandra S, Gunasinghe Pattiya Arachchillage KG, Kliuchnikov E, Maksudov F, Ayoub S, Barsegov V, Artés Vivancos JM. Single-molecule conductance of double-stranded RNA oligonucleotides. NANOSCALE 2022; 14:2572-2577. [PMID: 35107112 DOI: 10.1039/d1nr06925j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA : RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA. Microsecond Molecular Dynamics simulations explain this difference and provide structural insights into the higher stability of DNA : RNA duplex with atomic level of detail. The rotations of 2'-OH groups of the ribose rings and the bases in RNA strands destabilize the duplex structure by weakening base stacking interactions, affecting charge transport, and making single-molecule conductance of dsRNA more variable (dynamic disorder). The results demonstrate that a powerful combination of state-of-the-art biomolecular electronics techniques and computational approaches can provide valuable insights into biomolecules' biophysics with unprecedented spatial resolution.
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Affiliation(s)
- Subrata Chandra
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | | | - Evgenii Kliuchnikov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Steven Ayoub
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, 01854 MA, USA.
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27
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Yuan S, Qian Q, Zhou Y, Zhao S, Lin L, Duan P, Xu X, Shi J, Xu W, Feng A, Shi J, Yang Y, Hong W. Tracking Confined Reaction Based on Host-Guest Interaction Using Single-Molecule Conductance Measurement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104554. [PMID: 34796644 DOI: 10.1002/smll.202104554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The host-guest interaction acts as an essential part of supramolecular chemistry, which can be applied in confined reaction. However, it is challenging to obtain the dynamic process during confined reactions below micromolar concentrations. In this work, a new method is provided to characterize the dimerization process of the guest 1,2-bis(4-pyridinyl) ethylene in host cucurbit[8]curil using scanning tunneling microscope-break junction (STM-BJ) technique. The guest reaction kinetics is quantitatively by nuclear magnetic resonance (NMR) and in situ single-molecule junctions. It is found that in the single-molecule conductance measurements, the electrical signals of the reactants with a concentration as low as 5 × 10-6 m are clearly detected, and the reaction kinetics at micromolar concentrations are further obtained. However, in NMR measurements, the characteristic peak signal of the reactants is undetectable when the concentration of the reactants is lower than 0.5 × 10-3 m and it cannot be quantified. In addition, the strong electric field from the nanogap accelerates the reaction. This work reveals that single-molecule STM-BJ techniques are more sensitive for tracking confined reactions than that by NMR techniques and can be used to study effect of extremely strong electric field on kinetics.
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Affiliation(s)
- Saisai Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Qiaozan Qian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yu Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Shiqiang Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Luchun Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Ping Duan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xinghai Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jie Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wei Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Anni Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Pen-Tung Sah Institute of Micro-Nano Science and Technology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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28
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Xie Z, Diez Cabanes V, Van Nguyen Q, Rodriguez-Gonzalez S, Norel L, Galangau O, Rigaut S, Cornil J, Frisbie CD. Quantifying Image Charge Effects in Molecular Tunnel Junctions Based on Self-Assembled Monolayers of Substituted Oligophenylene Ethynylene Dithiols. ACS APPLIED MATERIALS & INTERFACES 2021; 13:56404-56412. [PMID: 34783518 DOI: 10.1021/acsami.1c16398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A number of factors contribute to orbital energy alignment with respect to the Fermi level in molecular tunnel junctions. Here, we report a combined experimental and theoretical effort to quantify the effect of metal image potentials on the highest occupied molecular orbital to Fermi level offset, εh, for molecular junctions based on self-assembled monolayers (SAMs) of oligophenylene ethynylene dithiols (OPX) on Au. Our experimental approach involves the use of both transport and photoelectron spectroscopy to extract the offsets, εhtrans and εhUPS, respectively. We take the difference in these quantities to be the image potential energy eVimage. In the theoretical approach, we use density functional theory (DFT) to calculate directly eVimage between positive charge on an OPX molecule and the negative image charge in the Au. Both approaches yield eVimage ∼ -0.1 eV per metal contact, meaning that the total image potential energy is ∼-0.2 eV for an assembled junction with two Au contacts. Thus, we find that the total image potential energy is 25-30% of the total offset εh, which means that image charge effects are significant in OPX junctions. Our methods should be generally applicable to understanding image charge effects as a function of molecular size, for example, in a variety of SAM-based junctions.
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Affiliation(s)
- Zuoti Xie
- Department of Materials Science and Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Valentin Diez Cabanes
- Laboratory for Chemistry of Novel Materials, University of Mons, Mons B-7000, Belgium
| | - Quyen Van Nguyen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sandra Rodriguez-Gonzalez
- Laboratory for Chemistry of Novel Materials, University of Mons, Mons B-7000, Belgium
- Department of Physical Chemistry, University of Malaga, Campus de Teatinos s/n, Malaga 29071, Spain
| | - Lucie Norel
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes F-3500, France
| | - Olivier Galangau
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes F-3500, France
| | - Stéphane Rigaut
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes F-3500, France
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, University of Mons, Mons B-7000, Belgium
| | - C Daniel Frisbie
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
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29
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Affiliation(s)
- Nadim Darwish
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
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30
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Pattiya Arachchillage KGG, Chandra S, Piso A, Qattan T, Artes Vivancos JM. RNA BioMolecular Electronics: towards new tools for biophysics and biomedicine. J Mater Chem B 2021; 9:6994-7006. [PMID: 34494636 DOI: 10.1039/d1tb01141c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The last half-century has witnessed the birth and development of a new multidisciplinary field at the edge between materials science, nanoscience, engineering, and chemistry known as Molecular Electronics. This field deals with the electronic properties of individual molecules and their integration as active components in electronic circuits and has also been applied to biomolecules, leading to BioMolecular Electronics and opening new perspectives for single-molecule biophysics and biomedicine. Herein, we provide a brief introduction and overview of the BioMolecular electronics field, focusing on nucleic acids and potential applications for these measurements. In particular, we review the recent demonstration of the first single-molecule electrical detection of a biologically-relevant nucleic acid. We also show how this could be used to study biomolecular interactions and applications in liquid biopsy for early cancer detection, among others. Finally, we discuss future perspectives and challenges in the applications of this fascinating research field.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Angela Piso
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Tiba Qattan
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
| | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, One University Ave, 01854 Lowell, MA, USA.
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31
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Mohammad H, Demir B, Akin C, Luan B, Hihath J, Oren EE, Anantram MP. Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics. NANOSCALE HORIZONS 2021; 6:651-660. [PMID: 34190284 DOI: 10.1039/d1nh00211b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
| | - Busra Demir
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Caglanaz Akin
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research, Yorktown Heights, NY 10598, USA
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, Davis, CA, USA
| | - Ersin Emre Oren
- Bionanodesign Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara, Turkey. and Department of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara, Turkey
| | - M P Anantram
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
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32
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Domulevicz L, Jeong H, Paul NK, Gomez-Diaz JS, Hihath J. Multidimensional Characterization of Single-Molecule Dynamics in a Plasmonic Nanocavity. Angew Chem Int Ed Engl 2021; 60:16436-16441. [PMID: 33847037 DOI: 10.1002/anie.202100886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/18/2021] [Indexed: 11/07/2022]
Abstract
Nanoscale manipulation and characterization of individual molecules is necessary to understand the intricacies of molecular structure, which governs phenomena such as reaction mechanisms, catalysis, local effective temperatures, surface interactions, and charge transport. Here we utilize Raman enhancement between two nanostructured electrodes in combination with direct charge transport measurements to allow for simultaneous characterization of the electrical, optical, and mechanical properties of a single molecule. This multi-dimensional information yields repeatable, self-consistent, verification of single-molecule resolution, and allows for detailed analysis of structural and configurational changes of the molecule in situ. These experimental results are supported by a machine-learning based statistical analysis of the spectral information and calculations to provide insight into the correlation between structural changes in a single-molecule and its charge-transport properties.
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Affiliation(s)
- Lucas Domulevicz
- Department of Electrical and Computer Engineering, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Hyunhak Jeong
- Department of Electrical and Computer Engineering, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Nayan K Paul
- Department of Electrical and Computer Engineering, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Juan Sebastian Gomez-Diaz
- Department of Electrical and Computer Engineering, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California Davis, One Shields Ave., Davis, CA, 95616, USA
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33
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Domulevicz L, Jeong H, Paul NK, Gomez‐Diaz JS, Hihath J. Multidimensional Characterization of Single‐Molecule Dynamics in a Plasmonic Nanocavity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lucas Domulevicz
- Department of Electrical and Computer Engineering University of California Davis One Shields Ave. Davis CA 95616 USA
| | - Hyunhak Jeong
- Department of Electrical and Computer Engineering University of California Davis One Shields Ave. Davis CA 95616 USA
| | - Nayan K. Paul
- Department of Electrical and Computer Engineering University of California Davis One Shields Ave. Davis CA 95616 USA
| | - Juan Sebastian Gomez‐Diaz
- Department of Electrical and Computer Engineering University of California Davis One Shields Ave. Davis CA 95616 USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering University of California Davis One Shields Ave. Davis CA 95616 USA
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34
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He L, Zhang J, He C, Zhao B, Xie Z, Chen W, Sonawane MR, Patil SR. Electronic characteristics of BRCA1 mutations in DNA. Biopolymers 2021; 112:e23465. [PMID: 34242395 DOI: 10.1002/bip.23465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/08/2022]
Abstract
The efficient and low-cost way for gene mutation detection and identification are conducive for the detection of disease. Here, we report the electronic characteristics of the gene of breast cancer 1 in four common mutation types: duplication, single nucleotide variant, deletion, and indel. The electronic characteristics are investigated by the combination of density functional theory and non-equilibrium Green's function formulation with decoherence. The magnitude of conductance of these DNA molecules and mutational changes are found to be detectable experimentally. In this study, we also find the significant mutation type dependent on the change of conductance. Hence these mutations are expected to be identifiable. We find deletion type mutation shows the largest change in relative conductance (~97%), whereas the indel mutation shows the smallest change in relative conductance (~27%). Therefore, this work presents a possibility of electronic detection and identification of mutations in DNA, which could be an efficient method as compared to the conventional methods.
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Affiliation(s)
- Lijun He
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jinsha Zhang
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chengyun He
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Boyang Zhao
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Zhiyang Xie
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Weizhong Chen
- The School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | | | - Sunil R Patil
- Department of Physics, Institute of Science, Nagpur, India
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35
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Wang Y, Alangari M, Hihath J, Das AK, Anantram MP. A machine learning approach for accurate and real-time DNA sequence identification. BMC Genomics 2021; 22:525. [PMID: 34243709 PMCID: PMC8268518 DOI: 10.1186/s12864-021-07841-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/24/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results. RESULTS This article presents a DNA sequence identification system based on the current spectra of ten short strand sequences, including a pair that differs by a single mismatch. By employing a gradient boosted tree classifier model trained on conductance histograms, we demonstrate that extremely high accuracy, ranging from approximately 96 % for molecules differing by a single mismatch to 99.5 % otherwise, is possible. Further, such accuracy metrics are achievable in near real-time with just twenty or thirty SMBJ measurements instead of hundreds or thousands. We also demonstrate that a tandem classifier architecture, where the first stage is a multiclass classifier and the second stage is a binary classifier, can be employed to boost the single mismatched pair's identification accuracy to 99.5 %. CONCLUSIONS A monolithic classifier, or more generally, a multistage classifier with model specific parameters that depend on experimental current spectra can be used to successfully identify DNA strands.
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Affiliation(s)
- Yiren Wang
- Department of Electrical and Computer Engineering, University of Washington, 98195, Seattle, WA, USA.
| | - Mashari Alangari
- Electrical and Computer Engineering Department, University of California Davis, 95616, Davis, CA, USA
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis, 95616, Davis, CA, USA
| | - Arindam K Das
- Department of Electrical Engineering, Eastern Washington University, 99004, Cheney, WA, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, 98195, Seattle, WA, USA.
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36
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Aggarwal A, Sahoo AK, Bag S, Kaliginedi V, Jain M, Maiti PK. Fine-tuning the DNA conductance by intercalation of drug molecules. Phys Rev E 2021; 103:032411. [PMID: 33862831 DOI: 10.1103/physreve.103.032411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Veerabhadrarao Kaliginedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manish Jain
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Lee HJ, Cho SJ, Kang H, He X, Yoon HJ. Achieving Ultralow, Zero, and Inverted Tunneling Attenuation Coefficients in Molecular Wires with Extended Conjugation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005711. [PMID: 33543557 DOI: 10.1002/smll.202005711] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Molecular tunnel junctions are organic devices miniaturized to the molecular scale. They serve as a versatile toolbox that can systematically examine charge transport behaviors at the atomic level. The electrical conductance of the molecular wire that bridges the two electrodes in a junction is significantly influenced by its chemical structure, and an intrinsically poor conductance is a major barrier for practical applications toward integrating individual molecules into electronic circuitry. Therefore, highly conjugated molecular wires are attractive as active components for the next-generation electronic devices, owing to the narrow highest occupied molecular orbital-lowest occupied molecular orbital gaps provided by their extended π-building blocks. This article aims to highlight the significance of highly conductive molecular wires in molecular electronics, the structures of which are inspired from conductive organic polymers, and presents a body of discussion on molecular wires exhibiting ultralow, zero, or inverted attenuation of tunneling probability at different lengths, along with future directions.
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Affiliation(s)
- Hyun Ju Lee
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Soo Jin Cho
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Hungu Kang
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Xin He
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Hyo Jae Yoon
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
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Hu Y, Zhuang X, Lin L, Liu J, Yao Z, Xiao Z, Shi J, Fang B, Hong W. Determination of Ag[I] and NADH Using Single-Molecule Conductance Ratiometric Probes. ACS Sens 2021; 6:461-469. [PMID: 33326215 DOI: 10.1021/acssensors.0c02038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The sensing platform based on single-molecule measurements provides a new perspective for constructing ultrasensitive systems. However, most of these sensing platforms are unavailable for the accurate determination of target analytes. Herein, we demonstrate a conductance ratiometric strategy combing with the single-molecule conductance techniques for ultrasensitive and precise determination. A single-molecule sensing platform was constructed with the 3,3',5,5'-tetramethylbenzidine (TMB) and oxidized TMB (oxTMB) as the conductance ratiometric probes, which was applied in the detection of Ag[I] and nicotinamide adenine dinucleotide (NADH). It was found that the charge transport properties of TMB and oxTMB were distinct with more than an order of magnitude change of the conductance, thus enabling conductance ratiometric analysis of the Ag[I] and NADH in the real samples. The proposed method is ultrasensitive and has an anti-interference ability in the complicated matrix. The limit of detection can be as low as attomolar concentrations (∼34 aM). We believe that the proposed conductance ratiometric approach is generally enough to have a promising potential for broad and complicated analysis.
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Affiliation(s)
- Yong Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaoyan Zhuang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Luchun Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhiyi Yao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Baishan Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Tang L, Nadappuram BP, Cadinu P, Zhao Z, Xue L, Yi L, Ren R, Wang J, Ivanov AP, Edel JB. Combined quantum tunnelling and dielectrophoretic trapping for molecular analysis at ultra-low analyte concentrations. Nat Commun 2021; 12:913. [PMID: 33568635 PMCID: PMC7876030 DOI: 10.1038/s41467-021-21101-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/06/2021] [Indexed: 01/04/2023] Open
Abstract
Quantum tunnelling offers a unique opportunity to study nanoscale objects with atomic resolution using electrical readout. However, practical implementation is impeded by the lack of simple, stable probes, that are required for successful operation. Existing platforms offer low throughput and operate in a limited range of analyte concentrations, as there is no active control to transport molecules to the sensor. We report on a standalone tunnelling probe based on double-barrelled capillary nanoelectrodes that do not require a conductive substrate to operate unlike other techniques, such as scanning tunnelling microscopy. These probes can be used to efficiently operate in solution environments and detect single molecules, including mononucleotides, oligonucleotides, and proteins. The probes are simple to fabricate, exhibit remarkable stability, and can be combined with dielectrophoretic trapping, enabling active analyte transport to the tunnelling sensor. The latter allows for up to 5-orders of magnitude increase in event detection rates and sub-femtomolar sensitivity. Probes that effectively utilize quantum tunneling are sought after for high-resolution study of nanoscale objects. Here the authors present an easily fabricated probe of two nanoelectrodes that enables highly sensitive quantum-tunneling-based sensing of single molecules.
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Affiliation(s)
- Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering; International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China. .,Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK. .,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China.
| | | | - Paolo Cadinu
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Zhiyu Zhao
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Liang Xue
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Long Yi
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Ren Ren
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Jiangwei Wang
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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40
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Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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41
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Zwolak M. Analytic expressions for the steady-state current with finite extended reservoirs. J Chem Phys 2020; 153:224107. [PMID: 33317280 PMCID: PMC8356363 DOI: 10.1063/5.0029223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Open-system simulations of quantum transport provide a platform for the study of true steady states, Floquet states, and the role of temperature, time dynamics, and fluctuations, among other physical processes. They are rapidly gaining traction, especially techniques that revolve around "extended reservoirs," a collection of a finite number of degrees of freedom with relaxation that maintains a bias or temperature gradient, and have appeared under various guises (e.g., the extended or mesoscopic reservoir, auxiliary master equation, and driven Liouville-von Neumann approaches). Yet, there are still a number of open questions regarding the behavior and convergence of these techniques. Here, we derive general analytical solutions, and associated asymptotic analyses, for the steady-state current driven by finite reservoirs with proportional coupling to the system/junction. In doing so, we present a simplified and unified derivation of the non-interacting and many-body steady-state currents through arbitrary junctions, including outside of proportional coupling. We conjecture that the analytic solution for proportional coupling is the most general of its form for isomodal relaxation (i.e., relaxing proportional coupling will remove the ability to find compact, general analytical expressions for finite reservoirs). These results should be of broad utility in diagnosing the behavior and implementation of extended reservoir and related approaches, including the convergence to the Landauer limit (for non-interacting systems) and the Meir-Wingreen formula (for many-body systems).
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Affiliation(s)
- Michael Zwolak
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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42
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Forzani ES, He H, Hihath J, Lindsay S, Penner RM, Wang S, Xu B. Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020). ACS NANO 2020; 14:12291-12312. [PMID: 32940998 PMCID: PMC7718722 DOI: 10.1021/acsnano.0c06017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.
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Affiliation(s)
- Erica S Forzani
- Biodesign Center for Bioelectronics and Biosensors, Departments of Chemical Engineering and Mechanical Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Huixin He
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California 95616, United States
| | - Stuart Lindsay
- Biodesign Center for Single Molecule Biophysics, Arizona State University, Tempe, Arizona 85287, United States
| | - Reginald M Penner
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona 85287, United States
| | - Bingqian Xu
- School of Electrical and Computer Engineering, University of Georgia, Athens, Georgia 30602, United States
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43
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Aggarwal A, Bag S, Venkatramani R, Jain M, Maiti PK. Multiscale modelling reveals higher charge transport efficiencies of DNA relative to RNA independent of mechanism. NANOSCALE 2020; 12:18750-18760. [PMID: 32970051 DOI: 10.1039/d0nr02382e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we compare the charge transport properties of multiple double-stranded (ds)RNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA : RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in the coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has a smaller end-to-end length relative to that of dsDNA.
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Affiliation(s)
- Abhishek Aggarwal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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44
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Gao Y, He Z, He X, Zhang H, Weng J, Yang X, Meng F, Luo L, Tang BZ. Dual-Color Emissive AIEgen for Specific and Label-Free Double-Stranded DNA Recognition and Single-Nucleotide Polymorphisms Detection. J Am Chem Soc 2019; 141:20097-20106. [DOI: 10.1021/jacs.9b09239] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yuting Gao
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhenyan He
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuewen He
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Haoke Zhang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
| | - Jun Weng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fanling Meng
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Liang Luo
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ben Zhong Tang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, People’s Republic of China
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45
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Veselinovic J, Alangari M, Li Y, Matharu Z, Artés JM, Seker E, Hihath J. Two-tiered electrical detection, purification, and identification of nucleic acids in complex media. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.05.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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46
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Taniguchi M. Paving the way to single-molecule chemistry through molecular electronics. Phys Chem Chem Phys 2019; 21:9641-9650. [PMID: 31062773 DOI: 10.1039/c9cp00264b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since our understanding of single-molecule junctions, in which single molecules are connected between nanoelectrodes, has deepened, we have paved the way to single-molecule chemistry. Herein, we review fundamental properties, including the number of molecules connected to the electrode, their structure and type, the bonding force between the single molecule and electrode and the thermopower and quantum interference in single-molecule junctions. Additionally, we review the application of single-molecule junctions to biomolecules. Finally, we explore single-molecule chemical reaction analysis, which is one direction of single-molecule junction research.
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Affiliation(s)
- Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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47
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Bouilly D. Detecting short RNA sequences of pathogens. NATURE NANOTECHNOLOGY 2018; 13:1094-1096. [PMID: 30397283 DOI: 10.1038/s41565-018-0303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Delphine Bouilly
- Institute for Research in Immunology and Cancer (IRIC) & Department of Physics, Université de Montréal, Montréal, Québec, Canada.
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