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Alfinito E. TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties. Int J Mol Sci 2023; 24:14492. [PMID: 37833940 PMCID: PMC10572628 DOI: 10.3390/ijms241914492] [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: 08/16/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead.
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Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, I-73100 Lecce, Italy
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2
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Skotadis E, Aslanidis E, Tsekenis G, Panagopoulou C, Rapesi A, Tzourmana G, Kennou S, Ladas S, Zeniou A, Tsoukalas D. Hybrid Nanoparticle/DNAzyme Electrochemical Biosensor for the Detection of Divalent Heavy Metal Ions and Cr 3. SENSORS (BASEL, SWITZERLAND) 2023; 23:7818. [PMID: 37765875 PMCID: PMC10535422 DOI: 10.3390/s23187818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is proposed for the detection of Pb2+, Cd2+, and Cr3+. The sensor takes advantage of a well-studied material that is known for its selective interaction with heavy metal ions (i.e., DNAzymes), which is combined with metallic nanoparticles. The double-helix structure of DNAzymes is known to dissociate into smaller fragments in the presence of specific heavy metal ions; this results in a measurable change in device resistance due to the collapse of conductive inter-nanoparticle DNAzyme bridging. The paper discusses the effect of DNAzyme anchoring groups (i.e., thiol and amino functionalization groups) on device performance and reports on the successful detection of all three target ions in concentrations that are well below their maximum permitted levels in tap water. While the use of DNAzymes for the detection of lead in particular and, to some extent, cadmium has been studied extensively, this is one of the few reports on the successful detection of chromium (III) via a sensor incorporating DNAzymes. The sensor showed great potential for its future integration in autonomous and remote sensing systems due to its low power characteristics, simple and cost-effective fabrication, and easy automation and measurement.
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Affiliation(s)
- Evangelos Skotadis
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
| | - Evangelos Aslanidis
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
| | - Georgios Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 11527 Athens, Greece;
| | - Chryssi Panagopoulou
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
| | - Annita Rapesi
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
| | - Georgia Tzourmana
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
| | - Stella Kennou
- Department of Chemical Engineering, University of Patras, 26504 Patras, Greece; (S.K.); (S.L.)
| | - Spyridon Ladas
- Department of Chemical Engineering, University of Patras, 26504 Patras, Greece; (S.K.); (S.L.)
| | - Angelos Zeniou
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Aghia Paraskevi, 15310 Attiki, Greece;
| | - Dimitris Tsoukalas
- Department of Applied Physics, National Technical University of Athens, 15780 Athens, Greece; (E.A.); (C.P.); (A.R.); (G.T.); (D.T.)
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3
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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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4
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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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5
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Marrs J, Lu Q, Pan V, Ke Y, Hihath J. Structure-Dependent Electrical Conductance of DNA Origami Nanowires. Chembiochem 2023; 24:e202200454. [PMID: 36342926 DOI: 10.1002/cbic.202200454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Indexed: 11/09/2022]
Abstract
Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si3 N4 ) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si3 N4 substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼1013 ohms) than on native Si3 N4 substrates without HMDS (∼1014 ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si3 N4 substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.
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Affiliation(s)
- Jonathan Marrs
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA
| | - Qinyi Lu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Victor Pan
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Joshua Hihath
- Department of Electrical and Computer Engineering, University of California, Davis, Davis, California, 95616, USA.,Biodesign Center for Bioelectronics, School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA
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6
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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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7
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Zhang D, Hermann T. Metalated Nucleic Acid Nanostructures. Methods Mol Biol 2023; 2709:97-103. [PMID: 37572274 DOI: 10.1007/978-1-0716-3417-2_5] [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] [Indexed: 08/14/2023]
Abstract
Nucleic acid nanotechnology takes advantage of the self-assembling property of nucleic acids to form a variety of shapes and structures. The incorporation of metal ions into these structures introduces functionality for sensor and molecular electronic applications. Here, we describe a protocol for the incorporation of silver ions into polygonal nanoshapes that self-assemble from RNA and DNA modules.
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Affiliation(s)
- Douglas Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
- Center for Drug Discovery Innovation, University of California, San Diego, CA, USA.
- Program in Materials Science and Engineering, University of California, San Diego, CA, USA.
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8
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Li C, Yan PJ, Chen Y, Yang R, Sun M. Spectral investigation on single molecular optoelectronics of ladder phenylenes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121283. [PMID: 35537258 DOI: 10.1016/j.saa.2022.121283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 06/14/2023]
Abstract
Atomic chains and organic conjugated molecules are of great important research value in molecular optoelectronics, due to their special optoelectronic properties. The fully conjugated nature of ladder phenylenes (LPs) provide some unique properties that have potential applications in the fabrication of molecular electronics devices. Our results reveal optoelectronic properties apply density function theory and non-equilibrium green's function theory, including unit-dependent light absorption, Raman scattering, phonon energy band structure, the chemical potential dependent density of states, electrical conductivity, I-V curve, transmission spectrum, etc. Our research provides theoretical guidance for the regulation of light-harvesting regions based on LPs structures, and theoretical support for the design of nano-scale optoelectronic devices.
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Affiliation(s)
- Chenyu Li
- School of Mathematics and Physics, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Pen-Ji Yan
- College of Chemistry and Chemical Engineering, Key Laboratory of Hexi Corridor Resources Utilization of Gansu Universities, Hexi University, Zhangye 734000, PR China
| | - Yichuan Chen
- School of Mathematics and Physics, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Rui Yang
- School of Mathematics and Physics, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Mengtao Sun
- School of Mathematics and Physics, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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9
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Nandi S, Coane C, Villegas AE, Ray A, Di Felice R. The impact of G-quadruplex dynamics on inter-tetrad electronic couplings: a hybrid computational study. Phys Chem Chem Phys 2022; 24:22513-22522. [PMID: 36106845 DOI: 10.1039/d2cp03505g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The G-quadruplex is a fascinating nucleic acid motif with implications in biology, medicine, and nanotechnologies. G-quadruplexes can form in the telomeres at the edges of chromosomes and in other guanine-rich regions of the genome. They can also be engineered for exploitation as biological materials for nanodevices. Their higher stiffness and higher charge transfer rates make them better candidates in nanodevices than duplex DNA. For the development of molecular nanowires, it is important to optimize electron transport along the wire axis. One powerful basis to do so is by manipulating the structure, based on known effects that structural changes have on electron transport. Here, we investigate such effects, by a combination of classical simulations of the structure and dynamics and quantum calculations of electronic couplings. We find that this structure-function relationship is complex. A single helix shape parameter alone does not embody such complexity, but rather a combination of distances and angles between stacked bases influences charge transfer efficiency. By analyzing linear combinations of shape descriptors for different topologies, we identify the structural features that most affect charge transfer efficiency. We discuss the transferability of the proposed model and the limiting effects of inherent flexibility.
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Affiliation(s)
- Samprita Nandi
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Colin Coane
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angel-Emilio Villegas
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Angana Ray
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA. .,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.,CNR Institute of Nanoscience, 41125 Modena, Italy
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10
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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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11
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Xie X, Li P, Xu Y, Zhou L, Yan Y, Xie L, Jia C, Guo X. Single-Molecule Junction: A Reliable Platform for Monitoring Molecular Physical and Chemical Processes. ACS NANO 2022; 16:3476-3505. [PMID: 35179354 DOI: 10.1021/acsnano.1c11433] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Monitoring and manipulating the physical and chemical behavior of single molecules is an important development direction of molecular electronics that aids in understanding the molecular world at the single-molecule level. The electrical detection platform based on single-molecule junctions can monitor physical and chemical processes at the single-molecule level with a high temporal resolution, stability, and signal-to-noise ratio. Recently, the combination of single-molecule junctions with different multimodal control systems has been widely used to explore significant physical and chemical phenomena because of its powerful monitoring and control capabilities. In this review, we focus on the applications of single-molecule junctions in monitoring molecular physical and chemical processes. The methods developed for characterizing single-molecule charge transfer and spin characteristics as well as revealing the corresponding intrinsic mechanisms are introduced. Dynamic detection and regulation of single-molecule conformational isomerization, intermolecular interactions, and chemical reactions are also discussed in detail. In addition to these dynamic investigations, this review discusses the open challenges of single-molecule detection in the fields of physics and chemistry and proposes some potential applications in this field.
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Affiliation(s)
- Xinmiao Xie
- Center for Molecular Systems and Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, PR China
| | - Peihui Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, PR China
| | - Yanxia Xu
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, PR China
| | - Li Zhou
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, PR China
| | - Yong Yan
- Center for Molecular Systems and Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, PR China
| | - Linghai Xie
- Center for Molecular Systems and Organic Devices (CMSOD), Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, PR China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, PR China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, PR China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, PR China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, PR China
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12
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Wang Y, Sadar J, Tsao CW, Mukherjee S, Qing Q. Nanopore chip with self-aligned transverse tunneling junction for DNA detection. Biosens Bioelectron 2021; 193:113552. [PMID: 34416434 DOI: 10.1016/j.bios.2021.113552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
To achieve better signal quality and resolution in nanopore sequencing, there has been strong interest in quantum tunneling based detection which requires integration of tunneling junctions in nanopores. However, there has been very limited success due to precision and reproducibility issues. Here we report a new strategy based on feedback-controlled electrochemical processes in a confined nanoscale space to construct nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip. We demonstrate high-yield (>93%) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate. We also observed events attributed to non-translocating DNA making contact with the transverse electrodes. Existing challenges for precise sequencing are discussed, including fast translocation speed, and interference from transient electrostatic signals from fast-moving DNAs. Our work can serve as a first step to provide an accessible, and reproducible platform enabling further optimizations for tunneling-based DNA detection, and potentially sequencing.
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Affiliation(s)
- Yuan Wang
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Joshua Sadar
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Ching-Wei Tsao
- School for Engineering of Matter, Transport & Energy, And Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States
| | - Sanjana Mukherjee
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States; Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States.
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13
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LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability. MATERIALS 2021; 14:ma14174930. [PMID: 34501020 PMCID: PMC8434186 DOI: 10.3390/ma14174930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022]
Abstract
To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. For the non-diagonal matrix elements referring to neighboring atoms, we employ the Slater–Koster two-center interaction transfer integrals. We use Harrison-type expressions with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation energies of heterocycles with those obtained from Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA structural variability, a task impossible for the plane Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.
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14
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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15
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Mantela M, Morphis A, Lambropoulos K, Simserides C, Di Felice R. Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study. J Phys Chem B 2021; 125:3986-4003. [PMID: 33857373 DOI: 10.1021/acs.jpcb.0c11489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.
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Affiliation(s)
- Marilena Mantela
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Andreas Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Konstantinos Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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16
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Mozneb M, Mirtaheri E, Sanabria AO, Li CZ. Bioelectronic properties of DNA, protein, cells and their applications for diagnostic medical devices. Biosens Bioelectron 2020; 167:112441. [PMID: 32763825 DOI: 10.1016/j.bios.2020.112441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/25/2023]
Abstract
From a couple of centuries ago, understanding physical properties of biological material, their interference with their natural host and their potential manipulation for employment as a conductor in medical devices, has gathered substantial interest in the field of bioelectronics. With the fast-emerging technologies for fabrication of diagnostic modalities, wearable biosensors and implantable devices, which electrical components are of essential importance, a need for developing novel conductors within such devices has evolved over the past decades. As the possibility of electron transport within small biological molecules, such as DNA and proteins, as well as larger elements such as cells was established, several discoveries of the modern charge characterization technologies were evolved. Development of Electrochemical Scanning Tunneling Microscopy and Nuclear Magnetic Resonance among many other techniques were of vital importance, following the discoveries made in sub-micron scales of biological material. This review covers the most recent understandings of electronic properties within different scale of biological material starting from nanometer range to millimeter-sized organs. We also discuss the state-of-the-art technology that's been made taking advantage of electronic properties of biological material for addressing diseases like Parkinson's Disease and Epilepsy.
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Affiliation(s)
- Maedeh Mozneb
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Elnaz Mirtaheri
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Arianna Ortega Sanabria
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
| | - Chen-Zhong Li
- Florida International University, Biomedical Engineering Department, 10555 West Flagler Street, Miami, FL, 33174, USA.
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17
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Derr JB, Tamayo J, Clark JA, Morales M, Mayther MF, Espinoza EM, Rybicka-Jasińska K, Vullev VI. Multifaceted aspects of charge transfer. Phys Chem Chem Phys 2020; 22:21583-21629. [PMID: 32785306 PMCID: PMC7544685 DOI: 10.1039/d0cp01556c] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.
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Affiliation(s)
- James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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18
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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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19
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Daraghma SMA, Talebi S, Periasamy V. Understanding the electronic properties of single- and double-stranded DNA. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:40. [PMID: 32557121 DOI: 10.1140/epje/i2020-11965-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Understanding the charge transfer mechanism through deoxyribonucleic acid (DNA) molecules remains a challenge for numerous theoretical and experimental studies in order to be utilized in nanoelectronic devices. Various methods have attempted to investigate the conductivity of double-stranded (ds-) and single-stranded DNA (ssDNA) molecules. However, different electronic behaviors of these molecules are not clearly understood due to the complexity and lack of accuracy of the methods applied in these studies. In this work however, we demonstrated an electronic method to study the electrical behavior of synthetic ssDNA or dsDNA integrated within printed circuit board (PCB)-based metal (gold)-semiconductor (DNA) Schottky junctions. The results obtained in this work are in agreement with other studies reporting dsDNA as having higher conductivity than ssDNA as observed by us in the range of 4-6μA for the former and 2-3μA for the latter at an applied bias of 3V. Selected solid-state parameters such as turn-on voltage, series resistance, shunt resistance, ideality factor, and saturation current were also calculated for the specifically designed ss- and dsDNA sequences using the thermionic emission model. The results also showed that the highest conductance was observed for dsDNA with guanine and cytosine base pairs, while the lowest conductance was for ssDNA with adenine and thymine bases. We believe the results of this preliminary work involving the gold-DNA Schottky junction may allow the interrogation of DNA charge transfer mechanisms and contribute to better understanding its elusive electronic properties.
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Affiliation(s)
- Souhad M A Daraghma
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sara Talebi
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vengadesh Periasamy
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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20
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Deng C, Liu H, Si S, Zhu X, Tu Q, Jin Y, Xiang J. An electrochemical aptasensor for amyloid-β oligomer based on double-stranded DNA as "conductive spring". Mikrochim Acta 2020; 187:239. [PMID: 32189141 DOI: 10.1007/s00604-020-4217-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023]
Abstract
In order to overcome the antibody-based sensor's shortcomings, an electrochemical aptamer (Apt)-based sensor was developed for amyloid-β40 oligomer (Aβ40-O). The aptasensor was constructed by locating Apt and ferrocence (Fc) on streptavidin-modified gold (SA-gold) nanoparticles. The obtained AptFc@SA-gold nanoparticles were linked onto the Au electrode via the connection of double-stranded DNA (dsDNA) as a "conductive spring." The determination of Aβ40-O was performed with square-wave voltammetry (SWV). Upon bio-recognition between Apt and Aβ40-O, the conformation of Apt changed and the formed Apt/Aβ40-O complex separated from the SA-gold surface. As a result, the surface charge of SA-gold positively shifted, weakening the electrostatic attraction between the SA-gold and the positively charged Au electrode surface (at potential range of 0.1~0.5 V, corresponding to the Fc redox transformation), and stretching the dsDNA chain. Based on the exponential decay of dsDNA's electron transfer efficiency on its chain stretching, the oxidation current density from Fc decreased and displayed linear correlation to the concentration of Aβ40-O. A wide linear range of 0.100 nM to 1.00 μM with a low detection limit of 93.0 pM was obtained. The aptasensor displayed excellent selectivity toward Aβ40-O in contrast to other possible interfering analogs (Aβ40 monomer, Aβ42 monomer, and oligomer) at × 100 higher concentrations. The recoveries for Aβ40-O-spiked artificial cerebrospinal fluid and healthy human serum were 94.0~104% and 92.8~95.4%, respectively. The electrochemical aptasensor meets the demands of clinic determination of Aβ40-O, which is significant for the early diagnosis of AD. Graphical abstract Schematic representation of the electrochemical aptasensor for amyloid-β oligomer based on the surface charge change induced by target binding.
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Affiliation(s)
- Chunyan Deng
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Hui Liu
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Shihui Si
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Xiaojun Zhu
- School of Information Science and Technology, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Qiuyun Tu
- Department of Geratology, The Third Xiangya Hospital, Central South University, Changsha, 410013, People's Republic of China
| | - Yan Jin
- Department of Geratology, The Third Xiangya Hospital, Central South University, Changsha, 410013, People's Republic of China
| | - Juan Xiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
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21
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Vittala SK, Han D. DNA-Guided Assemblies toward Nanoelectronic Applications. ACS APPLIED BIO MATERIALS 2020; 3:2702-2722. [PMID: 35025404 DOI: 10.1021/acsabm.9b01178] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeepa Kulala Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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22
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23
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Liu Y, Ren X, He L. A DFT study of energetic and structural properties of a full turn of A-form DNA under relaxed and stretching conditions. J Chem Phys 2019; 151:215102. [DOI: 10.1063/1.5129716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Yue Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xinguo Ren
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Lixin He
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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24
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Teo RD, Smithwick ER, Migliore A. 2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport. Phys Chem Chem Phys 2019; 21:22869-22878. [PMID: 31599901 PMCID: PMC7050622 DOI: 10.1039/c9cp04805g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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25
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Bag S, Maiti PK. Tuning molecular fluctuation to boost the conductance in DNA based molecular wires. Phys Chem Chem Phys 2019; 21:23514-23520. [PMID: 31617554 DOI: 10.1039/c9cp03589c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Inherent molecular fluctuations are known to have a significant influence on the charge transport properties of biomolecules like DNA, PNA and proteins. In this work, we show ways to control these fluctuations and further demonstrate their use to enhance the conductance of two widely studied molecular wires, namely dsDNA (DNA) and G4 Quadruplex (G4-Quad). We quantify the molecular fluctuation in terms of the root mean square deviation (RMSD) of the molecule. In the case of DNA, we use temperature to control the fluctuations, while in the case of G4-Quad the fluctuations are tuned by the ions inside the pore. The electronic coupling between the bases of dsDNA and G4-Quad, which measures the conductance of these molecular wires, shows a non-monotonic behaviour with the increase in fluctuation. We find values of fluctuation which give rise to maximum electronic coupling and hence high conductivity for both the cases. In the case of DNA, these optimal fluctuations (∼2.5 Å) are achieved at a temperature of 210 K, which gives rise to an electronic coupling of 0.135 eV between the DNA bases. The optimal fluctuations in G4-Quad are achieved (∼7 Å) in a 4 base pair long system with 2 Na+ ions inside the pore, giving rise to an electronic coupling of 0.09 eV.
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Affiliation(s)
- Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, Karnataka, India.
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26
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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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27
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Lin K, Burke A, King NB, Kahanda D, Mazaheripour A, Bartlett A, Dibble DJ, McWilliams MA, Taylor DW, Jocson J, Minary‐Jolandan M, Gorodetsky AA, Slinker JD. Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates. Chempluschem 2019; 84:416-419. [DOI: 10.1002/cplu.201800661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Kuo‐Yao Lin
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Anthony Burke
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Nolan B. King
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Dimithree Kahanda
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - David J. Dibble
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Marc A. McWilliams
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - David W. Taylor
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Majid Minary‐Jolandan
- Department of Mechanical Engineering The University of Texas at Dallas 800 W. Campbell Road, EC 38 Richardson TX 75080-3020 USA
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Jason D. Slinker
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
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28
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Abstract
Achieving high-yielding photoinduced charge separation through the π-stacked bases of DNA is a critical requirement for realizing numerous DNA-based technologies. In the current work, we combine two strategies for achieving high-yield charge separation. First, a chromophore with a high driving force for charge injection, naphthalenediimide (NDI), is used because it generates hot carriers that enhance charge-transfer rates. Second, a diblock DNA sequence is used with two or three adenines followed by a series of guanines to implement an energy landscape that accelerates charge separation while retarding charge recombination. The photoinduced dynamics of these NDI diblock oligomers with and without a terminal hole acceptor are probed by femtosecond transient absorption spectroscopy. The measured rate constants for various charge separation and recombination processes are interpreted within the context of a full kinetic model of these systems. We find that the A2 and A3 oligomers achieve similar charge separation yields (as high as 20-25%) for a given length, yet the critical recombination process that determines these yields occurs at different distances from the NDI chromophore and on different time scales. This type of analysis could be used to predict charge separation efficiencies in candidate DNA structures.
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Olshansky JH, Krzyaniak MD, Young RM, Wasielewski MR. Photogenerated Spin-Entangled Qubit (Radical) Pairs in DNA Hairpins: Observation of Spin Delocalization and Coherence. J Am Chem Soc 2019; 141:2152-2160. [DOI: 10.1021/jacs.8b13155] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jacob H. Olshansky
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Matthew D. Krzyaniak
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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30
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Mishra S, Poonia VS, Fontanesi C, Naaman R, Fleming AM, Burrows CJ. Effect of Oxidative Damage on Charge and Spin Transport in DNA. J Am Chem Soc 2018; 141:123-126. [PMID: 30541275 DOI: 10.1021/jacs.8b12014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A Hall device was used for measuring spin polarization on electrons that are either reorganized within the molecules or transmitted through the self-assembled monolayers of DNA adsorbed on the device surface. We were able to observe spin-dependent charge polarization and charge transport through double-stranded DNA of various lengths and through double-stranded DNA containing oxidative damage. We found enhancement in the spin-dependent transport through oxidatively damaged DNA. This phenomenon can be rationalized either by assuming that the damaged DNA is characterized by a higher barrier for conduction or by charge transfer through the DNA being conducted through at least two channels, one involves the bases and is highly conductive but less spin selective, while the other pathway is mainly through the ribophosphate backbone and it is the minor one in terms of charge transmission efficiency, but it is highly spin selective.
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Affiliation(s)
- Suryakant Mishra
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Vishvendra S Poonia
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Claudio Fontanesi
- Dip. di Ingegneria , DIEF, MO26 , Via P. Vivarelli 10 , 41125 Modena , Italy
| | - Ron Naaman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 S. 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 S. 1400 East , Salt Lake City , Utah 84112-0850 , United States
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