1
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Polycarpou G, Skourtis SS. Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:375301. [PMID: 38848732 DOI: 10.1088/1361-648x/ad559d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/07/2024] [Indexed: 06/09/2024]
Abstract
We argue that dry DNA charge transport in molecular junctions, over distances of tens of nanometers, can take place via independent intra-strand pathways involving the phosphate groups. Such pathways explain recent single-molecule experiments that compare currents in intact and nicked 100 base-pair double-stranded DNA. We explore the conditions that favor independent intra-strand transport channels with the participation of the phosphate groups, as opposed to purely base-mediated transport involving the pi-stacked bases and inter-strand transitions. Our computations demonstrate how long-distance transport pathways in DNA are tuned by the degree of solvation, which affects the level of dynamic disorder in the pi-stacking, and the energies of phosphate-group molecular orbitals.
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2
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Katrivas L, Makarovsky A, Kempinski B, Randazzo A, Improta R, Rotem D, Porath D, Kotlyar AB. Ag +-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:663. [PMID: 38668157 PMCID: PMC11055002 DOI: 10.3390/nano14080663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Anna Makarovsky
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Napoli, Italy;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy;
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
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3
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Wang J, Zhao Y, Li S, Shen L, Zhang H, Ding C, Wei C, Wang Y, Li Y, Hong W, Li M. Composition and sequence-controlled conductance of crystalline unimolecular monolayers. SCIENCE ADVANCES 2023; 9:eadh0667. [PMID: 37327333 DOI: 10.1126/sciadv.adh0667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/12/2023] [Indexed: 06/18/2023]
Abstract
Understanding how the charge travels through sequence-controlled molecules has been a formidable challenge because of simultaneous requirements in well-controlled synthesis and well-manipulated orientation. Here, we report electrically driven simultaneous synthesis and crystallization as a general strategy to study the conductance of composition and sequence-controlled unioligomer and unipolymer monolayers. The structural disorder of molecules and conductance variations on random positions can be extremely minimized, by uniform synthesis of monolayers unidirectionally sandwiched between electrodes, as an important prerequisite for the reproducible measurement on the micrometer scale. These monolayers show tunable current density and on/off ratios in four orders of magnitude with controlled multistate and massive negative differential resistance (NDR) effects. The conductance of monolayer mainly depends on the metal species in homo-metal monolayers, while the sequence becomes a matter in hetero-metal monolayers. Our work demonstrates a promising way to release an ultra-rich variety of electrical parameters and optimize the functions and performances of multilevel resistive devices.
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Affiliation(s)
- Jinxin Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yongjie Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shumu Li
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing Mass Spectrum Center, Beijing 100190, China
| | - Lingyun Shen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Hao Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Caijun Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Chang Wei
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yanfang Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Yongfang Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mao Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- University of Science and Technology of China, Hefei 230026, China
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4
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Dong J, O'Hagan MP, Willner I. Switchable and dynamic G-quadruplexes and their applications. Chem Soc Rev 2022; 51:7631-7661. [PMID: 35975685 DOI: 10.1039/d2cs00317a] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO2 nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
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Affiliation(s)
- Jiantong Dong
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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5
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Fardian-Melamed N, Katrivas L, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules. NANO LETTERS 2021; 21:8987-8992. [PMID: 34694812 DOI: 10.1021/acs.nanolett.1c02269] [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: 06/13/2023]
Abstract
Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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6
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Lat PK, Schultz CW, Yu H, Sen D. A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016668] [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)
- Prince Kumar Lat
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Clayton W. Schultz
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Hua‐Zhong Yu
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Dipankar Sen
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
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7
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Lat PK, Schultz CW, Yu H, Sen D. A Long and Reversibly Self‐Assembling 1D DNA Nanostructure Built from Triplex and Quadruplex Hybrid Tiles. Angew Chem Int Ed Engl 2021; 60:8722-8727. [DOI: 10.1002/anie.202016668] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/22/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Prince Kumar Lat
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Clayton W. Schultz
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Hua‐Zhong Yu
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Dipankar Sen
- Dept. of Molecular Biology & Biochemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
- Dept. of Chemistry Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
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8
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Katrivas L, Fardian-Melamed N, Rotem D, Porath D, Kotlyar A. Formation of Novel Octuplex DNA Molecules from Guanine Quadruplexes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006932. [PMID: 33475220 DOI: 10.1002/adma.202006932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Guanine quadruplex (G4)-DNA structures have sparked the interest of many scientists due to their important biological roles and their potential use in molecular nanoelectronics and nanotechnology. The high guanine content in G4-DNA endows it with mechanical stability, robustness, and improved charge transport properties-attractive attributes for a molecular nanowire. The self-driven formation of a novel G4-DNA-based nanostructure, coined guanine octuplex (G8)-DNA, is reported herein. Atomic force microscopy and scanning tunneling microscopy characterization of this molecule reveal its organized coiled-coil structure, which is found to be stable under different temperatures and surrounding conditions. G8-DNA exhibits enhanced stiffness, mechanical and thermodynamic stability when compared to its parent G4-DNA. These, along with its high guanine content, make G8-DNA a compelling new molecule, and a highly prospective candidate for molecular nanoelectronics.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and, The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and, The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
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9
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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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10
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Zhuravel R, Huang H, Polycarpou G, Polydorides S, Motamarri P, Katrivas L, Rotem D, Sperling J, Zotti LA, Kotlyar AB, Cuevas JC, Gavini V, Skourtis SS, Porath D. Backbone charge transport in double-stranded DNA. NATURE NANOTECHNOLOGY 2020; 15:836-840. [PMID: 32807877 DOI: 10.1038/s41565-020-0741-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Understanding charge transport in DNA molecules is a long-standing problem of fundamental importance across disciplines1,2. It is also of great technological interest due to DNA's ability to form versatile and complex programmable structures. Charge transport in DNA-based junctions has been reported using a wide variety of set-ups2-4, but experiments so far have yielded seemingly contradictory results that range from insulating5-8 or semiconducting9,10 to metallic-like behaviour11. As a result, the intrinsic charge transport mechanism in molecular junction set-ups is not well understood, which is mainly due to the lack of techniques to form reproducible and stable contacts with individual long DNA molecules. Here we report charge-transport measurements through single 30-nm-long double-stranded DNA (dsDNA) molecules with an experimental set-up that enables us to address individual molecules repeatedly and to measure the current-voltage characteristics from 5 K up to room temperature. Strikingly, we observed very high currents of tens of nanoamperes, which flowed through both homogeneous and non-homogeneous base-pair sequences. The currents are fairly temperature independent in the range 5-60 K and show a power-law decrease with temperature above 60 K, which is reminiscent of charge transport in organic crystals. Moreover, we show that the presence of even a single discontinuity ('nick') in both strands that compose the dsDNA leads to complete suppression of the current, which suggests that the backbones mediate the long-distance conduction in dsDNA, contrary to the common wisdom in DNA electronics2-4.
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Affiliation(s)
- Roman Zhuravel
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Haichao Huang
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Phani Motamarri
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Física Aplicada I, Escuela Politécnica Superior, Universidad de Sevilla, Seville, Spain
| | - Alexander B Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Vikram Gavini
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Materials Science & Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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11
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Fardian-Melamed N, Katrivas L, Eidelshtein G, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Silver-Intercalated Cytosine Nanowires. NANO LETTERS 2020; 20:4505-4511. [PMID: 32412760 DOI: 10.1021/acs.nanolett.0c01292] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag+-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity. However, a high-resolution morphological characterization of long Ag+-intercalated polycytosine DNA has hitherto not been carried out. Furthermore, the electronic level structure of this molecule has not been studied before. Here we present a scanning tunneling microscopy and spectroscopy study of this intriguing nanowire. Its temperature-independent morphological and electronic properties suggest substantial stability, while its emergent electronic levels and energy gap provide the basis for its high conductivity.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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12
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Fardian-Melamed N, Eidelshtein G, Rotem D, Kotlyar A, Porath D. Temperature Dependence of the STM Morphology and Electronic Level Structure of Silver-Containing DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905901. [PMID: 31885142 DOI: 10.1002/smll.201905901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Understanding the effect of external conditions, temperature in particular, on novel nanomaterials is of great significance. The powerful ability of scanning tunneling microscopy (STM) to characterize topography and electronic levels on a single molecule scale is utilized herein to characterize individual silver-containing poly(dG)-poly(dC) DNA molecules, at different temperatures. These measurements indicate that the molecule is a truly hybrid metal-organic nanomaterial with electronic states originating from both the DNA and the embedded silver. The temperature dependence of this density of states (DOS) leads to the temperature dependent STM apparent height of the molecule-a phenomenon that has not been observed before for other complex nanostructures.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Danny Porath
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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13
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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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14
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Asefifeyzabadi N, Taki M, Funneman M, Song T, Shamsi MH. Unique sequence-dependent properties of trinucleotide repeat monolayers: electrochemical, electrical, and topographic characterization. J Mater Chem B 2020; 8:5225-5233. [DOI: 10.1039/d0tb00507j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The sequence-dependent properties of the surface-assembled trinucleotide repeat interface on a gold surface were explored by electrochemical methods and surface probe microscopy.
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Affiliation(s)
- Narges Asefifeyzabadi
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Motahareh Taki
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Madison Funneman
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
| | - Tingjie Song
- Department of Chemistry
- University of Illinois at Urbana-Champaign
- USA
| | - Mohtashim Hassan Shamsi
- Department of Chemistry & Biochemistry
- 1245 Lincoln Dr
- Southern Illinois University at Carbondale
- USA
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15
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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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16
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Katrivas L, Kempinski B, Kuchuk K, Sivan U, Kotlyar A. Multiply Modified Repeating DNA Templates for Production of Novel DNA-Based Nanomaterial. Bioconjug Chem 2019; 30:2201-2208. [PMID: 31343869 DOI: 10.1021/acs.bioconjchem.9b00433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report synthesis of long (thousands of base pairs), uniform double-stranded (ds) DNA comprising short (6-15 base pairs) tandem repeats. The synthesis method is based on self-assembly of short (6-15 bases) half-complementary 5'-end phosphorylated single-stranded oligonucleotides into long ds polymer molecules and covalent association of the oligonucleotide fragments in the polymer by DNA ligase to yield complete non-nicked ds DNA. The method is very flexible in regard to the sequence of the oligonucleotides and their length. Human telomeric DNA comprising thousands of base pairs as well as methylated, mismatched, and fluorescent dye-modified uniform dsDNA molecules can be synthesized. We have demonstrated by high resolution frequency-modulation atomic force microscopy that the structure of DNA containing mismatches is strongly different from that of the non-mismatched one. The DNA molecules comprising groups capable of anchoring metal particles and other redox active elements along the whole length of the nucleic acid polymer should find use as wires or transistors in future nanoelectronic applications.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Kfir Kuchuk
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Uri Sivan
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
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17
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Migliore A. How To Extract Quantitative Information on Electronic Transitions from the Density Functional Theory "Black Box". J Chem Theory Comput 2019; 15:4915-4923. [PMID: 31314526 DOI: 10.1021/acs.jctc.9b00518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Electronic couplings and vertical excitation energies are crucial determinants of charge and excitation energy transfer rates in a broad variety of processes ranging from biological charge transfer to charge transport through inorganic materials, from molecular sensing to intracellular signaling. Density Functional Theory (DFT) is generally used to calculate these critical parameters, but the quality of the results is unpredictable because of the semiempirical nature of the available DFT approaches. This study identifies a small set of fundamental rules that enables accurate DFT computation of electronic couplings and vertical excitation energies in molecular complexes and materials. These rules are applied to predict efficient DFT approaches to coupling calculations. The result is an easy-to-use guide for reliable DFT descriptions of electronic transitions.
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Affiliation(s)
- Agostino Migliore
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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18
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Fardian-Melamed N, Eidelshtein G, Rotem D, Kotlyar A, Porath D. Scanning Tunneling Microscopy and Spectroscopy of Novel Silver-Containing DNA Molecules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902816. [PMID: 31265189 DOI: 10.1002/adma.201902816] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/11/2019] [Indexed: 06/09/2023]
Abstract
The quest for a suitable molecule to pave the way to molecular nanoelectronics has been met with obstacles for over a decade. Candidate molecules such as carbon nanotubes lack the appealing trait of self-assembly, while DNA seems to lack the desirable feature of conductivity. Silver-containing poly(dG)-poly(dC) DNA (E-DNA) molecules have recently been reported as promising candidates for molecular electronics, owing to the selectivity of their metallization, their thin and uniform structure, their resistance to deformation, and their maximum possible high conductivity. Ultrahigh vacuum (UHV) scanning tunneling microscopy (STM) of E-DNA presents an elaborate high-resolution morphology characterization of these unique molecules, along with a detailed depiction of their electronic level structure. The energy levels found for E-DNA indicate a novel truly hybrid metal-molecule structure, potentially more conductive than other DNA-based alternatives.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
- Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Danny Porath
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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19
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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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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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