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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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2
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Dai X, Li Q, Aldalbahi A, Wang L, Fan C, Liu X. DNA-Based Fabrication for Nanoelectronics. NANO LETTERS 2020; 20:5604-5615. [PMID: 32787185 DOI: 10.1021/acs.nanolett.0c02511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The bottom-up DNA-templated nanoelectronics exploits the unparalleled self-assembly properties of DNA molecules and their amenability with various types of nanomaterials. In principle, nanoelectronic devices can be bottom-up assembled with near-atomic precision, which compares favorably with well-established top-down fabrication process with nanometer precision. Over the past decade, intensive effort has been made to develop DNA-based nanoassemblies including DNA-metal, DNA-polymer, and DNA-carbon nanotube complexes. This review introduces the history of DNA-based fabrication for nanoelectronics briefly and summarizes the state-of-art advances of DNA-based nanoelectronics. In particular, the most widely applied characterization techniques to explore their unique electronic properties at the nanoscale are described and discussed, including scanning tunneling microscopy, conductive atomic force microscopy, and Kelvin probe force microscopy. We also provide a perspective on potential applications of DNA-based nanoelectronics.
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Affiliation(s)
- Xinpei Dai
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lihua Wang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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Vecchioni S, Capece MC, Toomey E, Nguyen L, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild L. Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology. Sci Rep 2019; 9:6942. [PMID: 31061396 PMCID: PMC6502794 DOI: 10.1038/s41598-019-43316-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.
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Affiliation(s)
- Simon Vecchioni
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Mark C Capece
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emily Toomey
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Le Nguyen
- School of Engineering, Brown University, Providence, RI, 02912, USA
| | - Austin Ray
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alissa Greenberg
- Department of History, Stanford University, Stanford, CA, 94305, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Jesica Urbina
- Geology, Minerals, Energy, & Geophysics Science Center, U.S. Geological Survey, Menlo Park, CA, 94025, USA
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Ivan G Paulino-Lima
- Blue Marble Space Institute of Science, NASA Ames Research Center, Planetary Systems Branch, Moffett Field, CA, 94035-0001, USA
| | - Vitor Pinheiro
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Joseph Shih
- Department of Natural Sciences and Mathematics, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Lynn Rothschild
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
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Hu Z, Sun G, Jiang W, Xu F, Zhang Y, Xia M, Pan X, Xing Z, Zhang S, Zhang X. Chemical-Modified Nucleotide-Based Elemental Tags for High-Sensitive Immunoassay. Anal Chem 2019; 91:5980-5986. [PMID: 30973226 DOI: 10.1021/acs.analchem.9b00405] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Multiplex biomolecular analysis with inductively coupled plasma mass spectrometry (ICP-MS) becomes increasingly important in clinical diagnosis and single cell analysis. However, the sensitivity of ICP-MS-based immunoassay is only comparable or lower than those of fluorescence methods at the present stage. Therefore, designing elemental tags with a large number of metal atoms is necessary to achieve high-sensitive detection. In this work, we proposed a new strategy to build up elemental tag loading with hundreds of rare earth ions by coupling alkyne-DNA chains with rare earth element (REE)-DOTA complexes a click chemistry reaction. There are about 2 orders of magnitude improvement in sensitivity compared with single metal-ion tags. DNA chains with multialkynyl groups were facilely prepared by PCR synthesis. Moreover, the DNA-based elemental tags own excellent water-solubility and biocompatibility. The tags would be potentially applied to mass cytometry and clinical diagnosis.
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Affiliation(s)
- Zhian Hu
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Gongwei Sun
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Wencan Jiang
- Department of Clinical Laboratory Medicine , Chinese People's Liberation Army General Hospital & Postgraduate Medical School , Beijing 100853 , China
| | - Fujian Xu
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Yuqing Zhang
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Mengchan Xia
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Xingyu Pan
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Zhi Xing
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Sichun Zhang
- Department of Chemistry Tsinghua University , Beijing 100084 , China
| | - Xinrong Zhang
- Department of Chemistry Tsinghua University , Beijing 100084 , China
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McConnell G, Mabbott S, Kanibolotsky AL, Skabara PJ, Graham D, Burley GA, Laurand N. Organic Semiconductor Laser Platform for the Detection of DNA by AgNP Plasmonic Enhancement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14766-14773. [PMID: 30227713 DOI: 10.1021/acs.langmuir.8b01313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Organic semiconductor lasers are a sensitive biosensing platform that respond to specific biomolecule binding events. So far, such biosensors have utilized protein-based interactions for surface functionalization but a nucleic acid-based strategy would considerably widen their utility as a general biodiagnostic platform. This manuscript reports two important advances for DNA-based sensing using an organic semiconductor (OS) distributed feedback (DFB) laser. First, the immobilization of alkyne-tagged 12/18-mer oligodeoxyribonucleotide (ODN) probes by Cu-catalyzed azide alkyne cycloaddition (CuAAC) or "click-chemistry" onto an 80 nm thick OS laser film modified with an azide-presenting polyelectrolyte monolayer is presented. Second, sequence-selective binding to these immobilized probes with complementary ODN-functionalized silver nanoparticles, is detected. As binding occurs, the nanoparticles increase the optical losses of the laser mode through plasmonic scattering and absorption, and this causes a rise in the threshold pump energy required for laser action that is proportional to the analyte concentration. By monitoring this threshold, detection of the complementary ODN target down to 11.5 pM is achieved. This complementary binding on the laser surface is independently confirmed through surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- G McConnell
- Institute of Photonics, Department of Physics , University of Strathclyde , Glasgow G12 8QQ , U.K
- Biomedical Engineering , University of Strathclyde , Glasgow G12 8QQ , U.K
| | - S Mabbott
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Glasgow G12 8QQ , U.K
| | - A L Kanibolotsky
- WestCHEM, School of Chemistry , University of Glasgow , Glasgow G12 8QQ , U.K
- Institute of Physical-Organic and Coal Chemistry , The National Academy of Sciences of Ukraine , 02160 Kyiv , Ukraine
| | - P J Skabara
- WestCHEM, School of Chemistry , University of Glasgow , Glasgow G12 8QQ , U.K
| | - D Graham
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Glasgow G12 8QQ , U.K
| | - G A Burley
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Glasgow G12 8QQ , U.K
| | - N Laurand
- Institute of Photonics, Department of Physics , University of Strathclyde , Glasgow G12 8QQ , U.K
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Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc Natl Acad Sci U S A 2018; 115:9992-9997. [PMID: 30224478 PMCID: PMC6176618 DOI: 10.1073/pnas.1811518115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite being evolved to process the four canonical nucleotides, DNA polymerases are known to incorporate and extend from modified nucleotides, which is the key to numerous core biotechnology applications. The structural basis for postincorporation elongation remained elusive. We successfully crystallized KlenTaq DNA polymerase in six complexes, providing high-resolution snapshots of the modification “moving” from the 3′ terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity. This highlights the unexpected plasticity of the system as origin of the broad substrate properties of the DNA polymerase and guide for the design of improved systems. DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.
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7
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Stern A, Eidelshtein G, Zhuravel R, Livshits GI, Rotem D, Kotlyar A, Porath D. Highly Conductive Thin Uniform Gold-Coated DNA Nanowires. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1800433. [PMID: 29726045 DOI: 10.1002/adma.201800433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/26/2018] [Indexed: 06/08/2023]
Abstract
Over the past decades, DNA, the carrier of genetic information, has been used by researchers as a structural template material. Watson-Crick base pairing enables the formation of complex 2D and 3D structures from DNA through self-assembly. Various methods have been developed to functionalize these structures for numerous utilities. Metallization of DNA has attracted much attention as a means of forming conductive nanostructures. Nevertheless, most of the metallized DNA wires reported so far suffer from irregularity and lack of end-to-end electrical connectivity. An effective technique for formation of thin gold-coated DNA wires that overcomes these drawbacks is developed and presented here. A conductive atomic force microscopy setup, which is suitable for measuring tens to thousands of nanometer long molecules and wires, is used to characterize these DNA-based nanowires. The wires reported here are the narrowest gold-coated DNA wires that display long-range conductivity. The measurements presented show that the conductivity is limited by defects, and that thicker gold coating reduces the number of defects and increases the conductive length. This preparation method enables the formation of molecular wires with dimensions and uniformity that are much more suitable for DNA-based molecular electronics.
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Affiliation(s)
- Avigail Stern
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Roman Zhuravel
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gideon I Livshits
- 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
| | - Alexander Kotlyar
- Department of Biochemistry, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat 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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8
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Yang S, Schmidt DO, Khetan A, Schrader F, Jakobi S, Homberger M, Noyong M, Paulus A, Kungl H, Eichel RA, Pitsch H, Simon U. Electrochemical and Electronic Charge Transport Properties of Ni-Doped LiMn₂O₄ Spinel Obtained from Polyol-Mediated Synthesis. MATERIALS 2018; 11:ma11050806. [PMID: 29772663 PMCID: PMC5978183 DOI: 10.3390/ma11050806] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 12/26/2022]
Abstract
LiNi0.5Mn1.5O4 (LNMO) spinel has been extensively investigated as one of the most promising high-voltage cathode candidates for lithium-ion batteries. The electrochemical performance of LNMO, especially its rate performance, seems to be governed by its crystallographic structure, which is strongly influenced by the preparation methods. Conventionally, LNMO materials are prepared via solid-state reactions, which typically lead to microscaled particles with only limited control over the particle size and morphology. In this work, we prepared Ni-doped LiMn2O4 (LMO) spinel via the polyol method. The cycling stability and rate capability of the synthesized material are found to be comparable to the ones reported in literature. Furthermore, its electronic charge transport properties were investigated by local electrical transport measurements on individual particles by means of a nanorobotics setup in a scanning electron microscope, as well as by performing DFT calculations. We found that the scarcity of Mn3+ in the LNMO leads to a significant decrease in electronic conductivity as compared to undoped LMO, which had no obvious effect on the rate capability of the two materials. Our results suggest that the rate capability of LNMO and LMO materials is not limited by the electronic conductivity of the fully lithiated materials.
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Affiliation(s)
- Shuo Yang
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Dirk Oliver Schmidt
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Abhishek Khetan
- Institute for Combustion Technology, RWTH Aachen University, 52056 Aachen, Germany.
| | - Felix Schrader
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Simon Jakobi
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Melanie Homberger
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Michael Noyong
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
| | - Anja Paulus
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
- Institute of Energy and Climate Research IEK-9: Fundamental Electrochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Hans Kungl
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
- Institute of Energy and Climate Research IEK-9: Fundamental Electrochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Rüdiger-Albert Eichel
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
- Institute of Energy and Climate Research IEK-9: Fundamental Electrochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Physical Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
| | - Heinz Pitsch
- Institute for Combustion Technology, RWTH Aachen University, 52056 Aachen, Germany.
| | - Ulrich Simon
- Institute of Inorganic Chemistry, RWTH Aachen University, 52074 Aachen, Germany.
- Jülich Aachen Research Alliance-JARA, 52428 Jülich, Germany.
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Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
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10
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Brun C, Elchinger PH, Nonglaton G, Tidiane-Diagne C, Tiron R, Thuaire A, Gasparutto D, Baillin X. Metallic Conductive Nanowires Elaborated by PVD Metal Deposition on Suspended DNA Bundles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700956. [PMID: 28677894 DOI: 10.1002/smll.201700956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Metallic conductive nanowires (NWs) with DNA bundle core are achieved, thanks to an original process relying on double-stranded DNA alignment and physical vapor deposition (PVD) metallization steps involving a silicon substrate. First, bundles of DNA are suspended with a repeatable process between 2 µm high parallel electrodes with separating gaps ranging from 800 nm to 2 µm. The process consists in the drop deposition of a DNA lambda-phage solution on the electrodes followed by a naturally evaporation step. The deposition process is controlled by the DNA concentration within the buffer solution, the drop volume, and the electrode hydrophobicity. The suspended bundles are finally metallized with various thicknesses of titanium and gold by a PVD e-beam evaporation process. The achieved NWs have a width ranging from a few nanometers up to 100 nm. The electrical behavior of the achieved 60 and 80 nm width metallic NWs is shown to be Ohmic and their intrinsic resistance is estimated according to different geometrical models of the NW section area. For the 80 nm width NWs, a resistance of about few ohms is established, opening exploration fields for applications in microelectronics.
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Affiliation(s)
- Christophe Brun
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Pierre-Henri Elchinger
- Université Grenoble Alpes, F-38000, Grenoble, France
- Laboratory of Plant & Cell Physiology, CEA/DRF/BIG, CNRS UMR5168, INRA UMR 1417, F-38054, Grenoble, France
| | - Guillaume Nonglaton
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Cheikh Tidiane-Diagne
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Raluca Tiron
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Aurélie Thuaire
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Didier Gasparutto
- Université Grenoble Alpes, F-38000, Grenoble, France
- INAC/SyMMES, UMR 5819 CEA CNRS UGA, MINATEC Campus, F-38054, Grenoble, France
| | - Xavier Baillin
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
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11
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Li X, Hu D, Tan Z, Bai J, Xiao Z, Yang Y, Shi J, Hong W. Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions. Top Curr Chem (Cham) 2017; 375:42. [PMID: 28337670 DOI: 10.1007/s41061-017-0123-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/18/2017] [Indexed: 11/26/2022]
Abstract
The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Duan Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Zhibing Tan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Zongyuan Xiao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
| | - Jia Shi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Collaborative Innovation Center of Chemistry for Energy Materials, Xiamen University, Xiamen, 361005, China.
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12
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Wünnemann P, Noyong M, Kreuels K, Brüx R, Gordiichuk P, van Rijn P, Plamper FA, Simon U, Böker A. Microstructured Hydrogel Templates for the Formation of Conductive Gold Nanowire Arrays. Macromol Rapid Commun 2016; 37:1446-52. [DOI: 10.1002/marc.201600287] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/17/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Wünnemann
- Lehrstuhl für Makromolekulare Materialien und Oberflächen; RWTH Aachen University; Forckenbeckstraße 50 52056 Aachen Germany
| | - Michael Noyong
- Institute of Inorganic Chemistry; RWTH Aachen University; JARA-FIT, Landoltweg 1 52074 Aachen Germany
| | - Klaus Kreuels
- Lehrstuhl für Makromolekulare Materialien und Oberflächen; RWTH Aachen University; Forckenbeckstraße 50 52056 Aachen Germany
| | - Roland Brüx
- Lehrstuhl für Makromolekulare Materialien und Oberflächen; RWTH Aachen University; Forckenbeckstraße 50 52056 Aachen Germany
| | - Pavlo Gordiichuk
- Zernike Institute for Advanced Materials; University of Groningen; A. Deusinglaan 1 9747AG Groningen The Netherlands
| | - Patrick van Rijn
- Zernike Institute for Advanced Materials; University of Groningen; A. Deusinglaan 1 9747AG Groningen The Netherlands
- University Medical Center Groningen Department of Biomedical Engineering-FB40; University of Groningen; A. Deusinglaan 1 9713 AV Groningen The Netherlands
- W. J. Kolff Institute for Biomedical Engineering and Materials Science-FB41; University of Groningen; A. Deusinglaan 1 9713AW Groningen The Netherlands
| | - Felix A. Plamper
- Institute of Physical Chemistry; RWTH Aachen University; Landoltweg 2 52074 Aachen Germany
| | - Ulrich Simon
- Institute of Inorganic Chemistry; RWTH Aachen University; JARA-FIT, Landoltweg 1 52074 Aachen Germany
| | - Alexander Böker
- Fraunhofer Institute for Applied Polymer Research (IAP) & Lehrstuhl für Polymermaterialien und Polymertechnologien; University of Potsdam; Geiselbergstraße 69 14476 Potsdam-Golm Germany
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13
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Eidelshtein G, Fardian-Melamed N, Gutkin V, Basmanov D, Klinov D, Rotem D, Levi-Kalisman Y, Porath D, Kotlyar A. Synthesis and Properties of Novel Silver-Containing DNA Molecules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:4839-4844. [PMID: 27116695 DOI: 10.1002/adma.201505049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
Migration of silver atoms from silver nano-particles selectively to a double-stranded poly(dG)-poly(dC) polymer leads to metallization of the DNA. As a result the DNA molecules become shorter and thicker (higher), as evident from the atomic force microscopy imaging analysis. The metalized molecules can be detected by transmission and scanning electron microscopy in contrast to the initial non-metalized ones.
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Affiliation(s)
- 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
| | - Natalie Fardian-Melamed
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Vitaly Gutkin
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dmitry Basmanov
- Institute of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
| | - Dmitry Klinov
- Institute of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
- Russia and Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. Dolgoprudny, 141700, Moscow Region, Russia
| | - Dvir Rotem
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yael Levi-Kalisman
- Institute for Life SciencesThe Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Danny Porath
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of 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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14
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Cuerva M, García-Fandiño R, Vázquez-Vázquez C, López-Quintela MA, Montenegro J, Granja JR. Self-Assembly of Silver Metal Clusters of Small Atomicity on Cyclic Peptide Nanotubes. ACS NANO 2015; 9:10834-10843. [PMID: 26439906 DOI: 10.1021/acsnano.5b03445] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Subnanometric noble metal clusters, composed by only a few atoms, behave like molecular entities and display magnetic, luminescent and catalytic activities. However, noncovalent interactions of molecular metal clusters, lacking of any ligand or surfactant, have not been seen at work. Theoretically attractive and experimentally discernible, van der Waals forces and noncovalent interactions at the metal/organic interfaces will be crucial to understand and develop the next generation of hybrid nanomaterials. Here, we present experimental and theoretical evidence of noncovalent interactions between subnanometric metal (0) silver clusters and aromatic rings and their application in the preparation of 1D self-assembled hybrid architectures with ditopic peptide nanotubes. Atomic force microscopy, fluorescence experiments, circular dichroism and computational simulations verified the occurrence of these interactions in the clean and mild formation of a novel peptide nanotube and metal cluster hybrid material. The findings reported here confirmed the sensitivity of silver metal clusters of small atomicity toward noncovalent interactions, a concept that could find multiple applications in nanotechnology. We conclude that induced supramolecular forces are optimal candidates for the precise spatial positioning and properties modulation of molecular metal clusters. The reported results herein outline and generalize the possibilities that noncovalent interactions will have in this emerging field.
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Affiliation(s)
- Miguel Cuerva
- Technological Research Institute (IIT), Physical Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
| | - Rebeca García-Fandiño
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
| | - Carlos Vázquez-Vázquez
- Technological Research Institute (IIT), Physical Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
| | - M Arturo López-Quintela
- Technological Research Institute (IIT), Physical Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
| | - Javier Montenegro
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
| | - Juan R Granja
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), Organic Chemistry Department, University of Santiago de Compostela (USC) , Santiago de Compostela 15782, Spain
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15
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Chen P, Schönebaum S, Simons T, Rauch D, Dietrich M, Moos R, Simon U. Correlating the Integral Sensing Properties of Zeolites with Molecular Processes by Combining Broadband Impedance and DRIFT Spectroscopy--A New Approach for Bridging the Scales. SENSORS (BASEL, SWITZERLAND) 2015; 15:28915-41. [PMID: 26580627 PMCID: PMC4701314 DOI: 10.3390/s151128915] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/02/2015] [Accepted: 11/05/2015] [Indexed: 11/17/2022]
Abstract
Zeolites have been found to be promising sensor materials for a variety of gas molecules such as NH₃, NOx, hydrocarbons, etc. The sensing effect results from the interaction of the adsorbed gas molecules with mobile cations, which are non-covalently bound to the zeolite lattice. The mobility of the cations can be accessed by electrical low-frequency (LF; mHz to MHz) and high-frequency (HF; GHz) impedance measurements. Recent developments allow in situ monitoring of catalytic reactions on proton-conducting zeolites used as catalysts. The combination of such in situ impedance measurements with diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), which was applied to monitor the selective catalytic reduction of nitrogen oxides (DeNOx-SCR), not only improves our understanding of the sensing properties of zeolite catalysts from integral electric signal to molecular processes, but also bridges the length scales being studied, from centimeters to nanometers. In this work, recent developments of zeolite-based, impedimetric sensors for automotive exhaust gases, in particular NH₃, are summarized. The electrical response to NH₃ obtained from LF impedance measurements will be compared with that from HF impedance measurements, and correlated with the infrared spectroscopic characteristics obtained from the DRIFTS studies of molecules involved in the catalytic conversion. The future perspectives, which arise from the combination of these methods, will be discussed.
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Affiliation(s)
- Peirong Chen
- Institute of Inorganic Chemistry (IAC) and Center for Automotive Catalytic Systems Aachen (ACA), RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany.
| | - Simon Schönebaum
- Institute of Inorganic Chemistry (IAC) and Center for Automotive Catalytic Systems Aachen (ACA), RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany.
| | - Thomas Simons
- Institute of Inorganic Chemistry (IAC) and Center for Automotive Catalytic Systems Aachen (ACA), RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany.
| | - Dieter Rauch
- Department of Functional Materials, Bayreuth Engine Research Center (BERC) and Zentrum für Energietechnik (ZET), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.
| | - Markus Dietrich
- Department of Functional Materials, Bayreuth Engine Research Center (BERC) and Zentrum für Energietechnik (ZET), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.
| | - Ralf Moos
- Department of Functional Materials, Bayreuth Engine Research Center (BERC) and Zentrum für Energietechnik (ZET), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.
| | - Ulrich Simon
- Institute of Inorganic Chemistry (IAC) and Center for Automotive Catalytic Systems Aachen (ACA), RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany.
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16
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Miller EJ, Garcia KJ, Holahan EC, Ciccarelli RM, Bergin RA, Casino SL, Bogaczyk TL, Krout MR, Findeis PM, Stockland RA. Resolved P-metalated nucleoside phosphoramidites. Inorg Chem 2014; 53:12680-2. [PMID: 25437274 DOI: 10.1021/ic5024357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of resolved P-metalated nucleoside phosphoramidites is described. These rare compounds were initially prepared with gold as the metal center; however, the gold can be removed using basic phosphines or solid-supported triphenylphosphine. Treatment of the free nucleoside phosphoramidite with a platinum source generated a unique platinated dinucleoside species with a diastereomeric ratio of >99:1.
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Affiliation(s)
- Erica J Miller
- Department of Chemistry, Bucknell University , Lewisburg, Pennsylvania 17837, United States
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17
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Kumar A, Kumar V. Biotemplated Inorganic Nanostructures: Supramolecular Directed Nanosystems of Semiconductor(s)/Metal(s) Mediated by Nucleic Acids and Their Properties. Chem Rev 2014; 114:7044-78. [DOI: 10.1021/cr4007285] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Vinit Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
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18
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Escorihuela J, Bañuls MJ, Puchades R, Maquieira Á. Site-specific immobilization of DNA on silicon surfaces by using the thiol–yne reaction. J Mater Chem B 2014; 2:8510-8517. [DOI: 10.1039/c4tb01108b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Covalent immobilization of ssDNA fragments onto silicon-based materials was performed using the thiol–yne reaction.
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Affiliation(s)
- Jorge Escorihuela
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - María-José Bañuls
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - Rosa Puchades
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
| | - Ángel Maquieira
- Centro de Reconocimiento Moleculary Desarrollo Tecnológico
- Departamento de Química
- Universitat Politècnica de València
- 46022 Valencia, Spain
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20
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Gilles S, Tuchscherer A, Lang H, Simon U. Dip-pen-based direct writing of conducting silver dots. J Colloid Interface Sci 2013; 406:256-62. [DOI: 10.1016/j.jcis.2013.05.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
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