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Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J. A Novel Ag
I
‐DNA Rod Comprising a One‐Dimensional Array of 11 Silver Ions within a Double Helical Structure. Angew Chem Int Ed Engl 2022; 61:e202204798. [DOI: 10.1002/anie.202204798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Takahiro Atsugi
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Akira Ono
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Miho Tasaka
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Natsumi Eguchi
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| | - Shoji Fujiwara
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
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2
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Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J. A Novel Ag
I
‐DNA Rod Comprising a One‐Dimensional Array of 11 Silver Ions within a Double Helical Structure. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Takahiro Atsugi
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Akira Ono
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Miho Tasaka
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Natsumi Eguchi
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
| | - Shoji Fujiwara
- Department of Materials & Life Chemistry Faculty of Engineering Kanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences Faculty of Science and Technology Sophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
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3
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Abstract
Metal-mediated base pairs enable a site-specific incorporation of transition metal ions into nucleic acid structures. The resulting nucleic acid-metal complex conjugates are of interest in the context of functionalized nucleic acids, as they bear metal-based functionality. It is desirable to devise nucleic acids with an externally triggered metal-binding affinity, as this may allow regulating this functionality. Toward this end, a caged deoxyribonucleoside analog HNPP was devised for the site-specific binding of copper(II) ions upon irradiation by light, based on the ligand 3-hydroxy-2-methylpyridin-4(1H)-one (H) and the photocleavable 2-(2-nitrophenyl)propoxy protecting group (NPP). The formation of both H-Cu(II)-H homo base pairs and H-Cu(II)-X hetero base pairs (involving a second artificial deoxyribonucleoside X, based on imidazole-4-carboxylate) was achieved upon irradiation of DNA duplexes bearing the respective HNPP:HNPP or HNPP:X mispairs in the presence of copper(II) ions. The H-Cu(II)-X pair shows an exceptional DNA duplex stabilization of up to 43 °C upon its formation, exceeding that of the H-Cu(II)-H pair. It therefore represents one of the most stabilizing Cu(II)-mediated base pairs reported so far. Our findings expand the scope of light-triggered metal-mediated base pair formation by introducing a copper(II)-binding ligand.
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Affiliation(s)
- Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster, Germany
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4
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Abdullahi YZ, Vatansever ZD, Ersan F, Akinci U, Akturk OU, Akturk E. Ferromagnetic TM 2BC (TM = Cr, Mn) monolayers for spintronic devices with high Curie temperature. Phys Chem Chem Phys 2021; 23:6107-6115. [PMID: 33683236 DOI: 10.1039/d0cp05802e] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transition metal boro-carbide (TM2BC) structures crystallize in the layered orthorhombic structure in their bulk phases. In this study, however, we find that TM2BC (TM = Cr, Mn) prefer a tetragonal (t) crystal structure in their monolayer phases due to the occurrence of strong sp2 bonds between the metal and B/C atoms instead of sp3 + sp2 bonds which exist in the orthorhombic phase. The calculated energy difference between the orthorhombic and the tetragonal structures based on density functional theory (DFT) is more than 1 eV per unit cell. In addition, t-Cr2BC and t-Mn2BC monolayers are dynamically and thermally stable with their magnetic metal electronic structures. For further investigations, we combine our DFT calculations with the Monte Carlo simulations and find that both t-TM2BC monolayers show ferromagnetic properties. The calculated Curie temperatures are 846 K and 128 K for t-Cr2BC and t-MnBC sheets, respectively. In addition, we examine the magnetic anisotropy energies (MAE) of t-TM2BC monolayers and find that both structures prefer out-of-plane as the easy axis magnetization direction and the applied electric field can easily modulate the MAE of the monolayers. Our theoretical calculations reveal that t-TM2BC (TM = Cr, Mn) sheets have great potential for the future design of controllable spintronic devices with their tunable MAE properties.
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Affiliation(s)
- Yusuf Zuntu Abdullahi
- Department of Physics, Aydin Adnan Menderes University, Aydin 09010, Turkey and Department of Physics, Faculty of Science, Kaduna State University, P.M.B. 2339 Kaduna State, Nigeria
| | - Zeynep Demir Vatansever
- Faculty of Science, Physics Department, Dokuz Eylul University, Tinaztepe Campus, 35390 Izmir, Turkey
| | - Fatih Ersan
- Department of Physics, Aydin Adnan Menderes University, Aydin 09010, Turkey
| | - Umit Akinci
- Faculty of Science, Physics Department, Dokuz Eylul University, Tinaztepe Campus, 35390 Izmir, Turkey
| | - Olcay Uzengi Akturk
- Department of Electrical and Electronic Engineering, Aydin Adnan Menderes University, 09100 Aydin, Turkey and Nanotechnology Application and Research Center, Aydin Adnan Menderes University, Aydin 09010, Turkey.
| | - Ethem Akturk
- Department of Physics, Aydin Adnan Menderes University, Aydin 09010, Turkey and Nanotechnology Application and Research Center, Aydin Adnan Menderes University, Aydin 09010, Turkey.
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5
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Shen F, Mao S, Mathivanan J, Wu Y, Chandrasekaran AR, Liu H, Gan J, Sheng J. Short DNA Oligonucleotide as a Ag + Binding Detector. ACS OMEGA 2020; 5:28565-28570. [PMID: 33195907 PMCID: PMC7658945 DOI: 10.1021/acsomega.0c03372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Ag+ has been known to mediate several natural metallo-base pairs. Based on the unique structural information of a short 8-mer DNA strand (5'-GCACGCGC-3') induced by Ag+, we constructed several fluorescent DNA beacons for the detection of Ag+ according to the increase in the fluorescence emission on Ag+ binding. This Ag+ detection assay is quick, sensitive, and easy to adapt and can function in a wide range of temperatures from 5 to 65 °C.
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Affiliation(s)
- Fusheng Shen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Song Mao
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Johnsi Mathivanan
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Ying Wu
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Arun Richard Chandrasekaran
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Hehua Liu
- Shanghai
Public Health Clinical Center, State Key Laboratory of Genetic Engineering,
Collaborative Innovation Center of Genetics and Development, School
of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai
Public Health Clinical Center, State Key Laboratory of Genetic Engineering,
Collaborative Innovation Center of Genetics and Development, School
of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jia Sheng
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
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6
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Ono A, Kanazawa H, Ito H, Goto M, Nakamura K, Saneyoshi H, Kondo J. A Novel DNA Helical Wire Containing Hg
II
‐Mediated T:T and T:G Pairs. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Akira Ono
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Hiroki Kanazawa
- Department of Materials and Life SciencesFaculty of Science and TechnologySophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
- Present address: IBMC-CNRSUniversité de Strasbourg 2 allée Konrad Roentgen 67084 Strasbourg France
| | - Hikari Ito
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Misato Goto
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Koudai Nakamura
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Hisao Saneyoshi
- Department of Materials & Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku Yokohama 221-8686 Kanagawa Japan
| | - Jiro Kondo
- Department of Materials and Life SciencesFaculty of Science and TechnologySophia University 7-1 Kioi-cho, Chiyoda-ku 102-8554 Tokyo Japan
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7
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Ono A, Kanazawa H, Ito H, Goto M, Nakamura K, Saneyoshi H, Kondo J. A Novel DNA Helical Wire Containing Hg II -Mediated T:T and T:G Pairs. Angew Chem Int Ed Engl 2019; 58:16835-16838. [PMID: 31507027 DOI: 10.1002/anie.201910029] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/09/2019] [Indexed: 12/22/2022]
Abstract
Numerous applications of metal-mediated base pairs (metallo-base-pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo-base-pairs are formed in DNA and RNA duplexes containing Watson-Crick base pairs. Recently, a crystal structure of a metal-DNA nanowire with an uninterrupted one-dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing HgII -mediated T:T and T:G base pairs and water-mediated C:C base pairs. The Hg-DNA wire does not contain any Watson-Crick base pairs. Crystals of the Hg-DNA wire, which is the first DNA wire structure driven by HgII ions, were obtained by mixing the short oligonucleotide d(TTTGC) and HgII ions. This study demonstrates the potential of metallo-DNA to form various structural components that can be used for functional nanodevices.
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Affiliation(s)
- Akira Ono
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Hiroki Kanazawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan.,Present address: IBMC-CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084, Strasbourg, France
| | - Hikari Ito
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Misato Goto
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Koudai Nakamura
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Hisao Saneyoshi
- Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan
| | - Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan
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9
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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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10
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Jash B, Müller J. Metal-Mediated Base Pairs: From Characterization to Application. Chemistry 2017; 23:17166-17178. [PMID: 28833684 DOI: 10.1002/chem.201703518] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/11/2022]
Abstract
The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.
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Affiliation(s)
- Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry, Corrensstr. 28/30, 48149, Münster, Germany
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11
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Liu H, Cai C, Haruehanroengra P, Yao Q, Chen Y, Yang C, Luo Q, Wu B, Li J, Ma J, Sheng J, Gan J. Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex. Nucleic Acids Res 2017; 45:2910-2918. [PMID: 27998930 PMCID: PMC5389650 DOI: 10.1093/nar/gkw1296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
Abstract
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C–HgII–T containing duplex, three T–HgII–T containing duplexes and one native duplex containing T–T pair without HgII. Our structures suggest that both C–T and T–T pairs are flexible in interacting with the HgII ion with various binding modes including N3–HgII–N3, N4–HgII–N3, O2–HgII–N3 and N3–HgII–O4. Our studies also reveal that the overall conformations of the C–HgII–T and T–HgII–T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C–HgII–T or T–HgII–T containing DNA nanodevices in the future.
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Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chen Cai
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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12
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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13
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201704891] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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14
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Molecular magnetism, quo vadis? A historical perspective from a coordination chemist viewpoint☆. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.004] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Lu N, Bu Y. Computational design of three Cu-induced triangular pyrimidines based DNA motifs with improved conductivity. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Novel DNA triangular pyrimidine derivatives are designed by metal decoration through replacement of H by Cu in the Watson–Crick hydrogen bond region. The DFT method is used to examine the coordination of triangle-arranged Cu with three pyrimidines in nonplanar three-bladed turbine geometries. The Cu···Cu cuprophilic bonds are ascribed to the partially occupied d orbitals without direct molecular orbital (MO) interactions. Four-center bonds depend on Cu–N/O bonds, which are contributed by p orbitals of N/O atoms along or perpendicular to the bond axis. The activity of frontier MOs is modulated, leading to the decrease of gaps, ionization potentials (IPs), and electron affinities (EAs) desired for the improvement of conductivity. The hole trapping ability is assured by virtue of the spin density distributed on Cu. On average, the single electron density is located on π orbitals of three aromatic base rings. There is paramagnetic electron delocalization on the inner d orbitals of triangle region. The analysis of electron localization function ELF-π and electrostatic potential maps reveals that the outer strong π–π stacking interaction together with the inner d orbital channel enable effective transduction of electrical signals along the Cu–DNA nanowires. The 3Cu-induced triangular pyrimidines have important potential applications as structural motifs of molecular electronic devices.
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Affiliation(s)
- Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian, P. R. China, 271018
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, P. R. China, 250100
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16
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Lu N, Bu Y, Wang H. Intensified effects of multi-Cu modification on the electronic properties of the modified base pairs containing hetero-ring-expanded pyrimidine bases. Phys Chem Chem Phys 2016; 18:2913-23. [PMID: 26733396 DOI: 10.1039/c5cp06133d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel DNA base pair derivatives (A2CunU, A2CunC, G3CunU, and G3CunC) are designed by aromatic expansion of pyrimidine bases with four kinds of hetero-rings (denoted by nC and nU, n = 1, 2, 3, and 4) and metal-decoration through Cu replacement of hydrogens in the Watson-Crick hydrogen bond region. Their structures and properties are calculated for examining the cooperative effects of the two modification ways. The calculated results reveal that multiple Cu decoration makes up the deficiencies of size-expansion, and exhibits not only increase of structural stability and reduction of ionization potentials, but also ideal shrink of the HOMO-LUMO gaps, notable enhancement of interbase coupling as well as remarkable redshifts of π → π* transitions for all M-x modified base pairs. The decrease extents of the gaps and ionization potentials follow the same order G3CunU > G3CunC > A2CunU > A2CunC, and in each series (denoted by different n), the gaps, ionization potentials and first π → π* transition energies have an order of 4 < 1 < 2 < 3. The Cu d orbitals function as bridges for π electron delocalization on the conjugated aromatic rings of two bases, leading to an enhancement of transverse electronic communication, as verified by spin density delocalization, orbital composition changes, redshift of the π → π* transition and also advocated by the electron-sharing indexes such as delocalization index, Mayer bond orders and multicenter bonding. Electron localization function ELF-π isosurfaces above the molecular plane further suggested that effective longitudinal conduction is closely relevant with the bicyclic domain involving good electron delocalization and strong π-π stacking between layers. This work presents theoretical evidence for the cooperative effects of metal decoration and ring-expansion modifications on the electronic properties of the modified base pairs and also proves that the base pairs designed here could be competent building blocks for the DNA-based nanowires with improved electron activity and excellent conductivity.
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Affiliation(s)
- Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China and School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China.
| | - Huatian Wang
- College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, P. R. China
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17
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Nair NN, Ribas-Arino J, Staemmler V, Marx D. Magnetostructural Dynamics from Hubbard-U Corrected Spin-Projection: [2Fe-2S] Complex in Ferredoxin. J Chem Theory Comput 2015; 6:569-75. [PMID: 26617310 DOI: 10.1021/ct900547w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A Hubbard-corrected spin-projected two-determinant approach, EBS+Uscf, is introduced to treat low-spin ground states of antiferromagnetically coupled transition metal complexes. In addition to providing access to total energies, forces, and ab initio simulations, it allows one to readily compute Heisenberg's exchange coupling J(t) on the fly. By studying the binuclear [2Fe-2S] cofactor in a metalloprotein, Anabaena Fd, within this consistent nonempirical procedure in combination with a QM/MM framework, it is illustrated that spin-projection, self-interaction corrections, thermal fluctuations, and protein matrix shifts are crucial in obtaining ⟨J⟩ close to the experiment.
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Affiliation(s)
- Nisanth N Nair
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Volker Staemmler
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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18
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015; 54:13323-6. [DOI: 10.1002/anie.201507894] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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19
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Espinosa Leal LA, Karpenko A, Swasey S, Gwinn EG, Rojas-Cervellera V, Rovira C, Lopez-Acevedo O. The Role of Hydrogen Bonds in the Stabilization of Silver-Mediated Cytosine Tetramers. J Phys Chem Lett 2015; 6:4061-6. [PMID: 26722777 DOI: 10.1021/acs.jpclett.5b01864] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H-) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
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Affiliation(s)
| | - Alexander Karpenko
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
| | - Steven Swasey
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Elisabeth G Gwinn
- Department of Physics, University of California , Santa Barbara, California 93106-9510, United States
| | - Victor Rojas-Cervellera
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica I Computacional (IQTCUB), Universitat de Barcelona , Martí I Franquès 1, 08208 Barcelona, Spain
| | - Olga Lopez-Acevedo
- COMP Centre of Excellence, Department of Applied Physics, Aalto University , P.O. Box 11100, 00076 Aalto, Finland
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20
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Kondo J, Tada Y, Dairaku T, Saneyoshi H, Okamoto I, Tanaka Y, Ono A. High‐Resolution Crystal Structure of a Silver(I)–RNA Hybrid Duplex Containing Watson–Crick‐like CSilver(I)C Metallo‐Base Pairs. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507894] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Yoshinari Tada
- Graduate School of Science and Technology, Sophia University, 7‐1 Kioi‐cho, Chiyoda‐ku, Tokyo 102‐8554 (Japan)
| | - Takenori Dairaku
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
| | - Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
| | - Yoshiyuki Tanaka
- Laboratory of Molecular Transformation, Graduate School of Pharmaceutical Sciences, Tohoku University, 6‐3 Aza‐Aoba, Aramaki, Aoba‐ku, Sendai 980‐8578 (Japan)
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro‐cho, 770‐8514 Tokushima (Japan)
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3‐27‐1 Rokkakubashi, Kanagawa‐ku, Yokohama 221‐8686 (Japan)
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21
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Takezawa Y, Nishiyama K, Mashima T, Katahira M, Shionoya M. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination. Chemistry 2015; 21:14713-6. [DOI: 10.1002/chem.201502772] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/11/2022]
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22
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Su M, Tomás-Gamasa M, Serdjukow S, Mayer P, Carell T. Synthesis and properties of a Cu(II) complexing pyrazole ligandoside in DNA. Chem Commun (Camb) 2014; 50:409-11. [PMID: 24263097 DOI: 10.1039/c3cc47561a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development of metal base pairs is of immense importance for the construction of DNA nanostructures. Here we report the synthesis of a biaryl pyrazole-phenol nucleoside that forms in DNA a stable self-pair upon complexation of a Cu(II) ion. A sequence with five consecutive pyrazole nucleotides allows the complexation of five Cu(II) ions in a row.
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Affiliation(s)
- M Su
- Department of Chemistry, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377, Munich, Germany.
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23
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Richters T, Krug O, Kösters J, Hepp A, Müller J. A family of "click" nucleosides for metal-mediated base pairing: unravelling the principles of highly stabilizing metal-mediated base pairs. Chemistry 2014; 20:7811-8. [PMID: 24838942 DOI: 10.1002/chem.201402221] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 12/12/2022]
Abstract
A family of artificial nucleosides has been developed by applying the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition. Starting from 2-deoxy-β-D-glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3-triazole involved in all three nucleobases is complemented by 1,2,4-triazole (TriTri), pyrazole (TriPyr), or pyridine (TriPy). Molecular structures of two metal complexes indicate that metal-mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new "click" nucleosides showed that they can bind Ag(I) to form metal-mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag(I). A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal-mediated base pairs.
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Affiliation(s)
- Tim Richters
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149 Münster (Germany), Fax: (+49) 251-8336007
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24
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs. Angew Chem Int Ed Engl 2014; 53:2385-8. [PMID: 24478025 DOI: 10.1002/anie.201309066] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/06/2013] [Indexed: 11/09/2022]
Abstract
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo (Japan).
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-HgII-T Base Pairs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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26
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Samanta PK, Pati SK. Structural and magnetic properties of a variety of transition metal incorporated DNA double helices. Chemistry 2013; 20:1760-4. [PMID: 24382746 DOI: 10.1002/chem.201302628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/30/2013] [Indexed: 12/22/2022]
Abstract
By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.
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Affiliation(s)
- Pralok K Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80-2208-2766/2767, Hompage: http://www.jncasr.ac.in/pati
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27
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Engelhard DM, Pievo R, Clever GH. Reversible Stabilization of Transition-Metal-Binding DNA G-Quadruplexes. Angew Chem Int Ed Engl 2013; 52:12843-7. [DOI: 10.1002/anie.201307594] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Indexed: 12/17/2022]
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28
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Engelhard DM, Pievo R, Clever GH. Reversible Stabilisierung von übergangsmetallbindenden DNA-G-Quadruplexen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307594] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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Samanta PK, Pati SK. Structural, electronic and photophysical properties of analogous RNA nucleosides: a theoretical study. NEW J CHEM 2013. [DOI: 10.1039/c3nj00633f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Takezawa Y, Shionoya M. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs. Acc Chem Res 2012; 45:2066-76. [PMID: 22452649 DOI: 10.1021/ar200313h] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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31
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32
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Samanta PK, Manna AK, Pati SK. Structural, Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight. Chem Asian J 2012; 7:2718-28. [DOI: 10.1002/asia.201200630] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Pralok K. Samanta
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Arun K. Manna
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
| | - Swapan K. Pati
- Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bangalore 560064 (India), Fax: (+91) 80‐2208‐2766/2767
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Samanta PK, Periyasamy G, Manna AK, Pati SK. Computational studies on structural and optical properties of single-stranded DNA encapsulated silver/gold clusters. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16068d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Base-pairing in the naturally occurring DNA and RNA oligonucleotide duplexes is based on π-stacking, hydrogen bonding, and shape complementarity between the nucleobases adenine, thymine, guanine, and cytosine as well as on the hydrophobic-hydrophilic balance in aqueous media. This complex system of multiple supramolecular interactions is the product of a long-term evolutionary process and thus highly optimized to serve its biological functions such as information storage and processing. After the successful implementation of automated DNA synthesis, chemists have begun to introduce artificial modifications inside the core of the DNA double helix in order to study various aspects of base pairing, generate new base pairs orthogonal to the natural ones, and equip the biopolymer with entirely new functions. The idea to replace the hydrogen bonding interactions with metal coordination between ligand-like nucleosides and suitable transition metal ions culminated in the development of a plethora of artificial base-pairing systems termed "metal base-pairs" which were shown to strongly enhance the DNA duplex stability. Furthermore, they show great potential for the use of DNA as a molecular wire in nanoscale electronic architectures. Although single electrons have proven to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides was identified as a serious obstacle. By exchanging some or all of the Watson-Crick base pairs in DNA with metal complexes, this problem may be solved. In the future, these research efforts are supposed to lead to DNA-like materials with superior conductivity for nano-electronic applications. Other fields of potential application such as DNA-based supramolecular architecture and catalysis may be strongly influenced by these developments as well. This text is meant to illustrate the basic concepts of metal-base pairing and give an outline over recent developments in this field.
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Affiliation(s)
- Guido H Clever
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Göttingen, Germany.
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Matsui T, Miyachi H, Baba T, Shigeta Y. Theoretical Study on Reaction Scheme of Silver(I) Containing 5-Substituted Uracils Bridge Formation. J Phys Chem A 2011; 115:8504-10. [DOI: 10.1021/jp200871f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Liu S, Clever GH, Takezawa Y, Kaneko M, Tanaka K, Guo X, Shionoya M. Direct Conductance Measurement of Individual Metallo-DNA Duplexes within Single-Molecule Break Junctions. Angew Chem Int Ed Engl 2011; 50:8886-90. [DOI: 10.1002/anie.201102980] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 11/10/2022]
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Liu S, Clever GH, Takezawa Y, Kaneko M, Tanaka K, Guo X, Shionoya M. Direct Conductance Measurement of Individual Metallo-DNA Duplexes within Single-Molecule Break Junctions. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102980] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Brancolini G, Felice RD. Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs. J Chem Phys 2011; 134:205102. [DOI: 10.1063/1.3593272] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Megger DA, Fonseca Guerra C, Hoffmann J, Brutschy B, Bickelhaupt FM, Müller J. Contiguous Metal‐Mediated Base Pairs Comprising Two Ag
I
Ions. Chemistry 2011; 17:6533-44. [DOI: 10.1002/chem.201002944] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/12/2011] [Indexed: 12/28/2022]
Affiliation(s)
- Dominik A. Megger
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jan Hoffmann
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - Bernhard Brutschy
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jens Müller
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
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Nakanishi Y, Matsui T, Kitagawa Y, Shigeta Y, Saito T, Kataoka Y, Kawakami T, Okumura M, Yamaguchi K. Electron Conductivity in Modified Models of Artificial Metal–DNA Using Green’s Function-Based Elastic Scattering Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Seubert K, Guerra CF, Bickelhaupt FM, Müller J. Chimeric GNA/DNA metal-mediated base pairs. Chem Commun (Camb) 2011; 47:11041-3. [DOI: 10.1039/c1cc13774c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Clever G, Reitmeier S, Carell T, Schiemann O. Antiferromagnetic Coupling of Stacked CuII-Salen Complexes in DNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906359] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Clever G, Reitmeier S, Carell T, Schiemann O. Antiferromagnetic Coupling of Stacked CuII-Salen Complexes in DNA. Angew Chem Int Ed Engl 2010; 49:4927-9. [DOI: 10.1002/anie.200906359] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Nagarajan S, Kumbhar A, Varghese B, Das TM. Structural and DNA cleavage of sugar-derived Schiff base ligands and their dinuclear Cu(II) complexes. Carbohydr Res 2010; 345:1077-83. [DOI: 10.1016/j.carres.2010.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 01/13/2010] [Accepted: 01/20/2010] [Indexed: 10/19/2022]
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Kang DW, Qu Z, Jiang H, Xie SJ. Transverse electric field modulated tunneling magnetoresistance in a DNA molecular device. Phys Chem Chem Phys 2010; 12:578-82. [PMID: 20066344 DOI: 10.1039/b917050b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum spin-dependent transport in a ferromagnetic(FM)/DNA/ferromagnetic(FM) device is theoretically investigated based on the lattice Green function method and the Landauer-Büttiker theory. The effect of a transverse electric field on magnetoresistance (MR) of the device is investigated. It is predicted that either the direction or strength of the transverse electric field can change the MR of the device. We suggest a possible application of modulating MR of the FM/DNA/FM device by a transverse electric field.
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Affiliation(s)
- Da-Wei Kang
- School of Physics, Shandong University, Jinan, 250100, China
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Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nat Chem 2010; 2:229-34. [PMID: 21124482 DOI: 10.1038/nchem.512] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 12/03/2009] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.
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Georgiades SN, Vilar R. Interaction of metal complexes with nucleic acids. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b918406f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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