1
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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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Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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4
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Chai Y, Guo X, Leonard P, Seela F. Heterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines. Chemistry 2020; 26:13973-13989. [PMID: 32667103 PMCID: PMC7702046 DOI: 10.1002/chem.202002765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Indexed: 02/05/2023]
Abstract
Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the Tm values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7-deazapurines resulted in stable parallel duplexes, thereby confirming Watson-Crick-type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α-d configuration display mirror-like shapes to those with the β-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with a limited number of silver pairs show a B-type double helix almost indistinguishable from natural DNA. Nonmelting silver ion-DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development LaboratoryWest China HospitalSichuan University610041SichuanP. R. China
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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5
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Ukale DU, Tähtinen P, Lönnberg T. 1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase. Chemistry 2020; 26:2164-2168. [PMID: 31913530 DOI: 10.1002/chem.201905434] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/25/2019] [Indexed: 12/19/2022]
Abstract
A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔTm =7.3 °C) HgII -mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two HgII ions coordinated to O2 and O4 of the thymine base.
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Affiliation(s)
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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6
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Chai Y, Leonard P, Guo X, Seela F. Silver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability. Chemistry 2019; 25:16639-16651. [PMID: 31583755 PMCID: PMC6972701 DOI: 10.1002/chem.201903915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/02/2019] [Indexed: 02/05/2023]
Abstract
Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral α-dC-dC base pairs can approach the stability of a Watson-Crick pair, whereas homochiral dC-dC pairs are significantly less stable. A positional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence. When the number of silver ions was equivalent to the number of duplex base pairs (12), non-melting silver-rich complexes were formed. Structural changes have been supported by circular dichroism (CD) spectra, which showed that the B-DNA structure was maintained whilst the silver ion concentration was low. At high silver ion concentration, silver-rich complexes displaying different CD spectra were formed.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of Respiratory and Critical Care MedicineTargeted Tracer Research and Development LaboratoryWest China HospitalSichuan UniversitySichuan610041P. R. China
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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7
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Funai T, Aotani M, Kiriu R, Nakamura J, Miyazaki Y, Nakagawa O, Wada S, Torigoe H, Ono A, Urata H. Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases. Chembiochem 2019; 21:517-522. [DOI: 10.1002/cbic.201900450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Megumi Aotani
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Risa Kiriu
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Junko Nakamura
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Yuki Miyazaki
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Osamu Nakagawa
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
- Present address: Graduate School of Pharmaceutical SciencesOsaka University 1–6 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shun‐ichi Wada
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Hidetaka Torigoe
- Department of Applied ChemistryFaculty of ScienceTokyo University of Science 1-3 Kagurazaka, Shinjuku-ku Tokyo 162-8601 Japan
| | - Akira Ono
- Department of Material and Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hidehito Urata
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
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8
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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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9
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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: 26] [Impact Index Per Article: 5.2] [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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10
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Zhou X, Kondhare D, Leonard P, Seela F. Anomeric 5-Aza-7-deaza-2'-deoxyguanosines in Silver-Ion-Mediated Homo and Hybrid Base Pairs: Impact of Mismatch Structure, Helical Environment, and Nucleobase Substituents on DNA Stability. Chemistry 2019; 25:10408-10419. [PMID: 31062885 DOI: 10.1002/chem.201901276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Nucleoside configuration (α-d vs. β-d), nucleobase substituents, and the helical DNA environment of silver-mediated 5-aza-7-deazaguanine-cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver-mediated base pairs of α-d and β-d anomeric 5-aza-7-deaza-2'-deoxyguanosines and anomeric 2'-deoxycytidines incorporated in 12-mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5-aza-7-deaza-2'-deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α-d/α-d and β-d/β-d homo base pairs or α-d/β-d and β-d/α-d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective Tm stability increases observed after silver ion addition differ significantly. Homo base pairs with β-d/β-d or α-d/α-d nucleoside combinations are more stable than α-d/β-d hybrid base pairs. The positional switch of silver-ion-mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5-position of the dC site of silver-mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal-DNA hybrid materials.
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Affiliation(s)
- Xinglong Zhou
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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11
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Fujii A, Nakagawa O, Kishimoto Y, Okuda T, Nakatsuji Y, Nozaki N, Kasahara Y, Obika S. 1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three Ag I Ions in a Duplex. Chemistry 2019; 25:7443-7448. [PMID: 30843298 DOI: 10.1002/chem.201900373] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 12/23/2022]
Abstract
Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned AgI ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three AgI ions. Nine equivalents of AgI led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three AgI ions are expected to be applicable to new DNA nanotechnologies.
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Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
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12
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Müller SL, Zhou X, Leonard P, Korzhenko O, Daniliuc C, Seela F. Functionalized Silver‐Ion‐Mediated α‐dC/β‐dC Hybrid Base Pairs with Exceptional Stability: α‐d‐5‐Iodo‐2′‐Deoxycytidine and Its Octadiynyl Derivative in Metal DNA. Chemistry 2019; 25:3077-3090. [DOI: 10.1002/chem.201805299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/04/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Sebastian Lars Müller
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Xinglong Zhou
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Oxana Korzhenko
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
| | - Constantin Daniliuc
- Institut für Organische ChemieUniversität Münster Corrensstrasse 40 48149 Münster Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for Nanotechnology Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für, Chemie neuer MaterialienUniversität Osnabrück Barbarastrasse 7 49069 Osnabrück Germany
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13
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Xing X, Feng Y, Yu Z, Hidaka K, Liu F, Ono A, Sugiyama H, Endo M. Direct Observation of the Double-Stranded DNA Formation through Metal Ion-Mediated Base Pairing in the Nanoscale Structure. Chemistry 2018; 25:1446-1450. [DOI: 10.1002/chem.201805394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/26/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Xiwen Xing
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Department of Biotechnology; Key Laboratory of Virology of Guangzhou; College of Life Science and Technology; Jinan University; Guangzhou P. R. China
| | - Yihong Feng
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Zutao Yu
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Kumi Hidaka
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Fenyong Liu
- Department of Biotechnology; Key Laboratory of Virology of Guangzhou; College of Life Science and Technology; Jinan University; Guangzhou P. R. China
| | - Akira Ono
- Department of Materials & Life Chemistry; Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences; Kyoto University
| | - Masayuki Endo
- Department of Chemistry; Graduate School of Science; Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
- Institute for Integrated Cell-Material Sciences; Kyoto University
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14
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Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Chembiochem 2018; 19:2372-2379. [PMID: 30168891 DOI: 10.1002/cbic.201800448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/08/2022]
Abstract
The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-HgII -T and cytosine (C)-AgI -C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2',4'-BNA/LNA in the field of MMBPs. 2',4'-BNA/LNA with 5-methylcytosine stabilized the MMBP of C with AgI ions. Moreover, the 2',4'-BNA/LNA sugar significantly improved the duplex-forming ability of the DNA/DNA complex, relative to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex-containing MMBPs. The results indicate that 2',4'-BNA/LNA can be applied not only to nucleic acid based therapies, but also to MMBP technologies.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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15
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Jash B, Müller J. Concomitant Site-Specific Incorporation of Silver(I) and Mercury(II) Ions into a DNA Duplex. Chemistry 2018; 24:10636-10640. [DOI: 10.1002/chem.201802470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
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16
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Guo X, Leonard P, Ingale SA, Liu J, Mei H, Sieg M, Seela F. 5-Aza-7-deaza-2'-deoxyguanosine and 2'-Deoxycytidine Form Programmable Silver-Mediated Base Pairs with Metal Ions in the Core of the DNA Double Helix. Chemistry 2018; 24:8883-8892. [PMID: 29573347 DOI: 10.1002/chem.201801273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 02/05/2023]
Abstract
5-Aza-7-deaza-2'-deoxyguanosine (dZ) forms a silver-mediated base pair with dC. The metal ion pair represents a mimic of the H-bonded Watson-Crick dG-dC pair. The modified nucleoside displays a similar shape as the parent 2'-deoxyguanosine from which it can be constructed by transposition of nitrogen-7 to the bridgehead position-5. It lacks the major groove binding site as the positional change moves the dG- acceptor position from nitrogen-7 to nitrogen-1. As a shape mimic of dG, it fits nicely in the DNA double helix. The purine-pyrimidine dZ-dC hetero pair shows a relationship to the pyrimidine-pyrimidine dC-dC homo base pair. The dZ-dC pair forms a mismatch in the absence of silver ions and matches after addition of metal ions. Base-pair formation was verified on self-complementary 6-mer duplexes and 12-mer DNA with random composition by UV-dependent Tm measurements. Modified silver-mediated and hydrogen-bonded canonical base pairs can coexist. The dZ-Ag+ -dC base pair is slightly less stable than the dG-dC pair, shows sequence dependence, and consumes one or two silver ions. These properties make the dZ-Ag+ -dC pair suitable for programmable incorporation of silver ions in DNA which cannot be achieved by canonical base pairs. If the silver ion content is higher than the total number of base pairs the duplexes turn into very stable structures in which all base pairs are considered to be in the silver-mediated pairing mode.
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Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Jiang Liu
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,State Key Laboratory of Oral Diseases and National Clinical, Research Center for Oral Diseases and Department of Oral Medicine, of West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Martha Sieg
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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17
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Guo X, Leonard P, Ingale SA, Seela F. Gemcitabine, Pyrrologemcitabine, and 2'-Fluoro-2'-Deoxycytidines: Synthesis, Physical Properties, and Impact of Sugar Fluorination on Silver Ion Mediated Base Pairing. Chemistry 2017; 23:17740-17754. [PMID: 28906062 DOI: 10.1002/chem.201703427] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Indexed: 01/06/2023]
Abstract
The stability of silver-mediated "dC-dC" base pairs relies not only on the structure of the nucleobase, but is also sensitive to structural modification of the sugar moiety. 2'-Fluorinated 2'-deoxycytidines with fluorine atoms in the arabino (up) and ribo (down) configuration as well as with geminal fluorine substitution (anticancer drug gemcitabine) and the novel fluorescent phenylpyrrolo-gemcitabine (ph PyrGem) have been synthesized. All the nucleosides display the recognition face of naturally occurring 2'-deoxycytidine. The nucleosides were converted into phosphoramidites and incorporated into 12-mer oligonucleotides by solid-phase synthesis. The addition of silver ions to DNA duplexes with a fluorine-modified "dC-dC" pair near the central position led to significant duplex stabilization. The increase in stability was higher for duplexes with fluorinated sugar residues than for those with an unchanged 2'-deoxyribose moiety. Similar observations were made for "dC-dT" pairs and to a minor extent for "dC-dA" pairs. The increase in silver ion mediated base-pair stability was reversed by annulation of a pyrrole ring to the cytosine moiety, as shown for 2'-fluorinated ph PyrGem in comparison with phenylpyrrolo-dC (ph PyrdC). This phenomenon results from stereoelectronic effects induced by fluoro substitution, which are transmitted from the sugar moiety to the silver ion mediated base pairs. The extent of the effect depends on the number of fluorine substituents, their configuration, and the structure of the nucleobase.
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Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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18
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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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19
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20
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Guo X, Seela F. Anomeric 2′-Deoxycytidines and Silver Ions: Hybrid Base Pairs with Greatly Enhanced Stability and Efficient DNA Mismatch Detection with α-dC. Chemistry 2017; 23:11776-11779. [DOI: 10.1002/chem.201703017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology; Center for Nanotechnology; Heisenbergstrasse 11 48149 Münster Germany
- Laboratorium für Organische und Bioorganische Chemie; Institut für Chemie neuer Materialien; Universität Osnabrück; Barbarastrasse 7 49069 Osnabrück Germany
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21
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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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22
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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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23
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Zhao H, Leonard P, Guo X, Yang H, Seela F. Silver-Mediated Base Pairs in DNA Incorporating Purines, 7-Deazapurines, and 8-Aza-7-deazapurines: Impact of Reduced Nucleobase Binding Sites and an Altered Glycosylation Position. Chemistry 2017; 23:5529-5540. [PMID: 28195414 DOI: 10.1002/chem.201605982] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 02/05/2023]
Abstract
Formation of silver-mediated DNA was studied with oligonucleotides incorporating 8-aza-7-deazapurine, 7-deazapurine, and purine nucleosides. The investigation was performed on non-self-complementary duplexes with one or two modifications and self-complementary duplexes with an alternating dA-dT motif. Homo base pairs as well as base pair mismatches of dA analogues with dC and Watson-Crick pairs with dT were studied by stoichiometric silver ion titration and Tm measurements. N8 -Glycosylated 8-aza-7-deazaadenine forms silver-ion-mediated base pairs capturing two silver ions (low silver content) whereas regularly glycosylated 8-aza-7-deazapurine, 7-deazapurine (c7 Ad ), and dA do not form comparable structures. Stable silver-mediated "dA-dC" base pair mismatches were detected for all nucleosides. Two silver ions per base pair are bound by 8-aza-7-deazapurine whereas c7 Ad binds only one silver ion. The situation is different when the equivalents of silver ions were increased to the number of total base pairs. Surprisingly, in 12-mer duplexes as well as in related 25-mer duplexes every base pair consumed one silver ion.
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Affiliation(s)
- Hang Zhao
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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24
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Terrón A, Moreno-Vachiano B, Bauzá A, García-Raso A, Fiol JJ, Barceló-Oliver M, Molins E, Frontera A. X-ray Crystal Structure of a Metalled Double-Helix Generated by Infinite and Consecutive C*-AgI
-C* (C*:N1
-Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions. Chemistry 2017; 23:2103-2108. [DOI: 10.1002/chem.201604331] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Angel Terrón
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Blas Moreno-Vachiano
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Angel García-Raso
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Juan Jesús Fiol
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Miquel Barceló-Oliver
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC); Campus de la Universitat Autònoma de Barcelona 08193 Bellaterra Spain
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
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25
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Kondo J, Sugawara T, Saneyoshi H, Ono A. Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine–2Ag(i)–4-thiothymine. Chem Commun (Camb) 2017; 53:11747-11750. [DOI: 10.1039/c7cc06153f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The crystal structures of 4-thiothymine–2AgI–4-thiothymine base pairs in B-form DNA duplexes have been solved.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Tokyo 102-8554
- Japan
| | - Toru Sugawara
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Hisao Saneyoshi
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
| | - Akira Ono
- Department of Materials & Life Chemistry
- Faculty of Engineering
- Kanagawa University
- Yokohama
- Japan
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26
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Mandal S, Hebenbrock M, Müller J. Ein zweikerniges Quecksilber(II)-vermitteltes Basenpaar in DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
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27
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Mandal S, Hebenbrock M, Müller J. A Dinuclear Mercury(II)-Mediated Base Pair in DNA. Angew Chem Int Ed Engl 2016; 55:15520-15523. [PMID: 27862734 DOI: 10.1002/anie.201608354] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/30/2016] [Indexed: 11/08/2022]
Abstract
The first dinuclear metal-mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N6 -ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N-M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of HgII and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T-HgII2 -ϵA base pair. This metal-mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature-dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.
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Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
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28
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Dairaku T, Furuita K, Sato H, Šebera J, Nakashima K, Kondo J, Yamanaka D, Kondo Y, Okamoto I, Ono A, Sychrovský V, Kojima C, Tanaka Y. Structure Determination of an AgI-Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with1H/15N/109Ag NMR Spectroscopy. Chemistry 2016; 22:13028-31. [DOI: 10.1002/chem.201603048] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Takenori Dairaku
- School of Pharmaceutical Sciences; Ohu University; 31-1 Misumido, Tomita-machi, Koriyama Fukushima 963-8611 Japan
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Kyoko Furuita
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Hajime Sato
- Application, Bruker BioSpin K. K.; 3-9 Moriya-cho, Kanagawa-ku, Yokohama Kanagawa 221-0022 Japan
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Katsuyuki Nakashima
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
| | - 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
| | - Daichi Yamanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Yoshinori Kondo
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
| | - Itaru Okamoto
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Akira Ono
- Department of Material & Life Chemistry, Faculty of Engineering; Kanagawa University; 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama Kanagawa 221-8686 Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic, v.v.i.; Flemingovo náměstí 2 16610 Praha 6 Czech Republic
- Czech Technical University in Prague; Faculty of Electrical Engineering, Department of Electrotechnology; Technická 2 166 27 Praha 6 Czech Republic
| | - Chojiro Kojima
- Institute for Protein Research; Osaka University; 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Yoshiyuki Tanaka
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai Miyagi 980-8578 Japan
- Faculty of Phamaceutical Scienes; Tokushima Bunri University; Yamashiro-cho Tokushima 770-8514 Japan
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29
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Yang H, Seela F. Silver Ions in Non-canonical DNA Base Pairs: Metal-Mediated Mismatch Stabilization of 2'-Deoxyadenosine and 7-Deazapurine Derivatives with 2'-Deoxycytidine and 2'-Deoxyguanosine. Chemistry 2016; 22:13336-46. [PMID: 27492501 DOI: 10.1002/chem.201602103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/18/2022]
Abstract
Novel silver-mediated dA-dC, dA*-dC, and dA*-dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA). 7-Deazapurine nucleosides enforce silver ion binding and direct metal-mediated base pair formation to their Watson-Crick face. New phosphoramidites were prepared from 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA, which contain labile isobutyryl protecting groups. Solid-phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher Tm values) were observed for oligonucleotide duplexes with non-canonical dA*-dC and dA-dC pairs in the presence of silver ions. The stability of the silver-mediated base pairs was pH dependent. Silver ion binding was not observed for the dA-dG mismatch but took place when mismatches were formed between 7-deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany), Fax.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany), Fax. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany.
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