1
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de Oliveira Martins E, Weber G. Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration. Biophys Chem 2024; 306:107156. [PMID: 38157701 DOI: 10.1016/j.bpc.2023.107156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
DNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and those available were obtained from a limited set of melting temperature at high sodium concentration. To our knowledge, there is currently no NN set of parameters for up to three mismatches covering all configurations at low sodium concentrations. Here, we are applying the NN model to a large set of 4096 published melting temperatures, covering all combinations of single, double and triple mismatches. Dealing with such a large set of temperature is challenging in several ways, bringing new methodological problems. Here, optimizing a large number of 252 independent parameters has required the development of a new method where we readjust the seed parameters using the definition of the Gibbs free energy. The new parameters predict the training set within 1.1 °C and the validation set to 2.7 °C.
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Affiliation(s)
- Erik de Oliveira Martins
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil; Escola Politécnica, Centro Universitário Católica do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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2
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Escher D, Schäfer T, Hebenbrock M, Müller J. 6-Pyrazolylpurine and its deaza derivatives as nucleobases for silver(I)-mediated base pairing with pyrimidines. J Biol Inorg Chem 2023; 28:791-803. [PMID: 37982840 PMCID: PMC10687122 DOI: 10.1007/s00775-023-02022-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 09/26/2023] [Indexed: 11/21/2023]
Abstract
The artificial nucleobase 6-pyrazolylpurine (6PP) and its deaza derivatives 1-deaza-6-pyrazolylpurine (1D6PP), 7-deaza-6-pyrazolylpurine (7D6PP), and 1,7-dideaza-6-pyrazolylpurine (1,7D6PP) were investigated with respect to their ability to differentiate between the canonical nucleobases cytosine and thymine by means of silver(I)-mediated base pairing. As shown by temperature-dependent UV spectroscopy and by circular dichroism spectroscopy, 6PP and (to a lesser extent) 7D6PP form stable silver(I)-mediated base pairs with cytosine, but not with thymine. 1D6PP and 1,7D6PP do not engage in the formation of stabilizing silver(I)-mediated base pairs with cytosine or thymine. The different behavior of 1D6PP, 7D6PP, and 1,7D6PP indicates that silver(I) binding occurs via the N1 position of the purine derivative, i.e. via the Watson-Crick face. The data show that 6PP is capable of differentiating between cytosine and thymine, which is potentially relevant in the context of detecting single-nucleotide polymorphisms.
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Affiliation(s)
- Daniela Escher
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Tim Schäfer
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 30, 48149, Münster, Germany.
- Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Universität Münster, Corrensstr. 30, 48149, Münster, Germany.
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3
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Nyenhuis M, Schönrath I, Kamzeeva PN, Zatsepin TS, Müller J, Doltsinis N, Aralov AV. Benzothiazole-substituted 1,3-diaza-2-oxophenoxazine as a luminescent nucleobase surrogate for silver(I)-mediated base pairing. Dalton Trans 2022; 51:13386-13395. [PMID: 35989665 DOI: 10.1039/d2dt01762h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A benzothiazole-substituted derivative (X) of 1,3-diaza-2-oxophenoxazine was evaluated with respect to its ability to engage in Ag(I)-mediated homo base pair formation in two different DNA duplexes. The metal binding was determined by a combination of temperature-dependent UV spectroscopy, CD spectroscopy, and fluorescence spectroscopy, indicating the incorporation of two Ag(I) ions to generate a dinuclear X-Ag(I)2-X base pair. Interestingly, a luminescence increase was observed upon metal binding. Theoretical luminescence spectra were calculated using time-dependent density functional theory (TDDFT) for all possible Ag(I)-mediated X : X base pair geometries to identify the species responsible for the increase in luminescence. The study shows that even bulky non-planar artificial nucleobases can be applied to form stabilizing metal-mediated base pairs.
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Affiliation(s)
- Marvin Nyenhuis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Isabell Schönrath
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Polina N Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
| | - Nikos Doltsinis
- Westfälische Wilhelms-Universität Münster, Institute for Solid State Theory and Center for Multiscale Theory and Computation, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany.
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
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4
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Mesoscopic model confirms strong base pair metal mediated bonding for T-Hg 2+-T and weaker for C-Ag +-C. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Heddinga MH, Müller J. Modulating aptamer function by copper(II)-mediated base pair formation. Org Biomol Chem 2022; 20:4787-4793. [PMID: 35640171 DOI: 10.1039/d2ob00788f] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two aptamers, one for ATP and one for arginine, were modified using an artificial 2'-dexoyribonucleoside based on the nucleobase surrogate imidazole-4-carboxylate. This synthetic nucleoside substitute does not engage in hydrogen bonding but is capable of forming Cu(II)-mediated base pairs instead. Hence, the addition of Cu(II) can be used to influence the ability of the aptamer derivatives to adopt the correct fold necessary for binding their respective target molecule. As a result, aptamer function can be modulated via the addition of Cu(II). The extent of modulation ability depends on the identity of the aptamer and on the exact location of the artificial nucleosides within the oligonucleotide sequence.
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Affiliation(s)
- Marius H Heddinga
- 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. .,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstraße 28/30, 48149 Münster, Germany
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6
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Aro-Heinilä A, Lepistö A, Äärelä A, Lönnberg TA, Virta P. 2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing. J Org Chem 2022; 87:137-146. [PMID: 34905374 PMCID: PMC8749955 DOI: 10.1021/acs.joc.1c02056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 01/02/2023]
Abstract
A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Assi Lepistö
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Antti Äärelä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | | | - Pasi Virta
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
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7
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Schönrath I, Aukam H, Jasper-Peter B, Müller J. Silver(I)-mediated base pairing involving an S-glycosidic GNA nucleoside analogue. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:23-35. [PMID: 34686119 DOI: 10.1080/15257770.2021.1994146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The 4S-Ag(I)-C base pair (4S, 3-((2-(methylthio)pyrimidin-4-yl)thio)propane-1,2-diol; C, deoxycytidine) represents the first metal-mediated base pair comprising an S-glycosidic nucleoside analogue. We report here the synthesis of the phosphoramidite suitable for the automated solid-phase synthesis of DNA oligonucleotides containing 4S and its silver(I)-binding ability. The DNA duplexes comprising a 4S:C mispair exhibit a large thermal stabilization upon the addition of one equivalent of silver ions, giving rise to the formation of the above-mentioned silver(I)-mediated base pair. By formally replacing the sulfur atom in the glycosidic bond by an oxygen atom, i.e., by applying 3-((2-(methylthio)pyrimidin-4-yl)oxy)propane-1,2-diol (4 O) as the artificial nucleoside analogue, the participation of this atom as a donor atom in silver(I)-mediated base pairing is shown to be neglectable.Supplemental data for this article is available online at.
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Affiliation(s)
- Isabell Schönrath
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hanne Aukam
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Beate Jasper-Peter
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Münster, Germany
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8
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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9
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Ukale D, Lönnberg T. Organomercury Nucleic Acids: Past, Present and Future. Chembiochem 2021; 22:1733-1739. [PMID: 33410571 PMCID: PMC8247973 DOI: 10.1002/cbic.202000821] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/30/2020] [Indexed: 11/19/2022]
Abstract
Synthetic efforts towards nucleosides, nucleotides, oligonucleotides and nucleic acids covalently mercurated at one or more of their base moieties are summarized, followed by a discussion of the proposed, realized and abandoned applications of this unique class of compounds. Special emphasis is given to fields in which active research is ongoing, notably the use of HgII -mediated base pairing to improve the hybridization properties of oligonucleotide probes. Finally, this minireview attempts to anticipate potential future applications of organomercury nucleic acids.
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Affiliation(s)
- Dattatraya Ukale
- 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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10
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Flamme M, Figazzolo C, Gasser G, Hollenstein M. Enzymatic construction of metal-mediated nucleic acid base pairs. Metallomics 2021; 13:6206861. [PMID: 33791776 DOI: 10.1093/mtomcs/mfab016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022]
Abstract
Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Chiara Figazzolo
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Centre de Recherches Interdisciplinaires CRI, 8 rue Charles V, 75004 Paris, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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11
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Escher D, Müller J. Silver(I)‐mediated hetero base pairs of 6‐pyrazolylpurine and its deaza derivatives. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202000481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster Institut für Anorganische und Analytische Chemie Corrensstr. 30 48149 Münster Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster Institut für Anorganische und Analytische Chemie Corrensstr. 30 48149 Münster Germany
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12
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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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13
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Kishimoto Y, Nakagawa O, Fujii A, Yoshioka K, Nagata T, Yokota T, Hari Y, Obika S. 2',4'-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance*. Chemistry 2021; 27:2427-2438. [PMID: 33280173 PMCID: PMC7898338 DOI: 10.1002/chem.202003982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 11/28/2022]
Abstract
Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2'-O,4'-C-Methylene-bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP (BH )) was previously reported. Herein, a novel BH analogue, 2',4'-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO (BAEO ), was designed. The BAEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing BAEO possessed up to 104 -, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2'-deoxycytidine (C), 2',4'-BNA/LNA with 5-methylcytosine (L), or 2'-deoxyribonucleoside with G-clamp (PAEO ), respectively. Moreover, duplexes formed by ODN bearing BAEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing BAEO was more resistant to 3'-exonuclease than ODNs with phosphorothioate linkages.
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
| | - Kotaro Yoshioka
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Tetsuya Nagata
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Takanori Yokota
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
- Department of Neurology and Neurological ScienceGraduate School of Medical and Dental SciencesTokyo Medical and Dental University1-5-45 Yushima, Bunkyo-kuTokyo113-8519Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical SciencesTokushima Bunri University180 Nishihamahoji, Yamashiro-choTokushima770-8514Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical SciencesOsaka University1–6 Yamadaoka SuitaOsaka565-0871Japan
- Core Research for Evolutional Science and Technology (CREST), (Japan) Sciences and Technology Agency (JST)7 GobanchoChiyoda-kuTokyo102-0076Japan
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14
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Schönrath I, Tsvetkov VB, Barceló-Oliver M, Hebenbrock M, Zatsepin TS, Aralov AV, Müller J. Silver(I)-mediated base pairing in DNA involving the artificial nucleobase 7,8-dihydro-8-oxo-1,N 6-ethenoadenine. J Inorg Biochem 2021; 219:111369. [PMID: 33878529 DOI: 10.1016/j.jinorgbio.2021.111369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/22/2022]
Abstract
The artificial nucleobase 7,8-dihydro-8-oxo-1,N6-ethenoadenine (X) was investigated with respect to its ability to engage in Ag(I)-mediated base pairing in DNA. Spectroscopic data indicate the formation of dinuclear X-Ag(I)2-X homo base pairs and mononuclear X-Ag(I)-C base pairs (C, cytosine). Density functional theory calculations and molecular dynamics simulations indicate that the nucleobase changes from its lactam tautomeric form prior to the formation of the Ag(I)-mediated base pair to the lactim form after the incorporation of the Ag(I) ions. Fluorescence spectroscopy indicates that the two Ag(I) ions of the homo base pair are incorporated sequentially. Isothermal titration calorimetry confirms that the affinity of one of the Ag(I) ions is about tenfold higher than that of the other Ag(I) ion. The computational analysis by means of density functional theory confirms a much larger reaction energy for the incorporation of the first Ag(I) ion. The thermal stabilization upon the formation of the dinuclear Ag(I)-mediated homo base pair exceeds the one previously observed for the closely related nucleobase 1,N6-ethenoadenine by far, despite very similar structures. This additional stabilization may stem from the presence of water molecules engaged in hydrogen bonding with the additional oxygen atom of the artificial nucleobase X. The highly stabilizing Ag(I)-mediated base pair is a valuable addition to established dinuclear metal-mediated base pairs.
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Affiliation(s)
- Isabell Schönrath
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Vladimir B Tsvetkov
- World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, 8/2 Trubetskaya Str., 119146 Moscow, Russia; Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia
| | - Miquel Barceló-Oliver
- Universitat de les Illes Balears, Departament de Química, carretera Valldemossa km 7.5, Ed. Mateu Orfila i Rotger, 07122 Palma de Mallorca, Spain
| | - Marian Hebenbrock
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205 Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia.
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany.
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15
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Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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16
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Light-induced formation of silver(I)-mediated base pairs in DNA: Possibilities and limitations. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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17
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Escher D, Müller J. Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge. Chemistry 2020; 26:16043-16048. [PMID: 32627879 PMCID: PMC7756626 DOI: 10.1002/chem.202002803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/18/2022]
Abstract
DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (1D6PP), 7‐deaza‐6PP (7D6PP) and 1,7‐dideaza‐6PP (1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of AgI. In 6PP and 7D6PP, the AgI ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in 1D6PP and 1,7D6PP, so that in 1D6PP an AgI coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the AgI‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of AgI, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.
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Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
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18
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Bachmann J, Schönrath I, Müller J, Doltsinis NL. Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair. Molecules 2020; 25:E4942. [PMID: 33114568 PMCID: PMC7663159 DOI: 10.3390/molecules25214942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) into the DNA. The dynamic distance constraint was employed to find initial structures, control the dissociation process in an unbiased fashion and to determine the free energy required. A strong influence of the exocyclic carbonyl or amino groups of neighbouring base pairs on both the bonding pattern and the mechanism of incorporation was observed. During the dissociation simulation, an amino group of an adenine moiety of the adjacent base pair acts as a turnstile to rotate the mercury(II) ion out of the DNA core region. The calculations provide an important insight into the mechanism of formation of this dinuclear metal-mediated base pair and indicate that the exact location of a transition metal ion in a metal-mediated base pair may be more ambiguous than derived from simple model building.
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Affiliation(s)
- Jim Bachmann
- Institute for Solid State Theory and Center for Multiscale Theory and Computation, Westfälische-Wilhelms Universität Münster, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany;
| | - Isabell Schönrath
- Institut für Anorganische und Analytische Chemie, Westfälische-Wilhelms Universität Münster, Corrensstraße 30, 48149 Münster, Germany;
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische-Wilhelms Universität Münster, Corrensstraße 30, 48149 Münster, Germany;
| | - Nikos L. Doltsinis
- Institute for Solid State Theory and Center for Multiscale Theory and Computation, Westfälische-Wilhelms Universität Münster, Wilhelm-Klemm-Straße 10, 48149 Münster, Germany;
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19
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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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20
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Fujii A, Nakagawa O, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties. Chembiochem 2019; 21:860-864. [PMID: 31568630 DOI: 10.1002/cbic.201900536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Indexed: 11/11/2022]
Abstract
1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities. A triplex-forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double-stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9-TAP-containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9-TAP moiety was maintained even in triplex (9-TAP:AT) formation, so 9-TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.
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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
| | - 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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21
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Naskar S, Müller J. Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs. Chemistry 2019; 25:16214-16218. [PMID: 31682036 PMCID: PMC6972992 DOI: 10.1002/chem.201903789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Indexed: 12/16/2022]
Abstract
By applying caged thymidine residues, DNA duplexes were created in which HgII‐mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal‐mediated base pairs was achieved.
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Affiliation(s)
- Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
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22
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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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23
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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24
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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25
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Sandmann N, Bachmann J, Hepp A, Doltsinis NL, Müller J. Copper(ii)-mediated base pairing involving the artificial nucleobase 3H-imidazo[4,5-f]quinolin-5-ol. Dalton Trans 2019; 48:10505-10515. [DOI: 10.1039/c9dt02043h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A highly stabilizing Cu(ii)-mediated base pair is introduced into DNA using a large artificial nucleobase.
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Affiliation(s)
- Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jim Bachmann
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Nikos L. Doltsinis
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
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