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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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2
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Lefringhausen N, Erbacher C, Elinkmann M, Karst U, Müller J. Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation. Bioconjug Chem 2024; 35:99-106. [PMID: 38157473 DOI: 10.1021/acs.bioconjchem.3c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Metal-mediated base pairs represent a topical alternative to canonical hydrogen-bonded base pairs. In this context, the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was introduced as an artificial nucleobase in a glycol nucleic acid-based nucleoside analogue into a DNA oligonucleotide in a way that the oligonucleotide contains a central block of six contiguous P residues. The ability to engage in Ag+-mediated base pairing was evaluated with respect to the four canonical nucleosides in positions complementary to P. Highly stabilizing Ag+-mediated base pairs were formed with cytosine and guanine (i.e., P-Ag+-C and P-Ag+-G base pairs), whereas the analogous base pairs with thymine and adenine were much less stable and hence formed incompletely. Surprisingly, the intermediate formation of a homodimeric duplex of the P-containing oligonucleotide was observed in all cases, albeit to a different extent. The homodimer is composed of P-Ag+-P base pairs and 18 overhanging mismatched canonical nucleobases. It demonstrates the obstacles present when designing metal-mediated base pairs as metal complexation may take place irrespective of the surrounding natural base pairs. Homodimer formation was found to be particularly prominent when the designated metal-mediated base pairs are of low stability, suggesting that homodimers and regular duplexes are formed in a competing manner.
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Affiliation(s)
- Nils Lefringhausen
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
| | - Catharina Erbacher
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Matthias Elinkmann
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Uwe Karst
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 48, Münster 48149, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
- Cells in Motion Interfaculty Centre (CiMIC) and Center for Soft Nanoscience (SoN), Universität Münster, Corrensstr. 28/30, Münster 48149, Germany
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3
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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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4
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Lefringhausen N, Seiffert V, Erbacher C, Karst U, Müller J. Chiral-at-Metal Silver-Mediated Base Pairs: Metal-Centred Chirality versus DNA Helical Chirality. Chemistry 2023; 29:e202202630. [PMID: 36219466 PMCID: PMC10098492 DOI: 10.1002/chem.202202630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/23/2022]
Abstract
When covalently incorporating ligands capable of forming chiral metal complexes into a DNA oligonucleotide duplex, an enantiospecific formation of metal-mediated base pairs is possible. We have been investigating the chirality of the silver-mediated base pair P-AgI -P (P, 1H-imidazo[4,5-f][1,10]phenanthroline) depending on the number of consecutive P : P pairs within a series of duplexes. Towards this end, both enantiomers of the nucleoside analogue 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-1-yl)propane-1,2-diol comprising an acyclic backbone were introduced into DNA duplexes, resulting in diastereomeric metal-mediated base pairs. The same chiral-at-metal complex is formed inside the duplex for up to five neighbouring P-AgI -P pairs, irrespective of whether (S)-P or (R)-P is used. With six silver-mediated base pairs, the chirality of the metal complex is inverted for (S)-P but not for (R)-P. This indicates an intricate balance of what determines the configuration of the metal complex, the intrinsically preferred metal-centred chirality or the DNA helical chirality.
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Affiliation(s)
- Nils Lefringhausen
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Victoria Seiffert
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany
| | - Catharina Erbacher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Uwe Karst
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 48, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149, Münster, Germany.,Westfälische Wilhelms-Universität Münster, Center for Soft Nanoscience (SoN) and Cells in Motion Interfaculty Centre (CiMIC), Corrensstr. 28/30, 48149, Münster, Germany
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5
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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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6
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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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7
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Hu L, Takezawa Y, Shionoya M. Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides. Chem Sci 2022; 13:3977-3983. [PMID: 35440985 PMCID: PMC8985573 DOI: 10.1039/d2sc00926a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (ImOA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The ImOC nucleobases were found to form stable ImOC–CuII–ImOC and ImOC–HgII–ImOC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The ImOC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The ImOC–CuII–ImOC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of CuII. Furthermore, we demonstrated the quantitative assembly of three CuII ions inside a DNA duplex with three consecutive ImOC–ImOC pairs, showing great potential of DNA-template based CuII nanoarray construction. The study of easily-prepared ImOC base pairs will provide a new design strategy for metal-responsive DNA materials. A novel 2-oxo-imidazole-4-carboxylate (ImOC) nucleobase, which can be easily derived from a commercially available uridine analogue, was found to form stable CuII- and HgII-mediated base pairs in DNA duplexes.![]()
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Affiliation(s)
- Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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8
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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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [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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9
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Abstract
Metal-mediated base pairs enable a site-specific incorporation of transition metal ions into nucleic acid structures. The resulting nucleic acid-metal complex conjugates are of interest in the context of functionalized nucleic acids, as they bear metal-based functionality. It is desirable to devise nucleic acids with an externally triggered metal-binding affinity, as this may allow regulating this functionality. Toward this end, a caged deoxyribonucleoside analog HNPP was devised for the site-specific binding of copper(II) ions upon irradiation by light, based on the ligand 3-hydroxy-2-methylpyridin-4(1H)-one (H) and the photocleavable 2-(2-nitrophenyl)propoxy protecting group (NPP). The formation of both H-Cu(II)-H homo base pairs and H-Cu(II)-X hetero base pairs (involving a second artificial deoxyribonucleoside X, based on imidazole-4-carboxylate) was achieved upon irradiation of DNA duplexes bearing the respective HNPP:HNPP or HNPP:X mispairs in the presence of copper(II) ions. The H-Cu(II)-X pair shows an exceptional DNA duplex stabilization of up to 43 °C upon its formation, exceeding that of the H-Cu(II)-H pair. It therefore represents one of the most stabilizing Cu(II)-mediated base pairs reported so far. Our findings expand the scope of light-triggered metal-mediated base pair formation by introducing a copper(II)-binding ligand.
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Affiliation(s)
- Shuvankar Naskar
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster, Germany
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10
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Pramanik S, Khamari L, Mukherjee S. Differentiating a Least-Stable Single Nucleotide Mismatch in DNA Via Metal Ion-Mediated Base Pairing and Using Thioflavin T as an Extrinsic Fluorophore. J Phys Chem Lett 2021; 12:2547-2554. [PMID: 33683888 DOI: 10.1021/acs.jpclett.1c00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Monitoring the DNA dynamics in solution has great potential to develop new nucleic acid-based sensors and devices. With spectroscopic approaches, both at the ensemble average and single-molecule resolution, this study is directed to differentiate a single nucleotide mismatch (SNM) via a metal ion-stabilized mismatched base-pairing (C-Ag+-C/C-Cu2+-T) (C = cytosine, T = thymine) and site-selective extrinsic fluorophore, specifically, Thioflavin T (ThT). This is the first approach of its kind where dynamic quantities like molecular diffusion coefficients and diffusion times have been utilized to distinguish the least-stable SNM (CC & CT) formed by the most discriminating nucleobase, specifically, cytosine in a 20-mer duplex DNA. Additionally, this work also quantifies metal ions (Ag+ and Cu2+) at lower concentrations using fluorescence correlation spectroscopy. Our results can provide greater molecular-level insights into the mismatch-dependent metal-DNA interactions and also illuminate ThT as a new fluorophore to monitor the dynamics involved in DNA-metal composites.
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Affiliation(s)
- Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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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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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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13
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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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14
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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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15
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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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16
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Aro-Heinilä A, Lönnberg T, Virta P. Covalently Mercurated Molecular Beacon for Discriminating the Canonical Nucleobases. Chembiochem 2020; 22:354-358. [PMID: 32827233 DOI: 10.1002/cbic.202000575] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Indexed: 12/14/2022]
Abstract
A highly nucleobase-discriminating metalated nucleoside analogue, 3-fluoro-2-mercuri-6-methylaniline, was incorporated into an oligonucleotide molecular beacon. Fluorescence emission spectra were measured after the addition of four different complementary strands, in which the nucleobase opposite the metalated analogue varies. The fluorescence results showed a clear binding selectivity at room temperature, in the order G>T>C>A. The selectivity is based on the different affinities between the metalated nucleoside analogue and the canonical nucleobases. The synthesized probe is capable of robust discrimination between the two purine as well as the two pyrimidine bases by fluorescence at room temperature, and more sophisticated temperature analysis allows clear separation of every canonical nucleobase. The probe would, hence, be a suitable method for the detection of single nucleotide polymorphisms.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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17
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Srivastava R. Nucleobase Pair-Metal Dimer/Dinuclear Metal Cation Interaction: A Theoretical Study. ACS OMEGA 2020; 5:18808-18817. [PMID: 32775882 PMCID: PMC7408194 DOI: 10.1021/acsomega.0c01931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Nucleobase pair-metal dimer/dinuclear metal cation interactions play an important role in biological applications because of their highly symmetrical structures and high stabilities. In this work, we have selected five adenine-adenine hydrogen bonding, adenine-thymine (AT), adenine-uracil, adenine-adenine stacking pairs, and Watson-Crick AT stacking pairs and studied their interaction with the coinage metal dimer M2 and M2 2+ metal cations, where M = Ag, Au, and Cu. Quantum chemical calculations have been carried out with density functional theory (DFT) and time-dependent DFT (TDDFT) methods. Electronic structures were analyzed by the partial density of states method. During interactions, we find that M-M distances are shorter than the sum of van der Waals radii of the corresponding two homocoinage metal atoms, which show the existence of significant metallophilic interactions. Results indicated that nucleobase-M2 2+ complexes are stronger as compared to nucleobase-M2 complexes. Also, the replacement of the hydrogen bond by the dinuclear metal cation-coordinated bond forms more stable alternative metallo-DNA sequences in AAST base pairs. TDDFT calculations reveal that nucleobase-Cu2 complexes and nucleobase-Ag2 2+/Au2 2+ complexes can be used for fluorescent markers and logic gate applications. Atom-in-molecules analysis predicted the noncovalent interaction in these complexes.
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Affiliation(s)
- Ruby Srivastava
- Bioinformatics, CSIR-Centre
for Cellular and Molecular Biology, Hyderabad 500607, India
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18
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Stable Hg(II)-mediated base pairs with a phenanthroline-derived nucleobase surrogate in antiparallel-stranded DNA. J Biol Inorg Chem 2020; 25:647-654. [PMID: 32277288 PMCID: PMC7239801 DOI: 10.1007/s00775-020-01788-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Metal-mediated base pairs involving artificial nucleobases have emerged as a promising means for the site-specific functionalization of nucleic acids with metal ions. In this context, a GNA-appended (GNA: glycol nucleic acid) nucleoside analogue containing the artificial nucleobase 1H-imidazo[4,5-f][1,10]phenanthroline (P) has already been applied successfully in a variety of homo- and heteroleptic metal-mediated base pairs, mainly involving Ag(I) ions. Herein, we report a thorough investigation of the Hg(II)-binding properties of P when incorporated into antiparallel-stranded DNA duplexes. The artificial nucleobase P is able to form Hg(II)-mediated homoleptic base pairs of the type P-Hg(II)-P with a [2 + 2] coordination environment. In addition, the heteroleptic P-Hg(II)-T pair was investigated. The addition of a stoichiometric amount of Hg(II) to a duplex comprising either a P:P pair or a P:T pair stabilizes the DNA duplex by 4.3 °C and 14.5 °C, respectively. The P-Hg(II)-T base pair, hence, represents the most stabilizing non-organometallic Hg(II)-mediated base pair reported to date. The formation of the Hg(II)-mediated base pairs was investigated by means of temperature-dependent UV spectroscopy and CD spectroscopy.
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19
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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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20
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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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21
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22
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Mistry L, El-Zubir O, Dura G, Clegg W, Waddell PG, Pope T, Hofer WA, Wright NG, Horrocks BR, Houlton A. Addressing the properties of "Metallo-DNA" with a Ag(i)-mediated supramolecular duplex. Chem Sci 2019; 10:3186-3195. [PMID: 30996900 PMCID: PMC6429620 DOI: 10.1039/c8sc05103h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/08/2019] [Indexed: 01/04/2023] Open
Abstract
The silver-nucleoside complex [Ag(i)-(N3-cytidine)2]+, 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA.
The silver-nucleoside complex [Ag(i)-(N3-cytidine)2], 1, self-assembles to form a supramolecular metal-mediated base-pair array highly analogous to those seen in metallo-DNA. A combination of complementary hydrogen-bonding, hydrophobic and argentophilic interactions drive the formation of a double-helix with a continuous silver core. Electrical measurements on 1 show that despite having Ag···Ag distances within <5% of the metallic radii, the material is electrically insulating. This is due to the electronic structure which features a filled valence band, an empty conduction band dominated by the ligand, and a band gap of 2.5 eV. Hence, as-prepared, such Ag(i)-DNA systems should not be considered molecular nanowires but, at best, proto-wires. The structural features seen in 1 are essentially retained in the corresponding organogel which exhibits thixotropic self-healing that can be attributed to the reversible nature of the intermolecular interactions. Photo-reduced samples of the gel exhibit luminescence confirming that these poly-cytidine sequences appropriately pre-configure silver ions for the formation of quantum-confined metal clusters in line with contemporary views on DNA-templated clusters. Microscopy data reveals the resulting metal cluster/particles are approximately spherical and crystalline with lattice spacing (111) similar to bulk Ag.
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Affiliation(s)
- Liam Mistry
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Osama El-Zubir
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Gema Dura
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - William Clegg
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Paul G Waddell
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Thomas Pope
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Werner A Hofer
- Chemistry , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Nick G Wright
- School of Engineering , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK
| | - Benjamin R Horrocks
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
| | - Andrew Houlton
- Chemical Nanoscience Laboratory , School of Natural & Environmental Sciences , Newcastle University , Newcastle upon Tyne , NE1 7RU , UK .
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23
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Metal-mediated base pairing in DNA involving the artificial nucleobase imidazole-4-carboxylate. J Inorg Biochem 2019; 191:85-93. [DOI: 10.1016/j.jinorgbio.2018.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/18/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
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24
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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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25
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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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26
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A stable zinc(II)-mediated base pair in a parallel-stranded DNA duplex. J Inorg Biochem 2018; 186:301-306. [DOI: 10.1016/j.jinorgbio.2018.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/12/2018] [Accepted: 07/01/2018] [Indexed: 12/16/2022]
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27
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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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28
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Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie und NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie und NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
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29
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Jash B, Müller J. Stable Copper(I)-Mediated Base Pairing in DNA. Angew Chem Int Ed Engl 2018; 57:9524-9527. [DOI: 10.1002/anie.201802201] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/26/2018] [Indexed: 12/17/2022]
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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30
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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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31
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Müller J. Metal-mediated base pairs in parallel-stranded DNA. Beilstein J Org Chem 2017; 13:2671-2681. [PMID: 29564004 PMCID: PMC5753045 DOI: 10.3762/bjoc.13.265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 01/03/2023] Open
Abstract
In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.
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Affiliation(s)
- Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany
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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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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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