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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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2
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Takezawa Y, Kanemaru D, Kudo N, Shionoya M. Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation. Dalton Trans 2023; 52:11025-11029. [PMID: 37309206 DOI: 10.1039/d3dt01508d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Incorporation of interstrand metal complexes into DNA is a versatile strategy for metal-dependent stabilization and structural induction of DNA supramolecular structures. In this study, we have synthesized DNA three-way junction (3WJ) structures modified with phenanthroline (phen) ligands. The phen-modified 3WJ was found to be thermally stabilized (ΔTm = +16.9 °C) by the formation of an interstrand NiII(phen)3 complex. Furthermore, NiII-mediated structure induction of 3WJs was demonstrated with the phen-modified strands and their unmodified counterparts. This study suggests that ligand-modified 3WJs would be useful structural motifs for the construction of metal-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Daisuke Kanemaru
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Naofumi Kudo
- 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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3
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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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4
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Levi-Acobas F, McKenzie LK, Hollenstein M. Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs. NEW J CHEM 2022. [DOI: 10.1039/d2nj00427e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polymerase-mediated synthesis of RNA-DNA metal base pairs.
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Affiliation(s)
- Fabienne Levi-Acobas
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Luke K. McKenzie
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- 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, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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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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6
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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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7
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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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8
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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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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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10
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020; 59:4091-4098. [DOI: 10.1002/anie.201913956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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11
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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] [Grants] [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 MünsterInstitut für Anorganische und Analytische ChemieCorrensstr. 3048149MünsterGermany
| | - Jens Müller
- Westfälische Wilhelms-Universität MünsterInstitut für Anorganische und Analytische ChemieCorrensstr. 3048149MünsterGermany
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12
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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: 71] [Impact Index Per Article: 14.2] [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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13
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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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15
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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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16
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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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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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18
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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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19
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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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20
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Engelhard DM, Stratmann LM, Clever GH. Structure-Property Relationships in Cu II -Binding Tetramolecular G-Quadruplex DNA. Chemistry 2017; 24:2117-2125. [PMID: 29139578 DOI: 10.1002/chem.201703409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Indexed: 12/29/2022]
Abstract
A series of artificial metal-base tetrads composed of a CuII cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [LA-D d(G4 )]4 (LA-D =ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)4 ] complex behaves analogously to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1-5 atoms) and thus demonstrating the robustness of the chosen ligand design. Only at long linker lengths, the stabilizing effect of copper binding is compensated by the loss of conformational freedom. A previously reported ligand LE with chiral backbone enables incorporation at any oligonucleotide position. We show that ligand chirality distinctly steers CuII -induced G-quadruplex stabilization. 5'-End formation of two metal-base tetrads by tetramolecular G-quadruplex [LE2 d(G)4 ]4 shows that stabilization in the presence of CuII is not additive. All results are based on UV/Vis thermal denaturation, thermal difference, circular dichroism experiments and molecular dynamics simulations.
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Affiliation(s)
- David M Engelhard
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Lukas M Stratmann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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21
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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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22
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Jash B, Müller J. Application of a Metal-Mediated Base Pair to the Detection of Medicinally Relevant Single Nucleotide Polymorphisms. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700665] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstr. 28/30 48149 Münster Germany
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Takezawa Y, Müller J, Shionoya M. Artificial DNA Base Pairing Mediated by Diverse Metal Ions. CHEM LETT 2017. [DOI: 10.1246/cl.160985] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 28/30, 48149 Münster, Germany
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033
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Mandal S, Müller J. Metal-mediated DNA assembly with ligand-based nucleosides. Curr Opin Chem Biol 2017; 37:71-79. [PMID: 28214670 DOI: 10.1016/j.cbpa.2017.01.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/22/2017] [Accepted: 01/24/2017] [Indexed: 01/12/2023]
Abstract
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids. It particularly focuses on recently developed metal-mediated base pairs with purine-derived nucleosides, gives an overview of metal-responsive systems relying on metal-mediated base pairs and summarizes various applications beyond metal-ion sensors.
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Affiliation(s)
- Soham Mandal
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*)
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstraße 30, 48149 Münster, Germany(*).
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Jash B, Scharf P, Sandmann N, Fonseca Guerra C, Megger DA, Müller J. A metal-mediated base pair that discriminates between the canonical pyrimidine nucleobases. Chem Sci 2017; 8:1337-1343. [PMID: 28451274 PMCID: PMC5360170 DOI: 10.1039/c6sc03482a] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 12/17/2022] Open
Abstract
A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag+-mediated base pair between P and cytosine, whereas the presence of Ag+ strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations. The molecular beacon significantly extends the application spectrum of nucleic acids with metal-mediated base pairs. It is of potential use in the detection of single-nucleotide polymorphisms.
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Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Philipp Scharf
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry , Amsterdam Center for Multiscale Modeling (ACMM) , VU Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands .
| | - Dominik A Megger
- Medizinisches Proteom-Center , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany .
- NRW Graduate School of Chemistry , Westfälische Wilhelms-Universität Münster , Corrensstraße 30 , 48149 Münster , Germany
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26
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DNA incorporation of a trans-chelating bis-pyridyl ligand for square-planar coordinated metal cations. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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