1
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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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2
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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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3
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Sun Q, Xie X, Song Y, Sun L. A review on silver-mediated DNA base pairs: methodology and application. Biomater Res 2022; 26:9. [PMID: 35256004 PMCID: PMC8900454 DOI: 10.1186/s40824-022-00254-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/13/2022] [Indexed: 12/27/2022] Open
Abstract
The investigation of the interaction between metal ions and DNA has always attracted much attention in the fields of bioinorganic chemistry, supramolecular coordination chemistry, and DNA nanotechnology. Its mode of action can be simply divided into two aspects. On the one hand, it is non-specific electrostatic adsorption, mainly including Na+, K+, Mg2+, Ca2+ and other physiologically regulating ions; on the other hand, it is specific covalent binding, such as Pt2+, Hg2+, Ag+ and other heavy metal ions. This article focuses on the mechanism of action between Ag+ and DNA mismatch pair C-C, and summarizes its main characterization methods and various applications. It aims to provide a certain reference for the field of biological devices. With the development of cryo-electron microscopy and liquidcell TEM, the structure of C-Ag+-C is expected to be further characterized, which will be more widely used.
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4
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Serec K, Babić SD, Tomić S. Magnesium ions reversibly bind to DNA double stranded helix in thin films. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 268:120663. [PMID: 34875504 DOI: 10.1016/j.saa.2021.120663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Effects of magnesium (Mg2+) ions on the stability and structural properties of double-stranded DNA are vitally important for DNA folding and functional behavior. Complementing our previous study on highly hydrated thin films of DNA with sodium counterions, with no buffer (pH ≈ 6) and surrounded with Mg2+ cations, here we use Fourier transform infrared spectroscopy and band shape analysis to explore in detail the vibrational signatures of DNA-magnesium interaction in the case when DNA charges are neutralized solely by Mg2+ cations, hereafter called MgDNA. Ion atmosphere has been controlled by the magnesium to phosphate molar concentration ratio r which varied between 0.0067 and 10. For r = 0 we find that spectral features in the base region remain similar as in DNA, whereas changes in the backbone region indicate that the B conformation becomes fully stabilized. With increasing r a pronounced structural reshaping occurs in the phosphate backbone region indicating a blue shift of the asymmetric band, while the symmetric band does not show any displacement in frequency. The band shape analysis of overlapping peaks in the respective phosphate regions demonstrates that the number of constituent modes as well as their positions in frequency do not change, whereas their intensities and bandwidths display disparate changes. The results reflect a variety of local environments at the DNA backbone due to a heterogeneous ion atmosphere with randomly distributed magnesium ions and local patterns of hydrogen bonds which change with increasing r. Remarkably, after crowded r = 10 ion atmosphere is depleted, Mg induced spectral changes vanish and structural features of MgDNA (r ≈ 0) are fully restored. Overall results strongly suggest that in MgDNA on highly hydrated thin films the hydrogen-base pairing remains preserved and that Mg2+ ions, similar to sodium ions, retain their mobility and interact with double helix via water-mediated electrostatic forces.
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Affiliation(s)
- Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia.
| | - Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
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5
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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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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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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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Murgunde BK, Rabinal MK. Tuning DNA electrical conductivity by silver photo-doping. Biomed Phys Eng Express 2020; 6:015017. [DOI: 10.1088/2057-1976/ab5c04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions. J CLUST SCI 2019. [DOI: 10.1007/s10876-019-01503-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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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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11
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Ukale DU, Lönnberg T. 2,6‐Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Tuomas Lönnberg
- Department of ChemistryUniversity of Turku Vatselankatu 2 20014 Turku Finland
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12
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Ukale DU, Lönnberg T. 2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018; 57:16171-16175. [PMID: 30358071 DOI: 10.1002/anie.201809398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/11/2018] [Indexed: 11/07/2022]
Abstract
A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear HgII -mediated base triples with adenine, cytosine, and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide. A single HgII -mediated base triple between 2,6-dimercuriphenol and two thymines increased both Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine⋅purine*pyrimidine triple helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA nanotechnology.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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13
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Hande M, Maity S, Lönnberg T. Palladacyclic Conjugate Group Promotes Hybridization of Short Oligonucleotides. Int J Mol Sci 2018; 19:ijms19061588. [PMID: 29843368 PMCID: PMC6032164 DOI: 10.3390/ijms19061588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 11/16/2022] Open
Abstract
Short oligonucleotides with cyclopalladated benzylamine moieties at their 5'-termini have been prepared to test the possibility of conferring palladacyclic anticancer agents sequence-selectivity by conjugation with a guiding oligonucleotide. Hybridization of these oligonucleotides with natural counterparts was studied by UV and CD (circular dichroism) melting experiments in the absence and presence of a competing ligand (2-mercaptoethanol). Cyclopalladated benzylamine proved to be strongly stabilizing relative to unmetalated benzylamine and modestly stabilizing relative to an extra A•T base pair. The stabilization was largely abolished in the presence of 2-mercaptoethanol, suggesting direct coordination of Pd(II) to a nucleobase of the complementary strand. In all cases, fidelity of Watson-Crick base pairing between the two strands was retained. Hybridization of the cyclopalladated oligonucleotides was characterized by relatively large negative enthalpy and entropy, consistent with stabilizing Pd(II) coordination partially offset by the entropic penalty of imposing conformational constraints on the flexible diethylene glycol linker between the oligonucleotide and the palladacyclic moiety.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Sajal Maity
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
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14
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Ukale DU, Lönnberg T. Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties. Chembiochem 2018; 19:1096-1101. [PMID: 29575511 DOI: 10.1002/cbic.201800112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/26/2022]
Abstract
Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular HgII -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than HgII -mediated base pairing.
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Affiliation(s)
| | - Tuomas Lönnberg
- University of Turku, Department of Chemistry, Vatselankatu 2, 20014, Turku, Finland
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15
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Maity SK, Lönnberg T. Oligonucleotides Incorporating Palladacyclic Nucleobase Surrogates. Chemistry 2018; 24:1274-1277. [DOI: 10.1002/chem.201705797] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Sajal Kumar Maity
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
| | - Tuomas Lönnberg
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
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16
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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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17
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Cao GJ. Dinuclear Metal-Mediated Homo Base Pairs with Metallophilic Interactions: Theoretical Studies of G 2M 22+ (M = Cu, Ag, and Au) Ions. Sci Rep 2017; 7:14896. [PMID: 29097669 PMCID: PMC5668421 DOI: 10.1038/s41598-017-14259-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022] Open
Abstract
Dinuclear metal-mediated homo base pairs are interesting clusters with highly symmetric structures and significant stabilities. The geometric and electronic structures of G2M22+ (G = Guanine, M = Cu, Ag or Au) cluster ions were studied with quantum chemical calculations. The lowest-energy isomers of G2M22+ cluster ions have C2h symmetries with an approximately antiparallel alignment of two sets of N-M∙∙∙O groups being formed in the planar structures. The M-M distances are shorter than the sum of van der Waals radii of corresponding two homo coinage metal atoms, showing that metallophilic interactions significantly exist in these complexes. They have the large HOMO−LUMO gaps of about 5.80 eV at the DFT level and the bond dissociation energies of more than 5.60 eV at the DFT/B3LYP level, indicating that these cluster dications are highly stable. The second lowest-energy isomers stabilized by an approximately parallel alignment of one set of O-M-O group and one set of N-M-N group are found to be close to the lowest-energy isomers in energy. The barrier between the two isomers of G2M22+ cluster ions is significantly large, also showing that these lowest-energy isomers are very stable.
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Affiliation(s)
- Guo-Jin Cao
- Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China.
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18
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Engelhard DM, Nowack J, Clever GH. Kupfer-vermittelte Topologieänderung und Thrombin-Inhibierung mit telomerischen DNA-G-Quadruplexen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David M. Engelhard
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Julia Nowack
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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19
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Engelhard DM, Nowack J, Clever GH. Copper-Induced Topology Switching and Thrombin Inhibition with Telomeric DNA G-Quadruplexes. Angew Chem Int Ed Engl 2017; 56:11640-11644. [DOI: 10.1002/anie.201705724] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Indexed: 11/10/2022]
Affiliation(s)
- David M. Engelhard
- Department of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Julia Nowack
- 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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20
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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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21
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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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22
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Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA Films Containing the Artificial Nucleobase Imidazole Mediate Charge Transfer in a Silver(I)-Responsive Way. Angew Chem Int Ed Engl 2017; 56:6098-6102. [DOI: 10.1002/anie.201700248] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/03/2017] [Indexed: 12/22/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Current address: Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
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23
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Léon JC, She Z, Kamal A, Shamsi MH, Müller J, Kraatz HB. DNA-Filme mit der künstlichen Nucleobase Imidazol vermitteln Ladungstransfer in einer Silber(I)-abhängigen Weise. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Zhe She
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Ajar Kamal
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
| | - Mohtashim Hassan Shamsi
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
- Department of Chemistry and Biochemistry; Southern Illinois University Carbondale; Carbondale USA
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Kanada
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24
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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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25
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Passays J, Rubay C, Marcélis L, Elias B. Synthesis and Photophysical Properties of Triazolyl Ir
III
Nucleosides. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201601227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Johan Passays
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Christophe Rubay
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Lionel Marcélis
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
| | - Benjamin Elias
- Institute of Condensed Matter and Nanosciences (IMCN) Université catholique de Louvain (UCL) Place Louis Pasteur 1/L4.01.02 1348 Louvain‐la‐Neuve Belgium
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26
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Guo X, Ingale SA, Yang H, He Y, Seela F. MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents. Org Biomol Chem 2017; 15:870-883. [PMID: 28045181 DOI: 10.1039/c6ob02560a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.
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Affiliation(s)
- Xiurong Guo
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Yang He
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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27
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Mandal S, Hebenbrock M, Müller J. Relative Strand Orientation in a DNA Duplex Controls the Nuclearity of a Metal-Mediated Base Pair. Chemistry 2016; 23:5962-5965. [PMID: 27901308 DOI: 10.1002/chem.201605327] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Indexed: 01/01/2023]
Abstract
1,N6 -Ethenoadenine (ϵA) and cytosine (C) are able to form two different metal-mediated base pairs. When the glycosidic bonds are arranged in a cisoid manner (i.e., in antiparallel-stranded DNA), the ϵA:C mispair binds one AgI ion, leading to a mononuclear ϵA-AgI -C base pair that contains a synergistic hydrogen bond. In contrast, a transoid orientation of the glycosidic bonds (as found in parallel-stranded DNA) results in the formation of a dinuclear metal-mediated base pair ϵA-AgI2 -C.
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Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149, Münster, Germany
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28
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Aro-Heinilä A, Lönnberg T. Fluorescent Oligonucleotide Probes for Screening High-Affinity Nucleobase Surrogates. Chemistry 2016; 23:1028-1031. [PMID: 27911048 DOI: 10.1002/chem.201605300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/16/2022]
Abstract
Double-helical oligonucleotide probes featuring a single-nucleotide gap opposed by one of the canonical nucleobases and flanked by the fluorescent nucleobase analogue pyrrolocytosine have been synthesized and titrated with PdII chelates of dipicolinamide and its N2 ,N6 -dialkylated derivatives. The fluorometric titrations revealed greatly increased affinity of the PdII chelates for the nucleobases opposing the gap compared to the respective free nucleotides in solution. Owing to the constrained environment of the single-nucleotide gap, the relative stabilities of the various PdII -mediated base pairs were also significantly different from those previously reported at monomer level.
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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
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29
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Mandal S, Hebenbrock M, Müller J. Ein zweikerniges Quecksilber(II)-vermitteltes Basenpaar in DNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
- NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Deutschland
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30
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Mandal S, Hebenbrock M, Müller J. A Dinuclear Mercury(II)-Mediated Base Pair in DNA. Angew Chem Int Ed Engl 2016; 55:15520-15523. [PMID: 27862734 DOI: 10.1002/anie.201608354] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/30/2016] [Indexed: 11/08/2022]
Abstract
The first dinuclear metal-mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N6 -ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N-M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of HgII and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T-HgII2 -ϵA base pair. This metal-mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature-dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.
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Affiliation(s)
- Soham Mandal
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstrasse 28/30, 48149, Münster, Germany
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31
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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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32
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Kumar J, Pratibha, Verma S. Crystallographic signatures of silver-purine frameworks with an azide functionality. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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33
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Structure and properties of a copper-mediated nucleobase pair from density functional theory investigation. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Taherpour S, Golubev O, Lönnberg T. On the feasibility of recognition of nucleic acid sequences by metal-ion-carrying oligonucleotides. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.01.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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36
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Schweizer K, Léon JC, Ravoo BJ, Müller J. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes. J Inorg Biochem 2016; 160:256-63. [DOI: 10.1016/j.jinorgbio.2016.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/08/2016] [Accepted: 03/12/2016] [Indexed: 12/26/2022]
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37
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Mandal S, Wang C, Prajapati RK, Kösters J, Verma S, Chi L, Müller J. Metal-Mediated Assembly of 1,N6-Ethenoadenine: From Surfaces to DNA Duplexes. Inorg Chem 2016; 55:7041-50. [DOI: 10.1021/acs.inorgchem.6b00927] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Can Wang
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
| | - Rajneesh K. Prajapati
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | | | - Sandeep Verma
- Department of Chemistry, DST Thematic Unit of Excellence
on Soft Nanofabrication, Indian Institute of Technology−Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Lifeng Chi
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Strasse 10, 48149 Münster, Germany
- Institute
of Functional Nano and Soft Materials, Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren’ai
Road, Suzhou, 215123 Jiangsu, People’s Republic of China
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38
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Metal-Dependent Nucleobase Recognition by Picolinamide. Chempluschem 2016; 81:978-984. [DOI: 10.1002/cplu.201600258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 12/14/2022]
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39
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Ukale D, Shinde VS, Lönnberg T. 5-Mercuricytosine: An Organometallic Janus Nucleobase. Chemistry 2016; 22:7917-23. [PMID: 27113075 DOI: 10.1002/chem.201600851] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/10/2022]
Abstract
The base-pairing properties of 5-mercuricytosine have been explored at the monomer level by NMR titrations and at the oligonucleotide level by melting temperature measurements. The NMR studies revealed a relatively high affinity for guanine, hypoxanthine, and uridine, that is, bases that are deprotonated upon coordination of Hg(II) . Within an oligonucleotide duplex, 5-mercuricytosine formed Hg(II) -mediated base pairs with thymine and guanine. In the former case, the duplex formed was as stable as the respective duplex comprising solely Watson-Crick base pairs. Based on detailed thermodynamic analysis of the melting curves, the stabilization by the Hg(II) -mediated base pairs may be attributed to a comparatively low entropic penalty of hybridization.
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Affiliation(s)
- Dattatraya Ukale
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.,Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Vaishali S Shinde
- Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.
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40
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Léon JC, Sinha I, Müller J. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes. Int J Mol Sci 2016; 17:554. [PMID: 27089326 PMCID: PMC4849010 DOI: 10.3390/ijms17040554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase.
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Affiliation(s)
- J Christian Léon
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149 Münster, Germany.
| | - Indranil Sinha
- 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.
| | - 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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41
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Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs. Bioinorg Chem Appl 2016; 2016:7485125. [PMID: 27034627 PMCID: PMC4791510 DOI: 10.1155/2016/7485125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/22/2015] [Accepted: 12/27/2015] [Indexed: 11/18/2022] Open
Abstract
A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters.
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42
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Withers JM, Telfer SG, Filichev VV. Towards metal-mediated g-quartet analogues: 1,2,4-triazole nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:277-88. [PMID: 25774720 DOI: 10.1080/15257770.2014.990156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We proposed that metal-coordinating nucleotides could be used to control the assembly of G-quadruplexes through the formation of an artificial metal-centered quartet. Several guanine-rich DNA sequences containing 1,2,4-triazole-functionalized nucleotides were investigated. These oligonucleotides were designed to form quartets mediated by metal-triazole bonding both on the surface of and within the G-quadruplex core. In contrast to duplex studies in which 1,2,4-triazole nucleosides serve as a mimic of Watson-Crick base-pairs, our results show that these nucleosides are not suitable components of an artificial metal-centered quartet.
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Affiliation(s)
- Jamie M Withers
- a Institute of Fundamental Sciences , Massey University , Palmerston North , New Zealand
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43
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Sinha I, Hepp A, Kösters J, Müller J. Metal complexes of 6-pyrazolylpurine derivatives as models for metal-mediated base pairs. J Inorg Biochem 2015; 153:355-360. [DOI: 10.1016/j.jinorgbio.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/10/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
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44
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Scharf P, Jash B, Kuriappan JA, Waller MP, Müller J. Sequence-Dependent Duplex Stabilization upon Formation of a Metal-Mediated Base Pair. Chemistry 2015; 22:295-301. [PMID: 26584591 DOI: 10.1002/chem.201503405] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 12/20/2022]
Abstract
An artificial nucleoside surrogate with 1H-imidazo[4,5-f][1,10]phenanthroline (P) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal-mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag(I) -mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B-DNA duplex.
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Affiliation(s)
- Philipp Scharf
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany).,Current address: University of Iceland, Science Institute, Dunhagi 3, 107 Reykjavík (Iceland)
| | - Biswarup Jash
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstrasse 28/30, 48149 Münster (Germany).,Westfälische Wilhelms-Universität Münster, Graduate School of Chemistry, Corrensstrasse 28/30, 48149 Münster (Germany)
| | - Jissy A Kuriappan
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstrasse 40, 48149 Münster (Germany)
| | - Mark P Waller
- Westfälische Wilhelms-Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstrasse 40, 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, Graduate School of Chemistry, Corrensstrasse 28/30, 48149 Münster (Germany).
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Pd(2+)-mediated base pairing in oligonucleotides. J Inorg Biochem 2015; 155:36-43. [PMID: 26606291 DOI: 10.1016/j.jinorgbio.2015.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/03/2015] [Accepted: 11/10/2015] [Indexed: 01/01/2023]
Abstract
Two short glycol nucleic acid (GNA) oligonucleotides, having either a terminal or an intrachain nucleobase replaced by the pyridine-2,6-dicarboxamide chelate of Pd(2+), have been synthesized and their hybridization properties studied by melting temperature measurements. In the termini of a double-stranded oligonucleotide, the Pd(2+) chelates provided dramatic stabilization of the duplex relative to its metal-free counterpart, in all likelihood owing to formation of Pd(2+)-mediated base pairs between pyridine-2,6-dicarboxamide and the opposing nucleobase. In contrast, no stabilization was observed when the Pd(2+) chelate was placed in the middle of the chain. Furthermore, the results could not be reproduced by adding a Pd(2+) salt in situ to the dilute oligonucleotide solutions but the palladated oligonucleotides had to be synthesized and purified prior to the hybridization studies. This behavior, presumably attributable to the relatively slow ligand-exchange reactions of Pd(2+), differs greatly from what is usually observed with more labile metal ions. The present results offer an explanation for the failure of previous attempts to incorporate Pd(2+)-mediated base pairs into oligonucleotides.
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Deng W, Zheng B, Ding W, Zhu H, Liang HJ. Metal-Triggered DNA Folding by Different Mechanisms. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1503051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Mandal S, Hepp A, Müller J. Unprecedented dinuclear silver(I)-mediated base pair involving the DNA lesion 1,N(6)-ethenoadenine. Dalton Trans 2015; 44:3540-3. [PMID: 25478946 DOI: 10.1039/c4dt02663b] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA lesion 1,N(6)-ethenoadenine (εA) has been investigated with respect to its metal-binding properties. A synthetic DNA duplex comprising an εA : εA mispair readily forms doubly silver(I)-mediated base pairs εA-Ag(I)2-εA, representing the first example for a dinuclear metal-mediated homo base pair of a purine derivative. It also constitutes the first example for a Hoogsteen-type metal-mediated homo base pair within a B-DNA duplex.
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Affiliation(s)
- Soham Mandal
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 28/30, 48149 Münster, Germany.
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Tan X, Litau S, Zhang X, Müller J. Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11305-11310. [PMID: 26421907 DOI: 10.1021/acs.langmuir.5b03183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.
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Affiliation(s)
- Xinxin Tan
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Stefanie Litau
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
| | - Xi Zhang
- Department of Chemistry, Key Lab of Organic Optoelectronics and Molecular Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster , Corrensstr. 28/30, 48149 Münster, Germany
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Litau S, Müller J. A tridentate “click” nucleoside for metal-mediated base pairing. J Inorg Biochem 2015; 148:116-20. [DOI: 10.1016/j.jinorgbio.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
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