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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Flamme M, Figazzolo C, Gasser G, Hollenstein M. Enzymatic construction of metal-mediated nucleic acid base pairs. Metallomics 2021; 13:6206861. [PMID: 33791776 DOI: 10.1093/mtomcs/mfab016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022]
Abstract
Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Chiara Figazzolo
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Centre de Recherches Interdisciplinaires CRI, 8 rue Charles V, 75004 Paris, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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3
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Escher D, Müller J. Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge. Chemistry 2020; 26:16043-16048. [PMID: 32627879 PMCID: PMC7756626 DOI: 10.1002/chem.202002803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/18/2022]
Abstract
DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (1D6PP), 7‐deaza‐6PP (7D6PP) and 1,7‐dideaza‐6PP (1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of AgI. In 6PP and 7D6PP, the AgI ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in 1D6PP and 1,7D6PP, so that in 1D6PP an AgI coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the AgI‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of AgI, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.
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Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
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4
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Chai Y, Leonard P, Guo X, Seela F. Silver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability. Chemistry 2019; 25:16639-16651. [PMID: 31583755 PMCID: PMC6972701 DOI: 10.1002/chem.201903915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/02/2019] [Indexed: 02/05/2023]
Abstract
Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral α-dC-dC base pairs can approach the stability of a Watson-Crick pair, whereas homochiral dC-dC pairs are significantly less stable. A positional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence. When the number of silver ions was equivalent to the number of duplex base pairs (12), non-melting silver-rich complexes were formed. Structural changes have been supported by circular dichroism (CD) spectra, which showed that the B-DNA structure was maintained whilst the silver ion concentration was low. At high silver ion concentration, silver-rich complexes displaying different CD spectra were formed.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of Respiratory and Critical Care MedicineTargeted Tracer Research and Development LaboratoryWest China HospitalSichuan UniversitySichuan610041P. R. China
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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5
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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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6
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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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7
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Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J. Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine. J Biol Inorg Chem 2019; 24:693-702. [DOI: 10.1007/s00775-019-01682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023]
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8
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Räisälä H, Lönnberg T. Covalently Palladated Oligonucleotides Through Oxidative Addition of Pd 0. Chemistry 2019; 25:4751-4756. [PMID: 30666718 DOI: 10.1002/chem.201806022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/11/2019] [Indexed: 12/13/2022]
Abstract
An 11-mer oligonucleotide incorporating a central (2-iodobenzoylamino)methyl residue has been synthesized and palladated by oxidative addition of Pd2 (dba)3 . UV melting profiles of the duplexes formed by the palladated oligonucleotide with its natural complements were biphasic and the higher melting temperatures (Tm ) exhibited considerable hysteresis. CD spectra, in turn, resembled those of canonical B-type double helices. Two-step denaturation, with the "low-Tm " melting involving only canonical base pairs and the "high-Tm " melting involving also dissociation of a PdII -mediated base pair, appears the most likely explanation for the observed UV melting profiles. As the latter step in all cases takes place at a higher temperature than denaturation of natural duplexes of the same length, the putative PdII -mediated base pairs are stabilizing.
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Affiliation(s)
- Harri Räisälä
- 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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9
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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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10
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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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11
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Jash B, Müller J. Concomitant Site-Specific Incorporation of Silver(I) and Mercury(II) Ions into a DNA Duplex. Chemistry 2018; 24:10636-10640. [DOI: 10.1002/chem.201802470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Biswarup Jash
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie and NRW Graduate School of Chemistry; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 48149 Münster Germany
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12
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Mandal S, Hebenbrock M, Müller J. A dinuclear silver(I)-mediated base pair in DNA formed from 1, N 6 -ethenoadenine and thymine. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.05.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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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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14
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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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15
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Buchanan HS, Pauff SM, Kosmidis TD, Taladriz-Sender A, Rutherford OI, Hatit MZC, Fenner S, Watson AJB, Burley GA. Modular, Step-Efficient Palladium-Catalyzed Cross-Coupling Strategy To Access C6-Heteroaryl 2-Aminopurine Ribonucleosides. Org Lett 2017; 19:3759-3762. [PMID: 28682638 DOI: 10.1021/acs.orglett.7b01602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two Pd-catalyzed methods to access 6-heteroaryl 2-aminopurine ribonucleosides from 6-chloroguanosine are described. First, Pd-132-catalyzed Suzuki-Miyaura cross-coupling using a series of boron substrates and 6-chloroguanosine forms 6-heteroaryl-2-aminopurines in a single step. The versatility of 6-chloroguanosine is further demonstrated using a modified Sonogashira coupling employing potassium iodide as an additive. Finally, the utility of the 6-alkynyl-2-aminopurine ribonucleoside as a dipolarophile in [3 + 2] cycloadditions is presented, affording triazoles and isoxazoles when reacted with azide and isonitrile 1,3-dipoles, respectively.
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Affiliation(s)
- Helena S Buchanan
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Steven M Pauff
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Tilemachos D Kosmidis
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Andrea Taladriz-Sender
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Olivia I Rutherford
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Marine Z C Hatit
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Sabine Fenner
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Allan J B Watson
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
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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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17
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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: 44] [Impact Index Per Article: 6.3] [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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18
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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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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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20
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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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21
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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: 38] [Impact Index Per Article: 4.8] [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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22
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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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23
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24
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Jana SK, Guo X, Mei H, Seela F. Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation. Chem Commun (Camb) 2016; 51:17301-4. [PMID: 26463426 DOI: 10.1039/c5cc06734k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices.
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Affiliation(s)
- Sunit Kumar Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, No. 1 Keyuan 4th Road, Gaopengdadao, Chengdu 610041, P. R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany.
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25
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Yang H, Seela F. Silver Ions in Non-canonical DNA Base Pairs: Metal-Mediated Mismatch Stabilization of 2'-Deoxyadenosine and 7-Deazapurine Derivatives with 2'-Deoxycytidine and 2'-Deoxyguanosine. Chemistry 2016; 22:13336-46. [PMID: 27492501 DOI: 10.1002/chem.201602103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/18/2022]
Abstract
Novel silver-mediated dA-dC, dA*-dC, and dA*-dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA). 7-Deazapurine nucleosides enforce silver ion binding and direct metal-mediated base pair formation to their Watson-Crick face. New phosphoramidites were prepared from 7-deaza-dA, 7-deaza-7-iodo-dA, and 7-cyclopropyl-7-deaza-dA, which contain labile isobutyryl protecting groups. Solid-phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher Tm values) were observed for oligonucleotide duplexes with non-canonical dA*-dC and dA-dC pairs in the presence of silver ions. The stability of the silver-mediated base pairs was pH dependent. Silver ion binding was not observed for the dA-dG mismatch but took place when mismatches were formed between 7-deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany), Fax.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany), Fax. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany.
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26
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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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27
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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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28
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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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29
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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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30
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31
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Yang H, Mei H, Seela F. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding. Chemistry 2015; 21:10207-19. [PMID: 26096946 DOI: 10.1002/chem.201500582] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 11/11/2022]
Abstract
Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany).
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32
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Sinha I, Hepp A, Schirmer B, Kösters J, Neugebauer J, Müller J. Regioselectivity of the C-metalation of 6-furylpurine: importance of directing effects. Inorg Chem 2015; 54:4183-5. [PMID: 25901643 DOI: 10.1021/acs.inorgchem.5b00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the C-metalation of 6-furylpurine with Pt(2+), Pd(2+), and Hg(2+). The ligand binds the metal ions in a bidentate fashion, involving the N7 purine atom and one of the furyl carbon atoms. The regioselectivity is determined by the metal ion. Pt(2+) and Pd(2+) coordinate the furyl moiety in its β position and Hg(2+) in its electronically preferred α position.
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Affiliation(s)
| | | | - Birgitta Schirmer
- §Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | | | - Johannes Neugebauer
- §Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
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33
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Sinha I, Fonseca Guerra C, Müller J. Ein hochgradig stabilisierendes Silber(I)-vermitteltes Basenpaar in paralleler DNA. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411931] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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Sinha I, Fonseca Guerra C, Müller J. A Highly Stabilizing Silver(I)-Mediated Base Pair in Parallel-Stranded DNA. Angew Chem Int Ed Engl 2015; 54:3603-6. [DOI: 10.1002/anie.201411931] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 02/06/2023]
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35
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Taherpour S, Lönnberg T. Fluorescence probing of metal-ion-mediated hybridization of oligonucleotides. RSC Adv 2015. [DOI: 10.1039/c4ra15136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The structure-dependent fluorescence of pyrrolocytosine has been harnessed to quantify the affinity of metal-ion-chelating oligonucleotides for their native counterparts.
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36
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Formation of mixed-ligand complexes of Pd2+ with nucleoside 5'-monophosphates and some metal-ion-binding nucleoside surrogates. Molecules 2014; 19:16976-86. [PMID: 25340302 PMCID: PMC6271181 DOI: 10.3390/molecules191016976] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/08/2014] [Accepted: 10/17/2014] [Indexed: 11/21/2022] Open
Abstract
Formation of mixed-ligand Pd2+ complexes between canonical nucleoside 5'-monophosphates and five metal-ion-binding nucleoside analogs has been studied by 1H-NMR spectroscopy to test the ability of these nucleoside surrogates to discriminate between unmodified nucleobases by Pd2+-mediated base pairing. The nucleoside analogs studied included 2,6-bis(3,5-dimethylpyrazol-1-yl)-, 2,6-bis(1-methylhydrazinyl)- and 6-(3,5-dimethylpyrazol-1-yl)-substituted 9-(β-d-ribofuranosyl)purines 1–3, and 2,4-bis(3,5-dimethylpyrazol-1-yl)- and 2,4-bis(1-methylhydrazinyl)-substituted 5-(β-d-ribofuranosyl)-pyrimidines 4–5. Among these, the purine derivatives 1-3 bound Pd2+ much more tightly than the pyrimidine derivatives 4, 5 despite apparently similar structures of the potential coordination sites. Compounds 1 and 2 formed markedly stable mixed-ligand Pd2+ complexes with UMP and GMP, UMP binding favored by 1 and GMP by 2. With 3, formation of mixed-ligand complexes was retarded by binding of two molecules of 3 to Pd2+.
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