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Megger DA, Megger N, Müller J. Metal-mediated base pairs in nucleic acids with purine- and pyrimidine-derived nucleosides. Met Ions Life Sci 2012; 10:295-317. [PMID: 22210344 DOI: 10.1007/978-94-007-2172-2_11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Metal-mediated base pairs are transition metal complexes formed from complementary nucleosides within nucleic acid double helices. Instead of relying on hydrogen bonds, they are stabilized by coordinative bonds. The nucleosides acting as ligands do not necessarily have to be artificial. In fact, several examples are known of naturally occurring nucleobases (e.g., thymine, cytosine) capable of forming stable metal-mediated base pairs that are highly selective towards certain metal ions. This chapter provides a comprehensive overview of metal-mediated base pairs formed from natural nucleosides or from closely related artificial nucleosides that are pyrimidine or purine derivatives. It addresses the different strategies that lead to the development of these base pairs. The article focuses on structural models for metal-mediated base pairs, their experimental characterization within a nucleic acid, and on their possible applications.
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Megger DA, Fonseca Guerra C, Hoffmann J, Brutschy B, Bickelhaupt FM, Müller J. Contiguous Metal‐Mediated Base Pairs Comprising Two Ag
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Ions. Chemistry 2011; 17:6533-44. [DOI: 10.1002/chem.201002944] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/12/2011] [Indexed: 12/28/2022]
Affiliation(s)
- Dominik A. Megger
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jan Hoffmann
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - Bernhard Brutschy
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jens Müller
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
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Seela F, Debelak H, Reuter H, Kastner G, Mikhailopulo IA. 1-Deaza-3′-O-methyladenosine: A Nucleoside with theSyn-conformation in the Solid State and in Solution. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/07328319808004671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Frank Seela
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Barbarastr 7, D-49069 , Osnabrück , Germany
| | - Harald Debelak
- a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität Osnabrück , Barbarastr 7, D-49069 , Osnabrück , Germany
| | - Hans Reuter
- b Anorganische Chemie , Institut für Chemie, Universität Ósnabrück , Barbarastr. 7, D-49069 , Osnabriick , Germany
| | - Guide Kastner
- b Anorganische Chemie , Institut für Chemie, Universität Ósnabrück , Barbarastr. 7, D-49069 , Osnabriick , Germany
| | - Igor A. Mikhailopulo
- c Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences , 220141 , Minsk , Zhodinskaya 5, Byelorussia
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Ono A, Torigoe H, Tanaka Y, Okamoto I. Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 2011; 40:5855-66. [DOI: 10.1039/c1cs15149e] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Affiliation(s)
- Jens Müller
- Faculty of Chemistry, Dortmund University of Technology, Otto‐Hahn‐Str. 6, 44227 Dortmund, Germany, Fax: +49 231 755 3797
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Müller J, Polonius FA, Freisinger E, Gil Bardají E. X-ray crystallographic study of several 2'-deoxy-beta-D-ribonucleosides with 1-deazapurine-derived aglycones. Carbohydr Res 2008; 343:397-403. [PMID: 18045576 DOI: 10.1016/j.carres.2007.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 10/19/2007] [Accepted: 11/05/2007] [Indexed: 11/25/2022]
Abstract
The 2'-deoxy-beta-D-ribonucleosides of 1,3-deazapurine (benzimidazole (1)), 1-deazapurine (both 1H-imidazo[4,5-b]pyridine (2) and 3H-imidazo[4,5-b]pyridine (3)), and 6-benzoylamino-1-deazapurine (7-benzoylamino-3H-imidazo[4,5-b]pyridine (4)) have been prepared and structurally characterized by X-ray crystallography. Especially compounds 1-3 can serve as artificial nucleosides that may substitute 2'-deoxy adenosine because they lack the exocyclic amino group and one or two of the endocyclic nitrogen atoms and hence have a much smaller potential to engage in hydrogen bonds. In the latter respect, they are candidates for nucleosides in metal-ion mediated base pairs. The unit cell of compound 3 contains two crystallographically independent molecules. Compound 4 was crystallized from methanol and water, respectively, giving rise to two different solvates. Despite the closely related aglycones, the sugar conformations in 1-4 are found to be highly variable (1: (2)T(1); 2: (3)T(2); 3: (3)E and E(4); 4: (2)E and (2)T(3)). The structures reported here confirm that there is no simple correlation between the sugar conformation and the character of the nucleoside, and they will hopefully contribute to a better understanding of the complex interplay of different effects that are in control of the conformational equilibrium.
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Affiliation(s)
- Jens Müller
- University of Dortmund, Department of Chemistry, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.
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Ramzaeva N, Michalek E, Kazimierczuk Z, Seela F, Rosemeyer H. Hoogsteen vs. Watson-Crick base pairing: incorporation of 2-substituted adenine- and 7-deazaadenine 2'-deoxy-beta-D-ribonucleosides into oligonucleotides. Chem Biodivers 2008; 4:2725-44. [PMID: 18081083 DOI: 10.1002/cbdv.200790222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Various 2-substituted 2'-deoxyadenosines and 7-deazaadenosines have been synthesized. The phosphonate building block 9 of 2-chloro-7-deaza-2'-deoxyadenosine (7-deazacladribine; 2) was prepared by 4,4'-dimethoxytritylation of the parent nucleoside (-->7), followed by protection of the amino function with a formamidine residue (-->8). The latter was reacted with PCl3/N-methylmorpholine/1,2,4-triazole to give compound 9. Moreover, 2-methoxy-2'-deoxyadenosine (2'-deoxyspongosine; 1b) was converted into the fully protected derivative 12, which was then transformed into the 2-cyanoethyl phosphoramidite 14. Also the 2-(trifluoromethyl)-substituted 2'-deoxyadenosines 19-21 were prepared by glycosylation of the chromophore 16 with the halogenose 17, followed by one-pot deprotection and nucleophilic displacement of the 6-Cl substituent. The new DNA building blocks 9 and 14 were used--together with formerly prepared cladribine derivative 4--for solid-phase synthesis of a series of oligodeoxyribonucleotides. These were studied with respect to their thermal stability as well as of the base pairing mode (Watson-Crick vs. Hoogsteen) of modified bases.
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Affiliation(s)
- Natalya Ramzaeva
- Organische Chemie I-Bioorganische Chemie, Institut für Chemie, Fachbereich Biologie/Chemie, Universität Osnabrück
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Polonius FA, Müller J. Ein durch Wasserstoffbrücken und Metallionenbindung vermitteltes, künstliches Basenpaar. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700315] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Polonius FA, Müller J. An Artificial Base Pair, Mediated by Hydrogen Bonding and Metal-Ion Binding. Angew Chem Int Ed Engl 2007; 46:5602-4. [PMID: 17585398 DOI: 10.1002/anie.200700315] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mikhailopoulo IA, Kalinichenko EN, Podkopaeva TL, Wenzel T, Rosemeyer H, Seela FL. Synthesis of 1-Deazaadenosine Analogues of (2′→5′) ApApA. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002397] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Igor A. Mikhailopoulo
- a Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences , 220141 , Minsk , Byelorussia
| | - Elena N. Kalinichenko
- a Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences , 220141 , Minsk , Byelorussia
| | - Tatjana L. Podkopaeva
- a Institute of Bioorganic Chemistry, Byelorussian Academy of Sciences , 220141 , Minsk , Byelorussia
| | - Thomas Wenzel
- b Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universiat Osnabrück , D-49076 , Osnabrück , Germany
| | - Helmut Rosemeyer
- b Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universiat Osnabrück , D-49076 , Osnabrück , Germany
| | - Frank L. Seela
- b Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universiat Osnabrück , D-49076 , Osnabrück , Germany
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Perrier S, Seela F, Schwartz A, Leng M, Chottard JC. The Human Telomeric Sequence (T2AG3)n is Efficiently Cross-Linked by AN1 Binding to the Platinum of a trans-Pt(NH3)2 Chelate of an Antisense Oligo-2′-O-Methylribonucleotide. Eur J Inorg Chem 2003. [DOI: 10.1002/ejic.200390216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Seela F, Mittelbach C. 7-Deaza-2′-deoxyinosine: A Stable Nucleoside with the Ambiguous Base Pairing Properties of 2′-Deoxyinosine. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908043087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Seela F, Debelak H, Reuter H, Kastner G, Mikhailopulo IA. Different conformations of 1-deazaadenosine and its 2′-deoxyribonucleoside in the solid state and in solution. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(98)01131-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Seela F, Bourgeois W, Rosemeyer H, Wenzel T. Synthesis of 4-Substituted 1H-Benzimidazole 2?-Deoxyribonucleosides and Utility of the 4-Nitro Compound as Universal Base. Helv Chim Acta 1996. [DOI: 10.1002/hlca.19960790216] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Seela F, Wenzel T. Oligodeoxyribonucleotides Containing 4-Aminobenzimidazole in Place of Adenine: Solid-phase synthesis and base pairing. Helv Chim Acta 1995. [DOI: 10.1002/hlca.19950780405] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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