1
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A metallo-DNA nanowire with uninterrupted one-dimensional silver array. Nat Chem 2017; 9:956-960. [DOI: 10.1038/nchem.2808] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
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2
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Tashiro R, Iwamoto M, Morinaga H, Emura T, Hidaka K, Endo M, Sugiyama H. Linking two DNA duplexes with a rigid linker for DNA nanotechnology. Nucleic Acids Res 2015; 43:6692-700. [PMID: 26130712 PMCID: PMC4538841 DOI: 10.1093/nar/gkv662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 11/14/2022] Open
Abstract
DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Masahiro Iwamoto
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Hironobu Morinaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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3
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O'Flaherty DK, Wilds CJ. Synthesis, Characterization, and Repair of a Flexible O(6) -2'-Deoxyguanosine-alkylene-O(6) -2'-deoxyguanosine Intrastrand Cross-Link. Chemistry 2015; 21:10522-9. [PMID: 26075346 DOI: 10.1002/chem.201501103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 12/19/2022]
Abstract
Oligonucleotides tethered by an alkylene linkage between the O(6) -atoms of two consecutive 2'-deoxyguanosines, which lack a phosphodiester linkage between these residues, have been synthesized as a model system of intrastrand cross-linked (IaCL) DNA. UV thermal denaturation studies of duplexes formed between these butylene- and heptylene-linked oligonucleotides with their complementary DNA sequences revealed about 20 °C reduction in stability relative to the unmodified duplex. Circular dichroism spectra of the model IaCL duplexes displayed a signature characteristic of B-form DNA, suggesting minimal global perturbations are induced by the lesion. The model IaCL containing duplexes were investigated as substrates of O(6) -alkylguanine DNA alkyltransferase (AGT) proteins from human and E. coli (Ada-C and OGT). Human AGT was found to repair both model IaCL duplexes with greater efficiency towards the heptylene versus butylene analog adding to our knowledge of substrates this protein can repair.
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Affiliation(s)
- Derek K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec (Canada)
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec (Canada).
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4
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Zhang L, Zhou L, Tian J, Li X. Hetero-ring-expansion design for purine analogs: A theoretical study on the structural, electronic, and excited-state properties. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Zhang L, Zhou L, Tian J, Li X. Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study. Phys Chem Chem Phys 2014; 16:4338-49. [DOI: 10.1039/c3cp54505a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Zhang L, Ren T, Tian J, Yang X, Zhou L, Li X. Excited State Properties of Naphtho-Homologated xxDNA Bases and Effect of Methanol Solution, Deoxyribose, and Base Pairing. J Phys Chem B 2013; 117:3983-92. [DOI: 10.1021/jp3123242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laibin Zhang
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Tingqi Ren
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Jianxiang Tian
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Xiuqin Yang
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, P. R. China
| | - Liuzhu Zhou
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
| | - Xiaoming Li
- School of
Physics and Engineering, Qufu Normal University, Qufu, 273165, P. R. China
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7
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Sun G, Noronha A, Wilds C. Preparation of N3-thymidine–butylene–N3-thymidine interstrand cross-linked DNA via an orthogonal deprotection strategy. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.07.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Hentschel S, Alzeer J, Angelov T, Schärer OD, Luedtke NW. Synthese von DNA-Interstrang-Crosslinks unter Verwendung einer photoaktivierbaren Nucleobase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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9
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Hentschel S, Alzeer J, Angelov T, Schärer OD, Luedtke NW. Synthesis of DNA Interstrand Cross-Links Using a Photocaged Nucleobase. Angew Chem Int Ed Engl 2012; 51:3466-9. [DOI: 10.1002/anie.201108018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Indexed: 12/16/2022]
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10
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Blas JR, Huertas O, Tabares C, Sumpter BG, Fuentes-Cabrera M, Orozco M, Ordejón P, Luque FJ. Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases. J Phys Chem A 2011; 115:11344-54. [DOI: 10.1021/jp205122c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- José Ramón Blas
- Departamento de Química Inorgánica, Orgánica y Bioquímica, Facultad de Medicina, Universidad de Castilla-La Mancha, Avda. Almansa 14, Albacete, 02006, Spain
| | - Oscar Huertas
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal 643, Barcelona, 08028, Spain
| | - Carolina Tabares
- Centre d’Investigació en Nanociència i Nanotecnologia-CIN2 (CSIC-ICN), Campus UAB, 08193 Bellaterra, Spain
| | - Bobby G. Sumpter
- Center for Nanophase Materials Sciences and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6494, USA
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831-6494, USA
| | - Modesto Orozco
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona Scientific Park, Josep Samitier 1-6, 08028 barcelona, Spain; Department of Life Sciences, Barcelona Supercomputing Centre, Jordi Girona 29, 08034 barcelona, Spain; Departament de Bioquímica, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Pablo Ordejón
- Centre d’Investigació en Nanociència i Nanotecnologia-CIN2 (CSIC-ICN), Campus UAB, 08193 Bellaterra, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Avgda. Diagonal 643, Barcelona, 08028, Spain
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11
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Stevens K, Claeys DD, Catak S, Figaroli S, Hocek M, Tromp JM, Schürch S, Van Speybroeck V, Madder A. Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone. Chemistry 2011; 17:6940-53. [PMID: 21598324 DOI: 10.1002/chem.201100067] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Indexed: 01/06/2023]
Abstract
Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.
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Affiliation(s)
- Kristof Stevens
- Laboratory for Organic and Biomimetic Chemistry, Department of Organic Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent, Belgium
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12
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Ono T, Yoshida K, Saotome Y, Sakabe R, Okamoto I, Ono A. Synthesis of covalently linked parallel and antiparallel DNA duplexes containing the metal-mediated base pairs T–Hg(ii)–T and C–Ag(i)–C. Chem Commun (Camb) 2011; 47:1542-4. [DOI: 10.1039/c0cc02028a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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13
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Op de Beeck M, Madder A. Unprecedented C-selective interstrand cross-linking through in situ oxidation of furan-modified oligodeoxynucleotides. J Am Chem Soc 2010; 133:796-807. [PMID: 21162525 DOI: 10.1021/ja1048169] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical reagents that form interstrand cross-links have been used for a long time in cancer therapy. They covalently link two strands of DNA, thereby blocking transcription. Cross-link repair enzymes, however, can restore the transcription processes, causing resistance to certain anti-cancer drugs. The mechanism of these cross-link repair processes has not yet been fully revealed. One of the obstacles in this study is the lack of sufficient amounts of well-defined, stable, cross-linked duplexes to study the pathways of cross-link repair enzymes. Our group has developed a cross-link strategy where a furan moiety is incorporated into oligodeoxynucleotides (ODNs). These furan-modified nucleic acids can form interstrand cross-links upon selective furan oxidation with N-bromosuccinimide. We here report on the incorporation of the furan moiety at the 2'-position of a uridine through an amido or ureido linker. The resulting modified ODNs display an unprecedented selectivity for cross-linking toward a cytidine opposite the modified residue, forming one specific cross-linked duplex, which could be isolated in good yield. Furthermore, the structure of the formed cross-linked duplexes could be unambiguously characterized.
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Affiliation(s)
- Marieke Op de Beeck
- Laboratory for Organic and Biomimetic Chemistry, University of Ghent, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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14
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Bárta J, Slavětínská L, Klepetářová B, Hocek M. Modular Synthesis of 5-Substituted Furan-2-yl C-2′-Deoxyribonucleosides and Biaryl Covalent Base-Pair Analogues. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Affiliation(s)
- Michal Hocek
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, United Kingdom, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, CZ-16610 Prague 6, Czech Republic
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16
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Angelov T, Guainazzi A, Schärer OD. Generation of DNA interstrand cross-links by post-synthetic reductive amination. Org Lett 2009; 11:661-4. [PMID: 19132933 DOI: 10.1021/ol802719a] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA interstrand cross-links (ICLs) are the clinically most relevant adducts formed by many antitumor agents. To facilitate the study of biological responses triggered by ICLs, we developed a new approach toward the synthesis of mimics of nitrogen mustard ICLs. 7-Deazaguanine residues bearing acetaldehyde groups were incorporated into complementary strands of DNA and cross-link formation induced by double reductive amination. Our strategy enables the synthesis of major groove cross-links in high yields and purity.
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Affiliation(s)
- Todor Angelov
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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17
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Jensen EA, Allen BD, Kishi Y, O'Leary DJ. Conformational analysis of a covalently cross-linked Watson-Crick base pair model. Bioorg Med Chem Lett 2008; 18:5884-7. [PMID: 18706810 PMCID: PMC2590868 DOI: 10.1016/j.bmcl.2008.07.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/24/2008] [Accepted: 07/28/2008] [Indexed: 11/30/2022]
Abstract
Low-temperature NMR experiments and molecular modeling have been used to characterize the conformational behavior of a covalently cross-linked DNA base pair model. The data suggest that Watson-Crick or reverse Watson-Crick hydrogen bonding geometries have similar energies and can interconvert at low temperatures. This low-temperature process involves rotation about the crosslink CH(2)C(5') (psi) carbon-carbon bond, which is energetically preferred over the alternate CH(2)N(3) (phi) carbon-nitrogen bond rotation.
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Affiliation(s)
- Erik A Jensen
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, CA 91711, USA
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18
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Wilds CJ, Xu F, Noronha AM. Synthesis and characterization of DNA containing an N1-2'-deoxyinosine-ethyl-N3-thymidine interstrand cross-link: a structural mimic of the cross-link formed by 1,3-bis-(2-chloroethyl)-1-nitrosourea. Chem Res Toxicol 2008; 21:686-95. [PMID: 18257558 DOI: 10.1021/tx700422h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Interstrand cross-links, which are generated by chemotherapeutic treatment with bis-alkylating agents, exert their therapeutic effect by connecting the nucleobases of adjacent DNA strands together and represent some of the most threatening forms of damage suffered by genomic DNA. However, one of the reasons for treatment failure using these agents is due to enhanced repair of this DNA damage. The pursuit of understanding the repair of interstrand cross-links by repair systems has necessitated the synthesis of sufficient quantities of such damaged DNA. We report the synthesis of a site-specific interstrand cross-linked duplex containing an ethylene-bridged N (1)-2'-deoxyinosine- N (3)-thymidine base pair prepared by solution and solid-phase synthesis as a mimic for the lesion formed by the therapeutic agent 1,3-bis-(2-chloroethyl)-1-nitrosourea using both a phosphoramidite and a bis-phosphoramidite approach. UV thermal denaturation experiments revealed that this cross-linked duplex was stabilized by 52 degrees C relative to the noncross-linked control, and circular dichroism studies indicated little deviation from a B-form structure compared to a duplex that contained a G-C base pair at the same position. Molecular models of the cross-linked duplex that were geometry optimized using the AMBER forcefield also suggest that this lesion induces minimal distortion in B-form DNA. This modified oligonucleotide will be useful for studies related to the investigation of interstrand cross-linked DNA repair.
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Affiliation(s)
- Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia UniVersity, Montreal, Quebec, Canada.
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19
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Alzeer J, Schärer OD. A modified thymine for the synthesis of site-specific thymine-guanine DNA interstrand crosslinks. Nucleic Acids Res 2006; 34:4458-66. [PMID: 16945959 PMCID: PMC1636361 DOI: 10.1093/nar/gkl587] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 07/26/2006] [Accepted: 07/28/2006] [Indexed: 01/14/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are highly cytotoxic lesions formed by a variety of important anti-tumor agents. Despite the clinical importance of ICLs, the mechanisms by which these lesions are repaired in mammalian cells have so far remained elusive. One of the obstacles in the study of ICL repair has been the limited availability of suitable methods for the synthesis of defined site-specific ICLs. We report here the synthesis of a site-specific ICL containing an ethylene-bridged G-T base pair based on the incorporation of a crosslink precursor containing a selectively reactive group on one strand using solid-phase synthesis. 3-(2-chloroethyl)thymidine was incorporated into oligonucleotides and underwent ICL formation upon annealing to a complementary strand by reacting with the base opposite to the modified T residue. A strong preference for ICL formation with a G residue opposite the reactive T was observed. Detailed characterization of the reaction product revealed that the alkylation reaction occurred with the O-6 group of G and a mechanism accounting for this preference is proposed. These G-T crosslinks introduced here will be useful for studies of ICL repair.
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Affiliation(s)
- Jawad Alzeer
- Institute of Molecular Cancer Research, University of ZurichWinterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Orlando D. Schärer
- Institute of Molecular Cancer Research, University of ZurichWinterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Pharmacological Sciences, Chemistry Graduate Building 619, Stony Brook UniversityStony Brook, NY11794-3400
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Schärer OD. DNA interstrand crosslinks: natural and drug-induced DNA adducts that induce unique cellular responses. Chembiochem 2005; 6:27-32. [PMID: 15637664 DOI: 10.1002/cbic.200400287] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Orlando D Schärer
- Institute of Molecular Cancer Research, University of Zürich, August Forel Strasse 7, 8008 Zürich, Switzerland.
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Huertas O, Blas JR, Soteras I, Orozco M, Luque FJ. Benzoderivatives of Nucleic Acid Bases as Modified DNA Building Blocks. J Phys Chem A 2005; 110:510-8. [PMID: 16405323 DOI: 10.1021/jp052126u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.
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Affiliation(s)
- Oscar Huertas
- Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain
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22
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Nauš P, Votruba I, Hocek M. Covalent Analogues of DNA Base-Pairs and Triplets VII. Synthesis and Cytostatic Activity of Bis(purin-6-yl)acetylene and -diacetylene Nucleosides. ACTA ACUST UNITED AC 2004. [DOI: 10.1135/cccc20041955] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The title bis(purin-6-yl)acetylene and -diacetylene nucleoside derivatives were prepared as covalent base-pair analogues starting from acyl-protected 6-ethynylpurine and 6-iodopurine nucleosides by the Sonogashira cross-coupling or oxidative alkyne-dimerization reactions followed by deprotection. The key starting acyl-protected 6-ethynylpurine nucleosides were prepared by a sequence of cross-coupling reactions of protected 6-halopurine nucleosides with (trimethylsilyl)acetylene followed by a modified desilylation with TBAF in presence of acetic acid. Surprisingly, the acyl-protected nucleosides exhibited significant cytostatic activity higher than the fully deprotected title compounds.
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23
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Tanaka R, Hirano S, Urabe H, Sato F. Concise and stereoselective synthesis of enamides and dienamides by a titanium-mediated coupling method. Org Lett 2003; 5:67-70. [PMID: 12509892 DOI: 10.1021/ol027209x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ynamide-titanium alkoxide complexes underwent hydrolysis or addition to aldehydes and ketones to give single, stereodefined di- or trisubstituted enamides in good yields. Alternatively, coupling of a variety of alkyne-titanium alkoxide complexes with terminal ynamides generated amino-substituted titanacyclopentadienes, hydrolysis or aldehyde addition of which afforded stereodefined dienamides. [reaction--see text]
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Affiliation(s)
- Ryoichi Tanaka
- Departments of Biological Information and Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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24
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Kryachko ES, Nguyen MT. Unnatural Covalent DNA Base Pairing: Quantum Chemical Study. J Phys Chem A 2002. [DOI: 10.1021/jp020810s] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eugene S. Kryachko
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Minh Tho Nguyen
- Department of Chemistry, University of Leuven, Celestijnenlaan 200 F, B-3001 Leuven, Belgium
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25
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Havelková M, Dvořák D, Hocek M. Covalent analogues of DNA base-pairs and triplets. Part 3: Synthesis of 1,4- and 1,3-bis(purin-6-yl)benzenes and 1-(1,3-dimethyluracil-5-yl)-3 or 4-(purin-9-yl)benzenes. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00833-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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27
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Hocek M, Votruba I. Covalent analogues of DNA base-pairs and triplets. Part 2: synthesis and cytostatic activity of bis(purin-6-yl)acetylenes,-diacetylenes and related compounds. Bioorg Med Chem Lett 2002; 12:1055-8. [PMID: 11909716 DOI: 10.1016/s0960-894x(02)00077-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The title bis(purin-6-yl)acetylenes, -diacetylenes, -ethylenes and -ethanes were prepared as covalent base-pair analogues starting from 6-ethynylpurines and 6-iodopurines by cross-coupling and homo-coupling reactions and hydrogenations. The bis(purin-6-yl)acetylenes and -diacetylenes exhibited significant cytostatic activity in vitro (IC(50)=0.4-1.0 micromol/l).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-16610 6 Prague, Czech Republic.
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Hocek M, Stará IG, Starý I, Dvořáková H. Covalent Analogues of DNA Base-Pairs and Triplets IV. Synthesis of Trisubstituted Benzenes Bearing Purine and/or Pyrimidine Rings by Cyclotrimerization of 6-Ethynylpurines and/or 5-Ethynyl-1,3-dimethyluracil. ACTA ACUST UNITED AC 2002. [DOI: 10.1135/cccc20021223] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ni-Catalyzed cyclotrimerizations of 6-ethynylpurines 3 or 5-ethynyl-1,3-dimethyluracil (4) afforded the 1,2,4-tris(purin-6-yl)benzenes 7 or 1,2,4-tris(1,3-dimetyhyluracil-5-yl)benzene (9), respectively. The symmetrical 1,3,5-tris(purin-6-yl)benzenes 8 were also formed as minor products in very low yields. Co-cyclotrimerization of 9-benzyl-6-ethynylpurine (3a) with 4 afforded the tris(purinyl)benzene 7a as a major product along with 1,2-bis(9-benzylpurin-6-yl)-4-(1,3-dimethyluracil-5-yl)benzene (10) and a complex mixture of other derivatives and isomers. Compounds 7-10 are analogues of Hoogsteen base-triplets.
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Hocek M, Dvořáková H, Císařová I. Covalent Analogues of DNA Base-Pairs and Triplets V. Synthesis of Purine-Purine and Purine-Pyrimidine Conjugates Connected by Diverse Types of Acyclic Carbon Linkages. ACTA ACUST UNITED AC 2002. [DOI: 10.1135/cccc20021560] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The title 1,2-bis(purin-6-yl)acetylenes, -diacetylenes, -ethylenes and -ethanes were prepared as covalent base-pair analogues starting from 6-ethynylpurines and 6-iodopurines by the Sonogashira cross-coupling or oxidative alkyne-dimerization reactions followed by hydrogenations. 6-[(1,3-Dimethyluracil-5-yl)ethynyl]purine (11) was prepared analogously and hydrogenated to the corresponding purine-pyrimidine conjugates linked via vinylene and ethylene linkers. Unlike the cytostatic bis(purin-6-yl)acetylenes and -diacetylenes, the purine-pyrimidine conjugates were inactive. Crystal structures of bis(purin-6-yl)acetylene 6a, -diacetylene 8a and -ethane 5a were determined by single-crystal X-ray diffraction.
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Li HY, Qiu YL, Kishi Y. Solution structure of n-type DNA oligomers possessing a covalently cross-linked Watson-Crick base pair model. Chembiochem 2001; 2:371-4. [PMID: 11828467 DOI: 10.1002/1439-7633(20010504)2:5<371::aid-cbic371>3.0.co;2-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H Y Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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