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Lin X, Chen J, Shahsavari S, Green N, Goyal D, Fang S. Synthesis of Oligodeoxynucleotides Containing Electrophilic Groups. Org Lett 2016; 18:3870-3. [PMID: 27447361 DOI: 10.1021/acs.orglett.6b01878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By use of 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) as a protecting group and linker for oligodeoxynucleotide (ODN) synthesis, deprotection and cleavage are achieved under non-nucleophilic oxidative conditions. The nucleophile-sensitive thioester and α-chloroacetyl groups are conveniently incorporated into ODN sequences. The technology could be universally useful for electrophilic ODN synthesis.
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Affiliation(s)
- Xi Lin
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Nathanael Green
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Deepti Goyal
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
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2
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Carrette LLG, Gyssels E, De Laet N, Madder A. Furan oxidation based cross-linking: a new approach for the study and targeting of nucleic acid and protein interactions. Chem Commun (Camb) 2016; 52:1539-54. [PMID: 26679922 DOI: 10.1039/c5cc08766j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coming of age story of furan oxidation cross-linking.
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Affiliation(s)
- L. L. G. Carrette
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - E. Gyssels
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - N. De Laet
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - A. Madder
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
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3
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Gyssels E, Carrette LLG, Vercruysse E, Stevens K, Madder A. Triplex crosslinking through furan oxidation requires perturbation of the structured triple-helix. Chembiochem 2015; 16:651-8. [PMID: 25630588 DOI: 10.1002/cbic.201402602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 01/08/2023]
Abstract
Short oligonucleotides can selectively recognize duplexes by binding in the major groove thereby forming triplexes. Based on the success of our recently developed strategy for furan-based crosslinking in DNA duplexes, we here investigated for the first time the use of the furan-oxidation crosslink methodology for the covalent locking of triplex structures by an interstrand crosslink. It was shown that in a triplex context, although crosslinking yields are surprisingly low (to nonexistent) when targeting fully complementary duplexes, selective crosslinking can be achieved towards mismatched duplex sites at the interface of triplex to duplex structures. We show the promising potential of furan-containing probes for the selective detection of single-stranded regions within nucleic acids containing a variety of structural motifs.
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Affiliation(s)
- Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent (Belgium)
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4
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Carrette LLG, Gyssels E, Loncke J, Madder A. A mildly inducible and selective cross-link methodology for RNA duplexes. Org Biomol Chem 2014; 12:931-5. [DOI: 10.1039/c3ob42374c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Kobori A, Nagae Y, Sugihara Y, Yamayoshi A, Murakami A. Rate-adjusted cross-linking reaction by photoresponsive α-bromoaldehyde (PBA)-conjugated ODN. Bioorg Med Chem Lett 2013; 23:5825-8. [PMID: 24055045 DOI: 10.1016/j.bmcl.2013.08.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/25/2013] [Accepted: 08/27/2013] [Indexed: 12/30/2022]
Abstract
We developed a photoresponsive α-bromoaldehyde-conjugated oligonucleotide (PBA-ODN). The PBA-ODN selectively reacted and formed covalent bonds with target oligonucleotides having adenine or cytosine at the frontal position of the aldehyde derivative. Kinetic studies revealed that PBA-ODN has increased kinetic rates for the formation of cross-linked duplexes compared with the corresponding α-chloroaldehyde-conjugated oligonucleotide (PCA-ODN).
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Affiliation(s)
- Akio Kobori
- Kyoto Institute of Technology, Graduate School of Science and Technology, Department of Biomolecular Engineering, Kyoto, Japan.
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6
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Nagatsugi F, Sasaki S. Synthesis of Reactive Oligonucleotides for Gene Targeting and Their Application to Gene Expression Regulation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20100010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Stevens K, Madder A. Furan-modified oligonucleotides for fast, high-yielding and site-selective DNA inter-strand cross-linking with non-modified complements. Nucleic Acids Res 2009; 37:1555-65. [PMID: 19151089 PMCID: PMC2655669 DOI: 10.1093/nar/gkn1077] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Among the various types of DNA damage, inter-strand cross-links (ICL) represent one of the most cytotoxic lesions. Processes such as transcription and replication can be fully blocked by ICLs, as shown by the mechanism of action of some anticancer drugs. However, repair of ICLs can be a possible cause of resistance. To study the mechanisms of cross-link repair stable, site-specifically cross-linked duplexes are needed. We here report on the synthesis of site-specifically cross-linked DNA using an acyclic furan containing nucleoside. Selective in situ oxidation of the incorporated furan moiety generates a highly reactive oxo-enal that instantly reacts with the complementary base in a non-modified strand, yielding one specific stable cross-linked duplex species. Varying sequence context showed that a strong selectivity for cross-linking to either complementary A or complementary C is operating, without formation of cross-links to neighboring or distant bases. Reaction times are very short and high isolated yields are obtained using only one equivalent of modified strand. The formed covalent link is stable and the isolated cross-linked duplexes can be stored for several months without degradation. Structural characterization of the obtained ICL was possible by comparison to the natural mutagenic adducts of cis-2-butene-1,4-dial, a metabolite of furan primarily responsible for furan carcinogenicity.
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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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8
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Ali MM, Oishi M, Nagatsugi F, Mori K, Nagasaki Y, Kataoka K, Sasaki S. Intracellular inducible alkylation system that exhibits antisense effects with greater potency and selectivity than the natural oligonucleotide. Angew Chem Int Ed Engl 2007; 45:3136-40. [PMID: 16572503 DOI: 10.1002/anie.200504441] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Md Monsur Ali
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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9
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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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Ali MM, Oishi M, Nagatsugi F, Mori K, Nagasaki Y, Kataoka K, Sasaki S. Intracellular Inducible Alkylation System That Exhibits Antisense Effects with Greater Potency and Selectivity than the Natural Oligonucleotide. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Kawasaki T, Nagatsugi F, Ali MM, Maeda M, Sugiyama K, Hori K, Sasaki S. Hybridization-promoted and cytidine-selective activation for cross-linking with the use of 2-amino-6-vinylpurine derivatives. J Org Chem 2005; 70:14-23. [PMID: 15624902 DOI: 10.1021/jo048298p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, we have proposed a new concept for cross-linking agents with inducible reactivity, in which the highly reactive cross-linking agent, the 2-amino-6-vinylpurine nucleoside analogue (1), can be regenerated in situ from its stable precursors, the phenylsulfide (4) and the phenylsulfoxide (3) derivatives, by a hybridization-promoted activation process with selectivity to cytidine. The phenylsulfide precursor (4) exhibited cross-linking ability despite its high stability toward strong nucleophiles such as amines and thiols. In this study, we investigated the substituent effects of the phenylsulfide group on the cross-linking reaction, and determined the 2-carboxy substituent of the phenylsulfide derivative (11k) as an efficient cross-linking agent with inducible reactivity. Detailed investigations have shown that the phenylsulfoxide (3) and phenylsulfide (4) precursors produce the 2-amino-6-vinylpurine nucleoside (1) as the common reactive species. It has been concluded that the nature of the inducible reactivity of the precursors (3 and 4) is acceleration of their elimination to the 2-amino-6-vinylpurine nucleoside (1) through the selective process in the duplex with the ODN having cytidine at the target site.
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Affiliation(s)
- Takeshi Kawasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Eppacher S, Christen M, Vasella A. Synthesis and Incorporation ofC(5?)-Ethynylated Uracil-Derived Phosphoramidites into RNA. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Sasaki S. [Creation of functional recognition molecules for chemical modification of gene expression]. YAKUGAKU ZASSHI 2002; 122:1081-93. [PMID: 12510386 DOI: 10.1248/yakushi.122.1081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial molecules that exhibit specific recognition of duplex DNA have attracted great interest because of their potential application in the manipulation of gene expression. Specific chemical reactions to the target base within the predetermined site would secure selective inhibition at either translation or transcription reactions. A more interesting application would be to alter the reacted base structure to induce a point mutation. In our study, we have focused our efforts on: 1) development of new cross-linking molecules with high efficiency as well as high selectivity; 2) establishment of a new molecular basis for the formation of nonnatural triplexes; and 3) synthetic approaches to the new minor groove binders. This paper summarizes our recent results using two new functional molecules: 2-amino-6-vinylpurine derivatives as new cross-linking agents; and W-shaped nucleic acid analogues as new recognition molecules for the formation of nonnatural-type triplexes.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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14
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Nagatsugi F, Matsuyama Y, Maeda M, Sasaki S. Selective cross-linking to the adenine of the TA interrupting site within the triple helix. Bioorg Med Chem Lett 2002; 12:487-9. [PMID: 11814825 DOI: 10.1016/s0960-894x(01)00783-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The triplex-forming oligonucleotide incorporating the new nucleoside derivative (2) that connects the 2-amino-6-vinylpurine moiety to the 2-deoxyribose unit with an ethyl spacer has exhibited highly selective cross-linking reaction to the adenine of the TA interrupting site within the triple helix.
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Affiliation(s)
- Fumi Nagatsugi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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