1
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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2
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Tera M, Harati Taji Z, Luedtke NW. Intercalation‐enhanced “Click” Crosslinking of DNA. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Masayuki Tera
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
- Bioorganic Research InstituteSuntory Foundation for Life Sciences (SUNBOR) 8-1-1 Seikadai, Seika, Soraku Kyoto 619-0284 Japan
| | - Zahra Harati Taji
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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3
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Tera M, Harati Taji Z, Luedtke NW. Intercalation-enhanced "Click" Crosslinking of DNA. Angew Chem Int Ed Engl 2018; 57:15405-15409. [PMID: 30240107 DOI: 10.1002/anie.201808054] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/22/2018] [Indexed: 01/05/2023]
Abstract
DNA-DNA cross-linking agents constitute an important family of chemotherapeutics that non-specifically react with endogenous nucleophiles and therefore exhibit undesirable side effects. Here we report a cationic Sondheimer diyne derivative "DiMOC" that exhibits weak, reversible intercalation into duplex DNA (Kd =15 μm) where it undergoes tandem strain-promoted cross-linking of azide-containing DNA to give DNA-DNA interstrand crosslinks (ICLs) with an exceptionally high apparent rate constant kapp =2.1×105 m-1 s-1 . This represents a 21 000-fold rate enhancement as compared the reaction between DIMOC and 5-(azidomethyl)-2'-deoxyuridine (AmdU) nucleoside. As single agents, 5'-bispivaloyloxymethyl (POM)-AmdU and DiMOC exhibited low cytotoxicity, but highly toxic DNA-DNA ICLs were generated by metabolic incorporation of AmdU groups into cellular DNA, followed by treatment of the cells with DiMOC. These results provide the first examples of intercalation-enhanced bioorthogonal chemical reactions on DNA, and furthermore, the first strain-promoted double click (SPDC) reactions inside of living cells.
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Affiliation(s)
- Masayuki Tera
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Bioorganic Research Institute, Suntory Foundation for Life Sciences (SUNBOR), 8-1-1 Seikadai, Seika, Soraku, Kyoto, 619-0284, Japan
| | - Zahra Harati Taji
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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4
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Affiliation(s)
- Joseph McMorrow
- School of Biological and Chemical Sciences,
Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Mark Freeley
- School of Biological and Chemical Sciences,
Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences,
Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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5
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Saneyoshi H, Yamamoto Y, Kondo K, Hiyoshi Y, Ono A. Conjugatable and Bioreduction Cleavable Linker for the 5'-Functionalization of Oligonucleotides. J Org Chem 2017; 82:1796-1802. [PMID: 28112510 DOI: 10.1021/acs.joc.6b02527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient conjugatable and bioreduction cleavable linker was designed and synthesized for the 5'-terminal ends of oligonucleotides. A phosphoramidite reagent bearing this linker was successfully applied to solid phase synthesis and incorporated at the 5'-terminal ends of oligonucleotides. The controlled pore glass (CPG)-supported oligonucleotides were subsequently conjugated to a diverse range of functional molecules using a CuAAC reaction. The synthesized oligonucleotide conjugates were then cleaved using a nitroreductase/NADH bioreduction system to release the naked oligonucleotides.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuta Yamamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Kazuhiko Kondo
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuki Hiyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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6
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Yang H, Seela F. "Bis-Click" Ligation of DNA: Template-Controlled Assembly, Circularisation and Functionalisation with Bifunctional and Trifunctional Azides. Chemistry 2017; 23:3375-3385. [PMID: 27869337 DOI: 10.1002/chem.201604857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Indexed: 12/14/2022]
Abstract
Ligation and circularisation of oligonucleotides containing terminal triple bonds was performed with bifunctional or trifunctional azides. Both reactions are high yielding. Template-assisted bis-click ligation of two individual non-complementary oligonucleotide strands was accomplished to yield heterodimers exclusively. In this context, the template fulfils two functions: it accelerates the ligation reaction and controls product assembly (heterodimer vs. homodimer formation). Intermolecular bis-click circularisation of one oligonucleotide strand took place without template assistance. For construction of oligonucleotides with terminal triple bonds in the nucleobase side chain, 7- or 5-functionalised 7-deaza-dA and dU residues were used. These oligonucleotides are directly accessible by solid-phase synthesis. When trifunctional azides were employed instead of bifunctional linkers, functionalisation of the remaining azido group was performed with small molecules such as 1-ethynyl pyrene, biotin propargyl amide or with ethynylated oligonucleotides. By this means, branched DNA was constructed.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,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.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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7
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Ponomarenko AI, Brylev VA, Sapozhnikova KA, Ustinov AV, Prokhorenko IA, Zatsepin TS, Korshun VA. Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Pradère U, Hall J. Site-Specific Difunctionalization of Structured RNAs Yields Probes for microRNA Maturation. Bioconjug Chem 2016; 27:681-7. [PMID: 26806029 DOI: 10.1021/acs.bioconjchem.5b00661] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modified oligonucleotides bearing multiple functional labels are valuable tools in RNA biology. Efficient synthetic access to singly modified short DNAs and RNAs has been developed in the past years and paved the way to a first generation of oligonucleotide tools. Here, we describe an efficient procedure for the site-specific hetero bis-labeling of long RNAs. We exemplified the method with the preparation of Cy3/Cy5 pre-microRNAs labeled at selected internal sites as probes for microRNA maturation.
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Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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9
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Jana SK, Leonard P, Ingale SA, Seela F. 2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation. Org Biomol Chem 2016; 14:4927-42. [DOI: 10.1039/c6ob00622a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of 2′-O-alkyl residues on the stability of iCd–dG and iCd–iGd base pairs was studied in DNA with parallel and antiparallel chain orientation.
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Affiliation(s)
- Sunit K. Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - 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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10
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Haldón E, Nicasio MC, Pérez PJ. Copper-catalysed azide-alkyne cycloadditions (CuAAC): an update. Org Biomol Chem 2015; 13:9528-50. [PMID: 26284434 DOI: 10.1039/c5ob01457c] [Citation(s) in RCA: 363] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The reactions of organic azides and alkynes catalysed by copper species represent the prototypical examples of click chemistry. The so-called CuAAC reaction (copper-catalysed azide-alkyne cycloaddition), discovered in 2002, has been expanded since then to become an excellent tool in organic synthesis. In this contribution the recent results described in the literature since 2010 are reviewed, classified according to the nature of the catalyst precursor: copper(I) or copper(II) salts or complexes, metallic or nano-particulated copper and several solid-supported copper systems.
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Affiliation(s)
- Estela Haldón
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química y Ciencias de los Materiales, Campus de El Carmen s/n, Universidad de Huelva, 21007-Huelva, Spain.
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11
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Pujari SS, Ingale SA, Seela F. High-density functionalization and cross-linking of DNA: "click" and "bis-click" cycloadditions performed on alkynylated oligonucleotides with fluorogenic anthracene azides. Bioconjug Chem 2014; 25:1855-70. [PMID: 25154019 DOI: 10.1021/bc5003532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High density functionalization of DNA with ethynyl and octadiynyl side chains followed by CuAAC "click labeling" with 9-azidomethylanthracene was performed. Alkynyl DNA was also cross-linked with fluorogenic 9,10-bis-azidomethylanthracene employing the "bis-click" reaction. By this means the fluorescence of the anthracene moiety was imparted to the virtually nonfluorescent DNA. Phosphoramidites of 8-aza-7-deaza-2'-deoxyadenosine with short and long linker arms in a steric nondemanding 7-position were utilized in solid phase oligodeoxynucleotide synthesis. High density alkynylated DNA-without anthracene residues-was found to be of comparable stability with both long and short linker arms. High density anthracene functionalized DNA became less stable with the short linker compared to that with the long linker connectivity. Interstrand cross-linked homodimers constructed from alkynylated oligonucleotides with fluorogenic 9,10-bis-azidomethylanthracene were hybridized with complementary strands to form double helices. They are more stable when the linker was located at a terminus than in a central position. Short linker anthracene adducts were destabilizing compared to long linker adducts. The fluorogenic anthracene residues not only have a significant effect on the duplex stability, but also impart fluorescence to the species. Fluorescence of cross-linked double helices with long linker connectivity was quenched when the cross-link was in a terminal position and was dequenched when the linker was connecting the two double helices at the center of the molecule. The fluorescence of the anthracene cross-linked double helices was strongly increased (dequenched) when the correct base pair was formed, while no change occurred upon mismatch formation.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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12
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Fomich MA, Kvach MV, Navakouski MJ, Weise C, Baranovsky AV, Korshun VA, Shmanai VV. Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides. Org Lett 2014; 16:4590-3. [PMID: 25156193 DOI: 10.1021/ol502155g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.
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Affiliation(s)
- Maksim A Fomich
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, 220072 Minsk, Belarus
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13
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Pujari SS, Leonard P, Seela F. Oligonucleotides with "clickable" sugar residues: synthesis, duplex stability, and terminal versus central interstrand cross-linking of 2'-O-propargylated 2-aminoadenosine with a bifunctional azide. J Org Chem 2014; 79:4423-37. [PMID: 24693949 DOI: 10.1021/jo500392j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Duplex DNA with terminal and internal sugar cross-links were synthesized by the CuAAC reaction from oligonucleotides containing 2'-O-propargyl-2-aminoadenosine as a clickable site and a bifunctional azide (4). Stepwise click chemistry was employed to introduce cross-links at internal and terminal positions. Copper turnings were used as catalyst, reducing the copper load of the reaction mixture and avoiding complexing agents. For oligonucleotide building block synthesis, a protecting group strategy was developed for 2'-O-propargyl-2-aminoadenosine owing to the rather different reactivities of the two amino groups. Phosphoramidites were synthesized bearing clickable 2'-O-propargyl residues (14 and 18) as well as a 2'-deoxyribofuranosyl residue (10). Hybridization experiments of non-cross-linked oligonucleotides with 2,6-diaminopurine as nucleobase showed no significant thermal stability changes over those containing adenine. Surprisingly, an isobutyryl group protecting the 2-amino function has no negative impact on the stability of DNA-DNA and DNA-RNA duplexes. Oligonucleotide duplexes with cross-linked 2'-O-propargylated 2-aminoadenosine (1) and 2'-O-propargylated adenosine (3) at terminal positions are significantly stabilized (ΔT(m) = +29 °C). The stability results from a molecularity change from duplex to hairpin melting and is influenced by the ligation position. Terminal ligation led to higher melting duplexes than corresponding hairpins, while duplexes with central ligation sites were less stable.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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14
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Arumugam S, Popik VV. Sequential "click" - "photo-click" cross-linker for catalyst-free ligation of azide-tagged substrates. J Org Chem 2014; 79:2702-8. [PMID: 24548078 PMCID: PMC3985855 DOI: 10.1021/jo500143v] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 02/07/2023]
Abstract
Heterobifunctional linker allows for selective catalyst-free ligation of two different azide-tagged substrates via strained-promoted azide-alkyne cycloaddition (SPAAC). The linker contains an azadibenzocyclooctyne (ADIBO) moiety on one end and a cyclopropenone-masked dibenzocyclooctyne (photo-DIBO) group on the other. The first azide-derivatized substrate reacts only at the ADIBO end of the linker as the photo-DIBO moiety is azide-inert. After the completion of the first SPAAC step, photo-DIBO is activated by brief exposure to 350 nm light from a fluorescent UV lamp. The unmasked DIBO group then reacts with the second azide-tagged substrate. Both click reactions are fast (k = 0.4 and 0.07 M(-1) s(-1), respectively) and produce quantitative yield of ligation in organic solvents or aqueous solutions. The utility of the new cross-linker has been demonstrated by conjugation of azide functionalized bovine serum albumin (azido-BSA) with azido-fluorescein and by the immobilization of the latter protein on azide-derivatized silica beads. The BSA-bead linker was designed to incorporate hydrolytically labile fragment, which permits release of protein under the action of dilute acid. UV activation of the second click reaction permits spatiotemporal control of the ligation process.
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Affiliation(s)
- Selvanathan Arumugam
- Department of Chemistry, University of
Georgia, Athens, Georgia 30602, United
States
| | - Vladimir V. Popik
- Department of Chemistry, University of
Georgia, Athens, Georgia 30602, United
States
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15
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16
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Pujari SS, Seela F. Parallel stranded DNA stabilized with internal sugar cross-links: synthesis and click ligation of oligonucleotides containing 2'-propargylated isoguanosine. J Org Chem 2013; 78:8545-61. [PMID: 23915305 DOI: 10.1021/jo4012706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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17
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Sun H, Peng X. Template-directed fluorogenic oligonucleotide ligation using "click" chemistry: detection of single nucleotide polymorphism in the human p53 tumor suppressor gene. Bioconjug Chem 2013; 24:1226-34. [PMID: 23806001 DOI: 10.1021/bc4001678] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel nonfluorescent alkyne-modified coumarin phosphoramidite was synthesized and successfully incorporated into oligonucleotides, which were then used in highly efficient DNA interstrand cross-linking and ligation reactions via "click" chemistry. The template-directed fluorogenic ligation "click" chemistry reaction was used for single nucleotide polymorphism analysis, where the target DNA catalyzes the ligation of two nonfluorescent probes to generate a fluorescent product. The upstream oligonucleotide probe is a nonfluorescent alkyne-modified coumarin and the downstream probe is an azide-modified oligonucleotide. When bound to a fully complementary template, the oligonucleotides ligated to produce a fluorescent product with a fluorophore at the ligation point. Wild-type and mutant p53 alleles were used to demonstrate that template-directed fluorogenic oligonucleotide ligation is sequence-specific and is capable of single nucleotide discrimination under mild conditions, even without the removal of unreacted probes.
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Affiliation(s)
- Huabing Sun
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
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18
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Hashidzume A, Nakamura T, Sato T. Copper-catalyzed azide-alkyne cycloaddition oligomerization of 3-azido-1-propyne derivatives. POLYMER 2013. [DOI: 10.1016/j.polymer.2013.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Kalachova L, Pohl R, Bednárová L, Fanfrlík J, Hocek M. Synthesis of nucleosides and dNTPs bearing oligopyridine ligands linked through an octadiyne tether, their incorporation into DNA and complexation with transition metal cations. Org Biomol Chem 2013; 11:78-89. [PMID: 23090069 DOI: 10.1039/c2ob26881g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modified nucleosides (dA(R)s and dC(R)s) bearing bipyridine or terpyridine ligands attached through an octadiyne linker were prepared by single-step aqueous-phase Sonogashira cross-coupling of 7-iodo-7-deaza-2'-deoxyadenosine and 5-iodo-2'-deoxycytidine with the corresponding bipyridine- or terpyridine-octadiynes and were triphosphorylated to the corresponding nucleoside triphosphates (dA(R)TPs and dC(R)TPs). The modified dN(R)TPs were successfully incorporated into the oligonucleotides by primer extension experiment (PEX) using different DNA polymerases and the PEX products were used for post-synthetic complexation with divalent metal cations. The complexation of these DNAs containing flexibly-tethered ligands was compared with the previously reported ones bearing rigid acetylene-linked ligands suggesting the possible formation of both inter- and intra-strand complexes with Ni(2+) or Fe(2+).
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Affiliation(s)
- Lubica Kalachova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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20
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Ingale SA, Seela F. Stepwise Click Functionalization of DNA through a Bifunctional Azide with a Chelating and a Nonchelating Azido Group. J Org Chem 2013; 78:3394-9. [DOI: 10.1021/jo400059b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sachin A. Ingale
- Laboratory of Bioorganic Chemistry
and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11,
48149 Münster, Germany
- Laboratorium für
Organische und Bioorganische
Chemie, Institut für Chemie, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück,
Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry
and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11,
48149 Münster, Germany
- Laboratorium für
Organische und Bioorganische
Chemie, Institut für Chemie, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück,
Germany
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21
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Ichikawa S, Ueno H, Sunadome T, Sato K, Matsuda A. Tris(azidoethyl)amine hydrochloride; a versatile reagent for synthesis of functionalized dumbbell oligodeoxynucleotides. Org Lett 2013; 15:694-7. [PMID: 23339424 DOI: 10.1021/ol400001w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triazole-cross-linked oligodeoxynucleotides were synthesized using the Cu(I) catalyzed alkyne-azide cycloaddition with tris(azidoethyl)amine hydrochloride and oligodeoxynucleotides possessing N-3-(propargyl)thymidine at both the 3'- and 5'-termini. Further installation of a functional molecule to the dumbbell oligodeoxynucleotides was achieved by utilizing the remaining azide group.
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Affiliation(s)
- Satoshi Ichikawa
- Kita-12, Nishi-6, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
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Niu TF, Gu L, Wang L, Yi WB, Cai C. Chemoselective Preparation of Unsymmetrical Bis(1,2,3-triazole) Derivatives and Application in Bis(1,2,3-triazole)-Modified Peptidomimetic Synthesis. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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El-Sagheer AH, Brown T. Click Chemistry – a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The copper-catalysed [3+2] alkyne azide cycloaddition reaction (the CuAAC reaction) is the classic example of ‘click’ chemistry, a relatively new concept that has been influential in many areas of science. It is used in the nucleic acid field for DNA cross-linking, oligonucleotide ligation and cyclisation, DNA and RNA labelling, attaching DNA to surfaces, producing modified nucleobases and backbones, synthesising ribozymes and monitoring nucleic acid biosynthesis. More recently a related click reaction, the ring strain-promoted azide–alkyne [3+2] cycloaddition (SPAAC) reaction has been used successfully in DNA strand ligation and labelling. This does not require copper catalysis, and therefore has many potential uses in vivo. In this review we discuss recent developments in nucleic acid click chemistry and their applications in biology, biotechnology and nanotechnology.
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Affiliation(s)
- Afaf H. El-Sagheer
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Chemistry Branch Dept. of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721 Egypt
| | - Tom Brown
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
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El-Sagheer AH, Brown T. Click nucleic acid ligation: applications in biology and nanotechnology. Acc Chem Res 2012; 45:1258-67. [PMID: 22439702 PMCID: PMC3423825 DOI: 10.1021/ar200321n] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Biochemical strategies that use a combination of synthetic oligonucleotides, thermostable DNA polymerases, and DNA ligases can produce large DNA constructs up to 1 megabase in length. Although these ambitious targets are feasible biochemically, comparable technologies for the chemical synthesis of long DNA strands lag far behind. The best available chemical approach is the solid-phase phosphoramidite method, which can be used to assemble DNA strands up to 150 bases in length. Beyond this point, deficiencies in the chemistry make it impossible to produce pure DNA. A possible alternative approach to the chemical synthesis of large DNA strands is to join together carefully purified synthetic oligonucleotides by chemical methods. Click ligation by the copper-catalyzed azide–alkyne (CuAAC) reaction could facilitate this process. In this Account, we describe the synthesis, characterization, and applications of oligonucleotides prepared by click ligation. The alkyne and azide oligonucleotide strands can be prepared by standard protocols, and the ligation reaction is compatible with a wide range of chemical modifications to DNA and RNA. We have employed click ligation to synthesize DNA constructs up to 300 bases in length and much longer sequences are feasible. When the resulting triazole linkage is placed in a PCR template, various DNA polymerases correctly copy the entire base sequence. We have also successfully demonstrated both in vitro transcription and rolling circle amplification through the modified linkage. This linkage has shown in vivo biocompatibility: an antibiotic resistance gene containing triazole linkages functions in E. coli. Using click ligation, we have synthesized hairpin ribozymes up to 100 nucleotides in length and a hammerhead ribozyme with the triazole linkage located at the substrate cleavage site. At the opposite end of the length scale, click-ligated, cyclic mini-DNA duplexes have been used as models to study base pairing. Cyclic duplexes have potential therapeutic applications. They have extremely high thermodynamic stability, have increased resistance to enzymatic degradation, and have been investigated as decoys for regulatory proteins. For potential nanotechnology applications, we have synthesized double stranded DNA catenanes by click ligation. Other researchers have studied covalently fixed multistranded DNA constructs including triplexes and quadruplexes.
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Affiliation(s)
- Afaf H. El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez 43721, Egypt
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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Xiong H, Seela F. Cross-linked DNA: site-selective "click" ligation in duplexes with bis-azides and stability changes caused by internal cross-links. Bioconjug Chem 2012; 23:1230-43. [PMID: 22554072 DOI: 10.1021/bc300074k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Heterodimeric interstrand cross-linked DNA was constructed by the "bis-click" reaction carried out on preformed oligonucleotide duplexes with the bis-azide 1. For this, alkynylated 8-aza-7-deazapurine or corresponding 5-substituted pyrimidine nucleosides were synthesized. Cross-linking resulted in chemoselective formation of heterodimeric duplexes while homodimers were suppressed. For product identification, heterodimeric DNA was prepared by the "stepwise click" reaction, while noncomplementary homodimers were accessible by "bis-click" chemistry, unequivocally. Studies on duplex melting of complementary cross-linked duplexes (heterodimers) revealed significantly increased Tm values compared to the non-cross-linked congeners. The stability of this cross-linked DNA depends on the linker length and the site of modification. Cross-linked homodimers hybridized with single-stranded complementary oligonucleotides show much lower stability.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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Pujari SS, Seela F. Cross-linked DNA: propargylated ribonucleosides as "click" ligation sites for bifunctional azides. J Org Chem 2012; 77:4460-5. [PMID: 22480133 DOI: 10.1021/jo300421p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
2'-O or 3'-O-propargylated adenosines and ribothymidines were used as click targets for cross-linking of oligonucleotides with aliphatic and aromatic azides. The cross-link generates a sugar modification at the 2'-O-ligation site. Inexpensive ribonucleosides were used as starting materials. Cross-linking of oligonucleotides was performed at internal or terminal positions. Hybridization of homodimers with two complementary single strands resulted in stable ligated DNA duplexes.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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Xiong H, Leonard P, Seela F. Construction and assembly of branched Y-shaped DNA: "click" chemistry performed on dendronized 8-aza-7-deazaguanine oligonucleotides. Bioconjug Chem 2012; 23:856-70. [PMID: 22443223 DOI: 10.1021/bc300013k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Branched DNA was synthesized from tripropargylated oligonucleotides by the Huisgen-Meldal-Sharpless cycloaddition using "stepwise and double click" chemistry. Dendronized oligonucleotides decorated with 7-tripropargylamine side chains carrying two terminal triple bonds were further functionalized with bis-azides to give derivatives with two terminal azido groups. Then, the branched side chains with two azido groups or two triple bonds were combined with DNA-fragments providing the corresponding clickable function. Both concepts afforded branched (Y-shaped) three-armed DNA. Annealing of branched DNA with complementary oligonucleotides yielded supramolecular assemblies. The concept of "stepwise and double click" chemistry combined with selective hybridization represents a flexible tool to generate DNA nanostructures useful for various purposes in DNA diagnostics, delivery, and material science applications.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Seela F, Xiong H, Budow S, Eickmeier H, Reuter H. A 2'-deoxycytidine long-linker click adduct forming two conformers in the asymmetric unit. Acta Crystallogr C 2012; 68:o174-8. [PMID: 22476151 DOI: 10.1107/s0108270112010682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/10/2012] [Indexed: 11/11/2022] Open
Abstract
The title compound {systematic name: 4-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-[6-(1-benzyl-1H-1,2,3-triazol-4-yl)hex-1-ynyl]pyrimidin-2(1H)-one}, C(24)H(28)N(6)O(4), shows two conformations in the crystalline state, viz. (I-1) and (I-2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N-glycosylic bonds of both conformers adopt similar anti conformations, with χ = -168.02 (12)° for conformer (I-1) and χ = -159.08 (12)° for conformer (I-2). The sugar residue of (I-1) shows an N-type (C3'-endo) conformation, with P = 33.1 (2)° and τ(m) = 29.5 (1)°, while the conformation of the 2'-deoxyribofuranosyl group of (I-2) is S-type (C3'-exo), with P = 204.5 (2)° and τ(m) = 33.8 (1)°. Both conformers participate in hydrogen-bond formation and exhibit identical patterns resulting in three-dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N-H...N, N-H... O, O-H...N and O-H...O).
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Münster, Germany.
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Heaney F. Nitrile Oxide/Alkyne Cycloadditions - A Credible Platform for Synthesis of Bioinspired Molecules by Metal-Free Molecular Clicking. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101823] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Xiong H, Seela F. Stepwise "click" chemistry for the template independent construction of a broad variety of cross-linked oligonucleotides: influence of linker length, position, and linking number on DNA duplex stability. J Org Chem 2011; 76:5584-97. [PMID: 21591729 DOI: 10.1021/jo2004988] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Münster, Germany
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Uhlig N, Li CJ. Alkynes as an eco-compatible “on-call” functionality orthogonal to biological conditions in water. Chem Sci 2011. [DOI: 10.1039/c1sc00164g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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