151
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Hocek M. Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J Org Chem 2014; 79:9914-21. [PMID: 25321948 DOI: 10.1021/jo5020799] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
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152
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Balintová J, Špaček J, Pohl R, Brázdová M, Havran L, Fojta M, Hocek M. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions. Chem Sci 2014; 6:575-587. [PMID: 28970873 PMCID: PMC5618110 DOI: 10.1039/c4sc01906g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/09/2014] [Indexed: 12/17/2022] Open
Abstract
A new azido-based DNA redox label which can be transformed into nitrophenyltriazole by a CuAAC click reaction was developed. It was used for the mapping of DNA–protein interactions with electrochemical detection.
New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA–protein interactions. 5-(4-Azidophenyl)-2′-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2′-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at –0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at –0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA–protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.
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Affiliation(s)
- Jana Balintová
- 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 .
| | - Jan Špaček
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Radek Pohl
- 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 .
| | - Marie Brázdová
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Luděk Havran
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Michal Hocek
- 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 . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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153
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Yotapan N, Charoenpakdee C, Wathanathavorn P, Ditmangklo B, Wagenknecht HA, Vilaivan T. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label. Beilstein J Org Chem 2014; 10:2166-74. [PMID: 25246975 PMCID: PMC4168962 DOI: 10.3762/bjoc.10.224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.
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Affiliation(s)
- Nattawut Yotapan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Pawinee Wathanathavorn
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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154
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Wamberg MC, Wieczorek R, Brier SB, de Vries JW, Kwak M, Herrmann A, Monnard PA. Functionalization of fatty acid vesicles through newly synthesized bolaamphiphile-DNA conjugates. Bioconjug Chem 2014; 25:1678-88. [PMID: 25144926 DOI: 10.1021/bc500289u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The surface functionalization of fatty acid vesicles will allow their use as nanoreactors for complex chemistry. In this report, the tethering of several DNA conjugates to decanoic acid vesicles for molecular recognition and synthetic purposes was explored. Due to the highly dynamic nature of these structures, only one novel bola-amphiphile DNA conjugate could interact efficiently with or spontaneously pierce into the vesicle bilayers without jeopardizing their self-assembly or stability. This molecule was synthesized via a Cu(I)-catalyzed [3 + 2] azide-alkyne cycloaddition (click reaction), and consists of a single hydrocarbon chain of 20 carbons having on one end a triazole group linked to the 5'-phosphate of the nucleic acid and on the other side a hydroxyl-group. Its insertion was so effective that a fluorescent label on the DNA complementary to the conjugate could be used to visualize fatty acid structures.
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Affiliation(s)
- Michael C Wamberg
- Center for Fundamental Living Technology (FLinT), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
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155
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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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156
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Agopcan Cinar S, Ercan S, Erol Gunal S, Dogan I, Aviyente V. The origin of exo-stereoselectivity of norbornene in hetero Diels–Alder reactions. Org Biomol Chem 2014; 12:8079-86. [DOI: 10.1039/c4ob01217h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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157
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Li Z, Weeraman CN, Gibbs-Davis JM. Following the azide-alkyne cycloaddition at the silica/solvent interface with sum frequency generation. Chemphyschem 2014; 15:2247-51. [PMID: 24800780 DOI: 10.1002/cphc.201402161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Indexed: 11/10/2022]
Abstract
The Cu(I) -catalyzed 1,3-dipolar azide-alkyne cycloaddition (CuAAC) has arisen as one of the most useful chemical transformations for introducing complexity onto surfaces and materials owing to its functional-group tolerance and high yield. However, methods for monitoring such reactions in situ at the widely used silica/solvent interface are hampered by challenges associated with probing such buried interfaces. Using the surface-specific technique broadband sum frequency generation (SFG), we monitored the reaction of a benzyl azide monolayer in real time at the silica/methanol interface. A strong peak at 2096 cm(-1) assigned to the azides was observed for the first time by SFG. Using a cyano-substituted alkyne, the decrease of the azide peak and the increase of the cyano peak (2234 cm(-1) ) were probed simultaneously. From the kinetic analysis, the reaction order with respect to copper was determined to be 2.1, suggesting that CuAAC on the surface follows a similar mechanism as in solution.
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Affiliation(s)
- Zhiguo Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2 (Canada)
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158
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MacKenzie DA, Sherratt AR, Chigrinova M, Cheung LLW, Pezacki JP. Strain-promoted cycloadditions involving nitrones and alkynes—rapid tunable reactions for bioorthogonal labeling. Curr Opin Chem Biol 2014; 21:81-8. [DOI: 10.1016/j.cbpa.2014.05.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
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159
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Kries H, Wachtel R, Pabst A, Wanner B, Niquille D, Hilvert D. Reprogramming Nonribosomal Peptide Synthetases for “Clickable” Amino Acids. Angew Chem Int Ed Engl 2014; 53:10105-8. [DOI: 10.1002/anie.201405281] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 12/21/2022]
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160
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Kries H, Wachtel R, Pabst A, Wanner B, Niquille D, Hilvert D. Reprogramming Nonribosomal Peptide Synthetases for “Clickable” Amino Acids. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405281] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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161
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Stubinitzky C, Cserép GB, Bätzner E, Kele P, Wagenknecht HA. 2′-Deoxyuridine conjugated with a reactive monobenzocyclooctyne as a DNA building block for copper-free click-type postsynthetic modification of DNA. Chem Commun (Camb) 2014; 50:11218-21. [DOI: 10.1039/c4cc02855d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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162
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Bhaumik A, Samanta S, Pathak T. Enantiopure 1,4,5-trisubstituted 1,2,3-triazoles from carbohydrates: applications of organoselenium chemistry. J Org Chem 2014; 79:6895-904. [PMID: 25010213 DOI: 10.1021/jo5009564] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A wide range of stable vinyl selenone-modified furanosides has been synthesized for the first time. These 2π-partners undergo 1,3-dipolar cycloaddition reactions with a wide range of organic azides to afford enantiopure trisubstituted triazoles. Furanosyl rings opened up during triazole synthesis to generate polyfunctionalized molecules, ready to undergo further transformations. This strategy is one of the most convenient methods for the synthesis of enantiopure 1,4,5-trisubstituted 1,2,3-triazoles where the chiral components are attached to C-4 or C-5 position of triazole ring. These triazoles are formed in a regioselective manner, and several pairs of regioisomeric triazoles have also been synthesized. The approach affords densely functionalized triazoles, which are amenable to further modifications because of the presence of aldehyde and hydroxyl groups. This powerful and practical route adds to the arsenals of chemists and biologists interested in the synthesis and applications of triazoles.
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Affiliation(s)
- Atanu Bhaumik
- Department of Chemistry, Indian Institute of Technology Kharagpur , Kharagpur 721302, India
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163
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Yeap WS, Murib MS, Cuypers W, Liu X, van Grinsven B, Ameloot M, Fahlman M, Wagner P, Maes W, Haenen K. Boron-Doped Diamond Functionalization by an Electrografting/Alkyne-Azide Click Chemistry Sequence. ChemElectroChem 2014. [DOI: 10.1002/celc.201402068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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164
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Miyazaki A, Asanuma M, Dodo K, Egami H, Sodeoka M. A "catch-and-release" protocol for alkyne-tagged molecules based on a resin-bound cobalt complex for peptide enrichment in aqueous media. Chemistry 2014; 20:8116-28. [PMID: 24788842 DOI: 10.1002/chem.201400056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/09/2023]
Abstract
The development of new and mild protocols for the specific enrichment of biomolecules is of significant interest from the perspective of chemical biology. A cobalt-phosphine complex immobilised on a solid-phase resin has been found to selectively bind to a propargyl carbamate tag, that is, "catch", under dilute aqueous conditions (pH 7) at 4 °C. Upon acidic treatment of the resulting resin-bound alkyne-cobalt complex, the Nicholas reaction was induced to "release" the alkyne-tagged molecule from the resin as a free amine. Model studies revealed that selective enrichment of the alkyne-tagged molecule could be achieved with high efficiency at 4 °C. The proof-of-concept was applied to an alkyne-tagged amino acid and dipeptide. Studies using an alkyne-tagged dipeptide proved that this protocol is compatible with various amino acids bearing a range of functionalities in the side-chain. In addition, selective enrichment and detection of an amine derived from the "catch and release" of an alkyne-tagged dipeptide in the presence of various peptides has been accomplished under highly dilute conditions, as determined by mass spectrometry.
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Affiliation(s)
- Ayako Miyazaki
- Sodeoka Live Cell Chemistry Project, ERATO, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan) and Synthetic Organic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Current address: Institute of Transformative, Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)
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165
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Xu Y, Suzuki Y, Ishizuka T, Xiao CD, Liu X, Hayashi T, Komiyama M. Finding a human telomere DNA-RNA hybrid G-quadruplex formed by human telomeric 6-mer RNA and 16-mer DNA using click chemistry: a protective structure for telomere end. Bioorg Med Chem 2014; 22:4419-21. [PMID: 24947481 DOI: 10.1016/j.bmc.2014.05.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 01/21/2023]
Abstract
Telomeric repeat-containing RNA is a non-coding RNA molecule newly found in mammalian cells. The telomere RNA has been found to localize to the telomere DNA, but how the newly discovered RNA molecule interacts with telomere DNA is less known. In this study, using the click chemistry we successfully found that a 6-mer human telomere RNA and 16-mer human telomere DNA sequence can form a DNA-RNA hybrid type G-quadruplex structure. Detection of the click-reaction products directly probes DNA-RNA G-quadruplex structures in a complicated solution, whereas traditional methods such as NMR and crystallography may not be suitable. Importantly, we found that formation of DNA-RNA G-quadruplex induced an exonuclease resistance for telomere DNA, indicating that such structures might be important for protecting telomeric DNA from enzyme digestion to avoid telomere DNA shortening. These results provide the direct evidence for formation of DNA-RNA hybrid G-quadruplex structure by human telomere DNA and RNA sequence, suggesting DNA-RNA hybrid G-quadruplex structure associated between telomere DNA and RNA may respond to chromosome end protection and/or present a valuable target for drug design.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
| | - Yuta Suzuki
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8904, Tokyo, Japan
| | - Takumi Ishizuka
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Chao-Da Xiao
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Xiao Liu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Tetsuya Hayashi
- Division of Microbial Genomics, Department of Genomics and Bioenvironmental Science, Frontier Science Research Center, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku 153-8904, Tokyo, Japan; Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577, Japan.
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166
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Dong Y, Liu D, Yang Z. A brief review of methods for terminal functionalization of DNA. Methods 2014; 67:116-22. [DOI: 10.1016/j.ymeth.2013.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/06/2013] [Accepted: 11/12/2013] [Indexed: 12/29/2022] Open
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167
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Zhang X, Wang Y, Fricke BL, Gu LQ. Programming nanopore ion flow for encoded multiplex microRNA detection. ACS NANO 2014; 8:3444-50. [PMID: 24654890 PMCID: PMC4004327 DOI: 10.1021/nn406339n] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/21/2014] [Indexed: 05/20/2023]
Abstract
Many efforts are being made in translating the nanopore into an ultrasensitive single-molecule platform for various genetic and epigenetic detections. However, compared with current approaches including PCR, the low throughput limits the nanopore applications in biological research and clinical settings, which usually requires simultaneous detection of multiple biomarkers for accurate disease diagnostics. Herein we report a barcode probe approach for multiple nucleic acid detection in one nanopore. Instead of directly identifying different targets in a nanopore, we designed a series of barcode probes to encode different targets. When the probe is bound with the target, the barcode group polyethylene glycol attached on the probe through click chemistry can specifically modulate nanopore ion flow. The resulting signature serves as a marker for the encoded target. Therefore counting different signatures in a current recording allows simultaneous analysis of multiple targets in one nanopore. The principle of this approach was verified by using a panel of cancer-derived microRNAs as the target, a type of biomarker for cancer detection.
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168
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Patterson DM, Nazarova LA, Prescher JA. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014; 9:592-605. [PMID: 24437719 DOI: 10.1021/cb400828a] [Citation(s) in RCA: 531] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.
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Affiliation(s)
- David M. Patterson
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Lidia A. Nazarova
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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169
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Kumar P, Hornum M, Nielsen LJ, Enderlin G, Andersen NK, Len C, Hervé G, Sartori G, Nielsen P. High-affinity RNA targeting by oligonucleotides displaying aromatic stacking and amino groups in the major groove. Comparison of triazoles and phenyl substituents. J Org Chem 2014; 79:2854-63. [PMID: 24611639 DOI: 10.1021/jo4025896] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense M, Denmark
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170
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Santner T, Hartl M, Bister K, Micura R. Efficient access to 3'-terminal azide-modified RNA for inverse click-labeling patterns. Bioconjug Chem 2014; 25:188-95. [PMID: 24358989 PMCID: PMC3898571 DOI: 10.1021/bc400513z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 12/14/2013] [Indexed: 01/22/2023]
Abstract
Labeled RNA becomes increasingly important for molecular diagnostics and biophysical studies on RNA with its diverse interaction partners, which range from small metabolites to large macromolecular assemblies, such as the ribosome. Here, we introduce a fast synthesis path to 3'-terminal 2'-O-(2-azidoethyl) modified oligoribonucleotides for subsequent bioconjugation, as exemplified by fluorescent labeling via Click chemistry for an siRNA targeting the brain acid-soluble protein 1 gene (BASP1). Importantly, the functional group pattern is inverse to commonly encountered alkyne-functionalized "click"-able RNA and offers increased flexibility with respect to multiple and stepwise labeling of the same RNA molecule. Additionally, our route opens up a minimal step synthesis of 2'-O-(2-aminoethyl) modified pyrimidine nucleoside phosphoramidites which are of widespread use to generate amino-modified RNA for N-hydroxysuccinimide (NHS) ester-based conjugations.
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Affiliation(s)
- Tobias Santner
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Hartl
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Bister
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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171
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Thiviyanathan V, Gorenstein DG. Aptamers and the next generation of diagnostic reagents. Proteomics Clin Appl 2014; 6:563-73. [PMID: 23090891 DOI: 10.1002/prca.201200042] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 01/06/2023]
Abstract
Antibodies have been extensively used as capture and detection reagents in diagnostic applications of proteomics-based technologies. Proteomic assays need high sensitivity and specificity, a wide dynamic range for detection, and accurate, reproducible quantification with small confidence values. However, several inherent limitations of monoclonal antibodies in meeting the emerging challenges of proteomics led to the development of a new class of oligonucleotide-based reagents. Natural and derivatized nucleic acid aptamers are emerging as promising alternatives to monoclonal antibodies. Aptamers can be effectively used to simultaneously detect thousands of proteins in multiplex discovery platforms, where antibodies often fail due to cross-reactivity problems. Through chemical modification, vast range of additional functional groups can be added at any desired position in the oligonucleotide sequence, therefore the best features of small molecule drugs, proteins, and antibodies can be brought together into aptamers, making aptamers the most versatile reagent in proteomics. In this review, we discuss the recent developments in aptamer technology, including new selection methods and the aptamers' application in proteomics.
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Affiliation(s)
- Varatharasa Thiviyanathan
- Centers for Proteomics & Systems Biology, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, USA
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172
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Hoshi M, Okimoto M, Oikawa A, Miyawaki S, Shimotori Y. One-pot synthesis of 1-arylmethyl-4-[( E)-alk-1-enyl]-1 H-1,2,3-triazoles via a cross-coupling/click reaction sequence. RSC Adv 2014. [DOI: 10.1039/c3ra45718d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
1-Arylmethyl-4-[(E)-alk-1-enyl]-1H-1,2,3-triazoles have been synthesized from terminal conjugated (E)-enynes, prepared by copper-mediated cross-coupling reaction of (E)-alk-1-enyldisiamylboranes with (trimethylsilyl)ethynyl bromide, benzyl bromides and sodium azide in a one-pot fashion.
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Affiliation(s)
- Masayuki Hoshi
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Mitsuhiro Okimoto
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Asuka Oikawa
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Shunsuke Miyawaki
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yasutaka Shimotori
- Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
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173
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Xu L, Mou XQ, Chen ZM, Wang SH. Copper-catalyzed intermolecular azidocyanation of aryl alkenes. Chem Commun (Camb) 2014; 50:10676-9. [DOI: 10.1039/c4cc04640d] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A copper-catalyzed Markovnikov-type intermolecular azidocyanation of aryl alkenes has been developed for the first time.
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Affiliation(s)
- Li Xu
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000, P. R. China
| | - Xue-Qing Mou
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000, P. R. China
| | - Zhi-Min Chen
- State Key Laboratory of Applied Organic Chemistry
- Lanzhou University
- Lanzhou 730000, P. R. China
| | - Shao-Hua Wang
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000, P. R. China
- State Key Laboratory of Applied Organic Chemistry
- Lanzhou University
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174
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Salam N, Sinha A, Roy AS, Mondal P, Jana NR, Islam SM. Synthesis of silver–graphene nanocomposite and its catalytic application for the one-pot three-component coupling reaction and one-pot synthesis of 1,4-disubstituted 1,2,3-triazoles in water. RSC Adv 2014. [DOI: 10.1039/c3ra47466f] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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175
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176
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Doluca O, Hale TK, Edwards PJB, González C, Filichev VV. Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA. Chempluschem 2013; 79:58-66. [PMID: 31986766 DOI: 10.1002/cplu.201300310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/29/2013] [Indexed: 12/19/2022]
Abstract
In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (ΦF ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (ΦF =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.
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Affiliation(s)
- Osman Doluca
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682.,International Burch University, Francuske Revolucije, 71210 Sarajevo (Bosnia and Herzegovina)
| | - Tracy K Hale
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Patrick J B Edwards
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Carlos González
- Instituto de Química Física Rocasalano, CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Vyacheslav V Filichev
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
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177
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Holzhauser C, Rubner MM, Wagenknecht HA. Energy-transfer-based wavelength-shifting DNA probes with "clickable" cyanine dyes. Photochem Photobiol Sci 2013; 12:722-4. [PMID: 23314253 DOI: 10.1039/c2pp25366f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The insertion of cyanine dye azides as energy donor dyes via postsynthetic "click"-type cycloaddition chemistry with e.g. a new thiazole orange azide combined with thiazole red yields dual emitting DNA probes with good fluorescence readout properties.
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Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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178
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Rudolf GC, Sieber SA. Copper-assisted click reactions for activity-based proteomics: fine-tuned ligands and refined conditions extend the scope of application. Chembiochem 2013; 14:2447-55. [PMID: 24166841 DOI: 10.1002/cbic.201300551] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 12/26/2022]
Abstract
Copper-catalysed alkyne-azide 1,3-dipolar cycloaddition (CuAAC) is the predominantly used bioconjugation method in the field of activity-based protein profiling (ABPP). Several limitations, however, including conversion efficiency, protein denaturation and buffer compatibility, restrict the scope of established procedures. We introduce an ABPP customised click methodology based on refined CuAAC conditions together with new accelerating copper ligands. A screen of several triazole compounds revealed the cationic quaternary {3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propyl}trimethylammonium trifluoroacetate (TABTA) to be a superior ligand. TABTA exhibited excellent in vitro conjugation kinetics and optimal ABPP labelling activity while almost exclusively preserving the native protein fold. The application of this CuAAC-promoting system is amenable to existing protocols with minimal perturbations and is even compatible with previously unusable buffer systems such as Tris⋅HCl.
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Affiliation(s)
- Georg C Rudolf
- Fakultät für Chemie, Lehrstuhl für Organische Chemie II, Technische Universität München, Lichtenbergstraße 4, 85748 Garching (Germany)
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179
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Obeid S, Bußkamp H, Welte W, Diederichs K, Marx A. Snapshot of a DNA polymerase while incorporating two consecutive C5-modified nucleotides. J Am Chem Soc 2013; 135:15667-9. [PMID: 24090271 DOI: 10.1021/ja405346s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Functional nucleotides are important in many cutting-edge biomolecular techniques. Often several modified nucleotides have to be incorporated consecutively. This structural study of KlenTaq DNA polymerase, a truncated form of Thermus aquaticus DNA polymerase, gives first insights how multiple modifications are processed by a DNA polymerase and, therefore, contribute to the understanding of these enzymes in their interplay with artificial substrates.
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Affiliation(s)
- Samra Obeid
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz , Universitätsstrasse 10, 78457 Konstanz, Germany
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180
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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181
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Kayet A, Pathak T. 1,5-Disubstituted 1,2,3-Triazolylation at C1, C2, C3, C4, and C6 of Pyranosides: A Metal-Free Route to Triazolylated Monosaccharides and Triazole-Linked Disaccharides. J Org Chem 2013; 78:9865-75. [DOI: 10.1021/jo401576n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anirban Kayet
- Department
of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Tanmaya Pathak
- Department
of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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182
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Ag-Promoted Azido-Carbocyclization of Activated Alkenes via CH Bond Cleavage. Chem Asian J 2013; 8:2932-5. [DOI: 10.1002/asia.201300960] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Indexed: 12/19/2022]
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183
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Sheng R, Luo T, Li H, Sun J, Wang Z, Cao A. 'Click' synthesized sterol-based cationic lipids as gene carriers, and the effect of skeletons and headgroups on gene delivery. Bioorg Med Chem 2013; 21:6366-77. [PMID: 24063908 DOI: 10.1016/j.bmc.2013.08.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/15/2013] [Accepted: 08/24/2013] [Indexed: 01/01/2023]
Abstract
In this work, we have successfully prepared a series of new sterol-based cationic lipids (1-4) via an efficient 'Click' chemistry approach. The pDNA binding affinity of these lipids was examined by EB displacement and agarose-gel retardant assay. The average particle sizes and surface charges of the sterol-based cationic lipids/pDNA lipoplexes were analyzed by dynamic laser light scattering instrument (DLS), and the morphologies of the lipoplexes were observed by atomic force microscopy (AFM). The cytotoxicity of the lipids were examined by MTT and LDH assay, and the gene transfection efficiencies of these lipid carriers were investigated by luciferase gene transfection assay in various cell lines. In addition, the intracellular uptake and trafficking/localization behavior of the Cy3-DNA loaded lipoplexes were preliminarily studied by fluorescence microscopy. The results demonstrated that the pDNA loading capacity, lipoplex particle size, zeta potential and morphology of the sterol lipids/pDNA lipoplexes depended largely on the molecular structure factors including sterol-skeletons and headgroups. Furthermore, the sterol-based lipids showed quite different cytotoxicity and gene transfection efficacy in A549 and HeLa cells. Interestingly, it was found that the cholesterol-bearing lipids 1 and 2 showed 7-10(4) times higher transfection capability than their lithocholate-bearing counterparts 3 and 4 in A549 and HeLa cell lines, suggested that the gene transfection capacity strongly relied on the structure of sterol skeletons. Moreover, the study on the structure-activity relationships of these sterol-based cationic lipid gene carriers provided a possible approach for developing low cytotoxic and high efficient lipid gene carriers by selecting suitable sterol hydrophobes and cationic headgroups.
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Affiliation(s)
- Ruilong Sheng
- Laboratory for Polymer Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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184
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Dadová J, Orság P, Pohl R, Brázdová M, Fojta M, Hocek M. Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins. Angew Chem Int Ed Engl 2013; 52:10515-8. [DOI: 10.1002/anie.201303577] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Indexed: 12/15/2022]
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185
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Dadová J, Orság P, Pohl R, Brázdová M, Fojta M, Hocek M. Vinylsulfonamide and Acrylamide Modification of DNA for Cross-linking with Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303577] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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186
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Stolz RM, Northrop BH. Experimental and Theoretical Studies of Selective Thiol–Ene and Thiol–Yne Click Reactions Involving N-Substituted Maleimides. J Org Chem 2013; 78:8105-16. [DOI: 10.1021/jo4014436] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert M. Stolz
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
| | - Brian H. Northrop
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
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187
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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188
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Holzhauser C, Wagenknecht HA. DNA and RNA “Traffic Lights”: Synthetic Wavelength-Shifting Fluorescent Probes Based on Nucleic Acid Base Substitutes for Molecular Imaging. J Org Chem 2013; 78:7373-9. [DOI: 10.1021/jo4010102] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
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189
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Ein chemo-enzymatischer Ansatz zur regiospezifischen Modifizierung der RNA-Kappe. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302874] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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190
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Schulz D, Holstein JM, Rentmeister A. A chemo-enzymatic approach for site-specific modification of the RNA cap. Angew Chem Int Ed Engl 2013; 52:7874-8. [PMID: 23794451 DOI: 10.1002/anie.201302874] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Indexed: 11/08/2022]
Abstract
Capped and gowned: A two-step approach can be used to site-specifically modify the 5'-cap of eukaryotic mRNAs. First, a trimethylguanosinesynthase variant recognizes the m(7)G cap structure and introduces bioorthogonal groups using S-adenosyl-L-methionine-based cosubstrates. Then, the enzymatically introduced reporter groups are further modified by thiol-ene or CuAAC click chemistry (see scheme).
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Affiliation(s)
- Daniela Schulz
- Universität Hamburg, Department Chemie, Institut für Biochemie und Molekularbiologie, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
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191
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Bergen K, Betz K, Welte W, Diederichs K, Marx A. Structures of KOD and 9°N DNA polymerases complexed with primer template duplex. Chembiochem 2013; 14:1058-62. [PMID: 23733496 DOI: 10.1002/cbic.201300175] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 12/29/2022]
Abstract
Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.
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Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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192
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Bare GA, Sherman JC. Multiple phosphate-linked nucleotide couplings via 5′ silyl ether protection in the phosphite triester and phosphoramidite approaches. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.04.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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193
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Ménová P, Raindlová V, Hocek M. Scope and limitations of the nicking enzyme amplification reaction for the synthesis of base-modified oligonucleotides and primers for PCR. Bioconjug Chem 2013; 24:1081-93. [PMID: 23682869 DOI: 10.1021/bc400149q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides (ONs) was developed by nicking enzyme amplification reaction (NEAR) using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease, and a modified deoxyribonucleoside triphosphate (dNTP) derivative. The scope and limitations of the methodology in terms of different nucleobases, length, sequences, and modifications has been thoroughly studied. The methodology including isolation of the modified ONs was scaled up to nanomolar amounts and the modified ONs were successfully used as primers in primer extension and PCR. Two simple and efficient methods for fluorescent labeling of the PCR products were developed, based either on direct fluorescent labeling of primers or on NEAR synthesis of ethynylated primers, PCR, and final click labeling with fluorescent azides.
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Affiliation(s)
- Petra Ménová
- 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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194
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Shi L, Jing C, Ma W, Li DW, Halls JE, Marken F, Long YT. Plasmon resonance scattering spectroscopy at the single-nanoparticle level: real-time monitoring of a click reaction. Angew Chem Int Ed Engl 2013; 52:6011-4. [PMID: 23616358 DOI: 10.1002/anie.201301930] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Indexed: 11/09/2022]
Abstract
A method based on plasmon resonance Rayleigh scattering (PRRS) spectroscopy and dark-field microscopy (DFM) was established for the real-time monitoring of a click reaction at the single-nanoparticle level. Click reactions on the surface of single gold nanoparticles (GNPs) result in interparticle coupling, which leads to a red-shift of the λmax (Δλmax =43 nm) in the PRRS spectra and a color change of the single gold nanoparticles in DFM (from green to orange).
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Bioreactor Engineering, & Department of Chemistry, East China University of Science and Technology, Shanghai, 200237, PR China
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195
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Shi L, Jing C, Ma W, Li DW, Halls JE, Marken F, Long YT. Plasmon Resonance Scattering Spectroscopy at the Single-Nanoparticle Level: Real-Time Monitoring of a Click Reaction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301930] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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196
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Synthesis of new 1,2,3-triazole derivatives of uracil and thymine with potential inhibitory activity against acidic corrosion of steels. Molecules 2013; 18:4613-27. [PMID: 23599018 PMCID: PMC6269733 DOI: 10.3390/molecules18044613] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 12/11/2022] Open
Abstract
Ten 1,4-disubstituted 1,2,3-triazoles were synthesized from one of 1-(azido-methyl)benzene, 1-(azidomethyl)-4-fluorobenzene, 1-(azidomethyl)-4-chlorobenzene, 1-(azidomethyl)-4-bromobenzene or 1-(azidomethyl)-4-iodobenzene, generated in situ from sodium azide and the corresponding benzyl halide, and dipropargyl uracil or dipropargyl thymine. Optimal experimental conditions were established for the conventional click chemistry. The corrosion inhibiting properties of some of these compounds, which were determined by means of an electrochemical technique, are also presented.
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197
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Deng QH, Bleith T, Wadepohl H, Gade LH. Enantioselective Iron-Catalyzed Azidation of β-Keto Esters and Oxindoles. J Am Chem Soc 2013; 135:5356-9. [DOI: 10.1021/ja402082p] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Qing-Hai Deng
- Catalysis Research Laboratory (CaRLa), Im Neuenheimer Feld 584, 69120 Heidelberg,
Germany
| | - Tim Bleith
- Anorganisch-Chemisches
Institut, Universität Heidelberg, Im Neuenheimer Feld
270, 69120 Heidelberg, Germany
| | - Hubert Wadepohl
- Anorganisch-Chemisches
Institut, Universität Heidelberg, Im Neuenheimer Feld
270, 69120 Heidelberg, Germany
| | - Lutz H. Gade
- Catalysis Research Laboratory (CaRLa), Im Neuenheimer Feld 584, 69120 Heidelberg,
Germany
- Anorganisch-Chemisches
Institut, Universität Heidelberg, Im Neuenheimer Feld
270, 69120 Heidelberg, Germany
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198
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Miguel-Fernández S, Martínez de Salinas S, Díez J, Gamasa MP, Lastra E. 1,3-Dipolar Cycloadditions of Ruthenium(II) Azido Complexes with Alkynes and Nitriles. Inorg Chem 2013; 52:4293-302. [DOI: 10.1021/ic302264t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- S. Miguel-Fernández
- Departamento de Química Orgánica
e Inorgánica, Instituto de Química Organometálica
“Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de
Asturias, Spain
| | - S. Martínez de Salinas
- Departamento de Química Orgánica
e Inorgánica, Instituto de Química Organometálica
“Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de
Asturias, Spain
| | - J. Díez
- Departamento de Química Orgánica
e Inorgánica, Instituto de Química Organometálica
“Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de
Asturias, Spain
| | - M. P. Gamasa
- Departamento de Química Orgánica
e Inorgánica, Instituto de Química Organometálica
“Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de
Asturias, Spain
| | - E. Lastra
- Departamento de Química Orgánica
e Inorgánica, Instituto de Química Organometálica
“Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de
Asturias, Spain
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199
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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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200
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Sadhu KK, Röthlingshöfer M, Winssinger N. DNA as a Platform to Program Assemblies with Emerging Functions in Chemical Biology. Isr J Chem 2013. [DOI: 10.1002/ijch.201200100] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kalyan K. Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
- Department of Organic Chemistry, University of Geneva, 30 quai Ernest Ansermet, CH‐1211 Geneva 4 (Switzerland) phone: +41‐22‐379‐61‐05 fax: +41‐22‐379‐32‐15
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