51
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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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52
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Synthesis and enzymatic incorporation of photolabile dUTP analogues into DNA and their applications for DNA labeling. Bioorg Med Chem 2013; 21:6205-11. [PMID: 23719284 DOI: 10.1016/j.bmc.2013.04.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 11/22/2022]
Abstract
Two novel photolabile nucleotide triphosphate (NTP) analogues were synthesized through Sonogashira coupling and their enzymatic incorporation into DNA was evaluated with three different DNA polymerases (Taq, Vent exo- and T4) by polymerase chain reaction. Both nucleotide triphosphate analogues were recognized by these DNA polymerases as substrates for primer extension. Light irradiation of PCR products removed the photolabile group and released the amino and carboxyl moieties. Further site-specific dual-labeling for oligodeoxynucleotides (ODNs) and random labeling for a long DNA construct with fluorophores were successfully achieved with incorporation of the photolabile amine modified deoxyuridine triphosphate (dUnTP).
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53
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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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54
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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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55
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Beckendorf S, Asmus S, Mück-Lichtenfeld C, García Mancheño O. “Click” Bis-Triazoles as Neutral CH⋅⋅⋅Anion-Acceptor Organocatalysts. Chemistry 2012; 19:1581-5. [DOI: 10.1002/chem.201203360] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/08/2012] [Indexed: 12/20/2022]
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56
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Duprey JLHA, Takezawa Y, Shionoya M. Metal-locked DNA three-way junction. Angew Chem Int Ed Engl 2012; 52:1212-6. [PMID: 23238966 DOI: 10.1002/anie.201207338] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Jean-Louis H A Duprey
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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57
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58
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Hollenstein M. Synthesis of deoxynucleoside triphosphates that include proline, urea, or sulfonamide groups and their polymerase incorporation into DNA. Chemistry 2012; 18:13320-30. [PMID: 22996052 DOI: 10.1002/chem.201201662] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/21/2012] [Indexed: 01/02/2023]
Abstract
To expand the chemical array available for DNA sequences in the context of in vitro selection, I present herein the synthesis of five nucleoside triphosphate analogues containing side chains capable of organocatalysis. The synthesis involved the coupling of L-proline-containing residues (dU(tP)TP and dU(cP)TP), a dipeptide (dU(FP)TP), a urea derivative (dU(Bpu)TP), and a sulfamide residue (dU(Bs)TP) to a suitably protected common intermediate, followed by triphosphorylation. These modified dNTPs were shown to be excellent substrates for the Vent (exo(-)) and Pwo DNA polymerases, as well as the Klenow fragment of E. coli DNA polymerase I, although they were only acceptable substrates for the 9°N(m) polymerase. All of the modified dNTPs, with the exception of dU(Bpu)TP, were readily incorporated into DNA by the polymerase chain reaction (PCR). Modified oligonucleotides efficiently served as templates for PCR for the regeneration of unmodified DNA. Thermal denaturation experiments showed that these modifications are tolerated in the major groove. Overall, these heavily modified dNTPs are excellent candidates for SELEX.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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59
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Ming X, Seela F. A Nucleobase-Discriminating Pyrrolo-dC Click Adduct Designed for DNA Fluorescence Mismatch Sensing. Chemistry 2012; 18:9590-600. [DOI: 10.1002/chem.201103385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/17/2012] [Indexed: 11/10/2022]
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60
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Schmidt MJ, Summerer D. A Need for Speed: Genetic Encoding of Rapid Cycloaddition Chemistries for Protein Labelling in Living Cells. Chembiochem 2012; 13:1553-7. [DOI: 10.1002/cbic.201200321] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Indexed: 01/08/2023]
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61
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Schiesser S, Hackner B, Pfaffeneder T, Müller M, Hagemeier C, Truss M, Carell T. Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing. Angew Chem Int Ed Engl 2012; 51:6516-20. [PMID: 22644704 DOI: 10.1002/anie.201202583] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Indexed: 01/24/2023]
Abstract
Eraserhead: Stem cells seem to erase epigenetic information by decarboxylation of the newly discovered epigenetic base 5-carboxycytosine (caC; see picture). This reaction is likely to involve a nucleophilic attack of the C5-C6 double bond.
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Affiliation(s)
- Stefan Schiesser
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstrasse 5-13, 81377 München, Germany
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62
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Schiesser S, Hackner B, Pfaffeneder T, Müller M, Hagemeier C, Truss M, Carell T. Mechanismus und Stammzellaktivität der Decarboxylierung von 5-Carboxycytosin, bestimmt mittels Isotopenverfolgung. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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63
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Raindlová V, Pohl R, Klepetářová B, Havran L, Šimková E, Horáková P, Pivoňková H, Fojta M, Hocek M. Synthesis of Hydrazone-Modified Nucleotides and Their Polymerase Incorporation onto DNA for Redox Labeling. Chempluschem 2012. [DOI: 10.1002/cplu.201200056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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64
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Plass T, Milles S, Koehler C, Szymański J, Mueller R, Wießler M, Schultz C, Lemke EA. Amino Acids for Diels-Alder Reactions in Living Cells. Angew Chem Int Ed Engl 2012; 51:4166-70. [DOI: 10.1002/anie.201108231] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/17/2012] [Indexed: 01/03/2023]
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65
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Plass T, Milles S, Koehler C, Szymański J, Mueller R, Wießler M, Schultz C, Lemke EA. Amino Acids for Diels-Alder Reactions in Living Cells. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108231] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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66
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Raindlová V, Pohl R, Hocek M. Synthesis of aldehyde-linked nucleotides and DNA and their bioconjugations with lysine and peptides through reductive amination. Chemistry 2012; 18:4080-7. [PMID: 22337599 DOI: 10.1002/chem.201103270] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 11/06/2022]
Abstract
5-(5-Formylthienyl)-, 5-(4-formylphenyl)- and 5-(2-fluoro-5-formylphenyl)cytosine 2'-deoxyribonucleoside mono- (dC(R)MP) and triphosphates (dC(R)TP) were prepared by aqueous Suzuki-Miyaura cross-coupling of 5-iodocytosine nucleotides with the corresponding formylarylboronic acids. The dC(R)TPs were excellent substrates for DNA polymerases and were incorporated into DNA by primer extension or PCR. Reductive aminations of the model dC(R)MPs with lysine or lysine-containing tripeptide were studied and optimized. In aqueous phosphate buffer (pH 6.7) the yields of the reductive aminations with tripeptide III were up to 25 %. Bioconjugation of an aldehyde-containing DNA with a lysine-containing tripeptide was achieved through reductive amination in yields of up to 90 % in aqueous phosphate buffer.
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Affiliation(s)
- Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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67
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Ligeour C, Meyer A, Vasseur JJ, Morvan F. Bis- and Tris-Alkyne Phosphoramidites for Multiple 5′-Labeling of Oligonucleotides by Click Chemistry. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101763] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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68
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Rubner MM, Achatz DE, Mader HS, Stolwijk JA, Wegener J, Harms GS, Wolfbeis OS, Wagenknecht HA. DNA “Nanolamps”: “Clicked” DNA Conjugates with Photon Upconverting Nanoparticles as Highly Emissive Biomaterial. Chempluschem 2012. [DOI: 10.1002/cplu.201100055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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69
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Ghosh PS, Hamilton AD. Supramolecular dendrimers: convenient synthesis by programmed self-assembly and tunable thermoresponsivity. Chemistry 2012; 18:2361-5. [PMID: 22267264 DOI: 10.1002/chem.201103051] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Indexed: 11/08/2022]
Abstract
We report here the noncovalent synthesis of thermosensitive dendrimers. Short oligoguanosine strands were linked to the focal point of a dendron by using "click chemistry", and quadruplex formation was used to drive the self-assembly process in the presence of metal ions. The dynamic nature of these noncovalent assemblies can be exploited to create combinatorial libraries of dendrimers as demonstrated by the co-assembly of two components. These supramolecular dendrimers showed thermoresponsive behavior that can be tuned by varying the templating cations or the number of guanines in the oligonucleotide strand.
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Affiliation(s)
- Partha S Ghosh
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107, USA
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70
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Rubner MM, Holzhauser C, Bohländer PR, Wagenknecht HA. A “Clickable” Styryl Dye for Fluorescent DNA Labeling by Excitonic and Energy Transfer Interactions. Chemistry 2012; 18:1299-302. [DOI: 10.1002/chem.201102622] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 11/30/2011] [Indexed: 12/18/2022]
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71
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Spork AP, Wiegmann D, Granitzka M, Stalke D, Ducho C. Stereoselective synthesis of uridine-derived nucleosyl amino acids. J Org Chem 2011; 76:10083-98. [PMID: 22059552 DOI: 10.1021/jo201935w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Novel hybrid structures of 5'-deoxyuridine and glycine were conceived and synthesized. Such nucleosyl amino acids (NAAs) represent simplified analogues of the core structure of muraymycin nucleoside antibiotics, making them useful synthetic building blocks for structure-activity relationship (SAR) studies. The key step of the developed synthetic route was the efficient and highly diastereoselective asymmetric hydrogenation of didehydro amino acid precursors toward protected NAAs. It was anticipated that the synthesis of unprotected muraymycin derivatives via this route would require a suitable intermediate protecting group at the N-3 of the uracil base. After initial attempts using PMB- and BOM-N-3 protection, both of which resulted in problematic deprotection steps, an N-3 protecting group-free route was envisaged. In spite of the pronounced acidity of the uracil-3-NH, this route worked equally efficient and with identical stereoselectivities as the initial strategies involving N-3 protection. The obtained NAA building blocks were employed for the synthesis of truncated 5'-deoxymuraymycin analogues.
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Affiliation(s)
- Anatol P Spork
- Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37 077 Göttingen, Germany
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72
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73
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Baccaro A, Steck AL, Marx A. Barcoded nucleotides. Angew Chem Int Ed Engl 2011; 51:254-7. [PMID: 22083884 DOI: 10.1002/anie.201105717] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/15/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Baccaro
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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74
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Cheng Y, Dai C, Peng H, Zheng S, Jin S, Wang B. Design, synthesis, and polymerase-catalyzed incorporation of click-modified boronic acid-TTP analogues. Chem Asian J 2011; 6:2747-52. [PMID: 21887745 DOI: 10.1002/asia.201100229] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 11/06/2022]
Abstract
DNA molecules are known to be important materials in sensing, aptamer selection, nanocomputing, and construction of unique architectures. The incorporation of modified nucleobases affords unique DNA properties for applications in areas that would otherwise be difficult or not possible. Earlier, we demonstrated that the boronic acid moiety can be introduced into DNA through polymerase-catalyzed reactions. In order to study whether such incorporation by polymerase is a general phenomenon, we designed and synthesized four boronic acid-modified thymidine triphosphate (TTP) analogues. The synthesis of certain analogues was through the use of a single dialkyne tether for both the Sonogashira coupling with thymidine and the later Cu-mediated [3+2] cycloaddition for linking the boronic acid moiety. This approach is much more efficient than the previously described method, and paves the way for the preparation of a large number of boronic acid-modified TTPs with a diverse set of structural features. All analogues showed very good stability under polymerase chain reaction (PCR) conditions and were recognized as a substrate by DNA polymerase, and thus incorporated into DNA.
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Affiliation(s)
- Yunfeng Cheng
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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75
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Lallana E, Riguera R, Fernandez-Megia E. Zuverlässige und effiziente Konjugation von Biomolekülen über Huisgen-Azid-Alkin-Cycloadditionen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101019] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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76
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Lallana E, Riguera R, Fernandez-Megia E. Reliable and Efficient Procedures for the Conjugation of Biomolecules through Huisgen Azide-Alkyne Cycloadditions. Angew Chem Int Ed Engl 2011; 50:8794-804. [DOI: 10.1002/anie.201101019] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Indexed: 12/20/2022]
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77
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102898] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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78
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Kielkowski P, Macíčková-Cahová H, Pohl R, Hocek M. Transient and Switchable (Triethylsilyl)ethynyl Protection of DNA against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2011; 50:8727-30. [DOI: 10.1002/anie.201102898] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/30/2011] [Indexed: 12/13/2022]
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79
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Abendroth F, Bujotzek A, Shan M, Haag R, Weber M, Seitz O. DNA-controlled bivalent presentation of ligands for the estrogen receptor. Angew Chem Int Ed Engl 2011; 50:8592-6. [PMID: 21793134 DOI: 10.1002/anie.201101655] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/02/2011] [Indexed: 12/31/2022]
Affiliation(s)
- Frank Abendroth
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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80
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Abendroth F, Bujotzek A, Shan M, Haag R, Weber M, Seitz O. DNA-gesteuerte bivalente Präsentation von Liganden für den Östrogenrezeptor. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101655] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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81
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Stephenson AWI, Partridge AC, Filichev VV. Synthesis of β-pyrrolic-modified porphyrins and their incorporation into DNA. Chemistry 2011; 17:6227-38. [PMID: 21503985 DOI: 10.1002/chem.201003200] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/01/2011] [Indexed: 12/20/2022]
Abstract
A synthetic methodology for the synthesis of various β-pyrrolic-functionalised porphyrins and their covalent attachment to 2'-deoxyuridine and DNA is described. Palladium(0)-catalysed Sonogashira and copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reactions were used to insert porphyrins into the structure of 2'-deoxyuridine and DNA. Insertion of a porphyrin into the middle of single-stranded CT oligonucleotides possessing a 5'-terminal run of four cytosines was shown to trigger the formation of pH- and temperature-dependent i-motif structures. Porphyrin insertion also led to the aggregation of single-stranded purine-pyrimidine sequences, which could be dissociated by heating at 90 °C for 5 min. Parallel triplexes and anti-parallel duplexes were formed in the presence of the appropriate complementary strand(s). Depending on the modification, porphyrins were placed in the major and minor grooves of duplexes and were used as bulged intercalating insertions in duplexes and triplexes. In general, the thermal stabilisation of parallel triplexes possessing porphyrin-modified triplex-forming oligonucleotide (TFO) strands was observed, whereas anti-parallel duplexes were destabilised. These results are compared and discussed on the basis of the results of molecular modelling calculations.
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Affiliation(s)
- Adam W I Stephenson
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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82
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Kitaoka M, Tsuruda Y, Tanaka Y, Goto M, Mitsumori M, Hayashi K, Hiraishi Y, Miyawaki K, Noji S, Kamiya N. Transglutaminase-mediated synthesis of a DNA-(enzyme)n probe for highly sensitive DNA detection. Chemistry 2011; 17:5387-92. [PMID: 21469233 DOI: 10.1002/chem.201003744] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Indexed: 12/29/2022]
Abstract
A new synthetic strategy for DNA-enzyme conjugates with a novel architecture was explored using a natural cross-linking catalyst, microbial transglutaminase (MTG). A glutamine-donor substrate peptide of MTG was introduced at the 5-position on the pyrimidine of deoxyuridine triphosphate to prepare a DNA strand with multiple glutamine-donor sites by polymerase chain reaction (PCR). A substrate peptide that contained an MTG-reactive lysine residue was fused to the N terminus of a thermostable alkaline phoshatase from Pyrococcus furiosus (PfuAP) by genetic engineering. By combining enzymatically the substrate moieties of MTG introduced to the DNA template and the recombinant enzyme, a DNA-(enzyme)(n) conjugate with 1:n stoichiometry was successfully obtained. The enzyme/DNA ratio of the conjugate increased as the benzyloxycarbonyl-L-glutaminylglycine (Z-QG) moiety increased in the DNA template. The potential utility of the new conjugate decorated with signaling enzymes was validated in a dot blot hybridization assay. The DNA-(enzyme)(n) probe could clearly detect 10(4) copies of the target nucleic acid with the complementary sequence under harsh hybridization conditions, thereby enabling a simple detection procedure without cumbersome bound/free processes associated with a conventional hapten-antibody reaction-based DNA-detection system.
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Affiliation(s)
- Momoko Kitaoka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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83
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Ding P, Wunnicke D, Steinhoff HJ, Seela F. Site-directed spin-labeling of DNA by the azide-alkyne 'click' reaction: nanometer distance measurements on 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine nitroxide conjugates spatially separated or linked to a 'dA-dT' base pair. Chemistry 2011; 16:14385-96. [PMID: 21117098 DOI: 10.1002/chem.201001572] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleobase-directed spin-labeling by the azide-alkyne 'click' (CuAAC) reaction has been performed for the first time with oligonucleotides. 7-Deaza-7-ethynyl-2'-deoxyadenosine (1) and 5-ethynyl-2'-deoxyuridine (2) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4-azido-2,2,6,6-tetramethylpiperidine 1-oxyl (4-azido-TEMPO, 3) was performed by post-modification in solution. Two spin labels (3) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a 'dA-dT' base pair. Modification at the 5-position of the pyrimidine base or at the 7-position of the 7-deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1-2 nm, were measured. The spin-spin distance was 1.8±0.2 nm for DNA duplex 17(dA*(7,10))⋅11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin-labeled 'dA-dT' base pair 15(dA*(7))⋅16(dT*(6)). The 'click' approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.
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Affiliation(s)
- Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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Staiger N, Marx A. A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides. Chembiochem 2011; 11:1963-6. [PMID: 20734370 DOI: 10.1002/cbic.201000384] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nadine Staiger
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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85
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Macíčková-Cahová H, Pohl R, Hocek M. Cleavage of Functionalized DNA Containing 5-Modified Pyrimidines by Type II Restriction Endonucleases. Chembiochem 2011; 12:431-8. [DOI: 10.1002/cbic.201000644] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Indexed: 12/18/2022]
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86
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Stephenson AWI, Bomholt N, Partridge AC, Filichev VV. Significantly enhanced DNA thermal stability resulting from porphyrin H-aggregate formation in the minor groove of the duplex. Chembiochem 2011; 11:1833-9. [PMID: 20677201 DOI: 10.1002/cbic.201000326] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adam W I Stephenson
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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87
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Aigner M, Hartl M, Fauster K, Steger J, Bister K, Micura R. Chemical synthesis of site-specifically 2'-azido-modified RNA and potential applications for bioconjugation and RNA interference. Chembiochem 2011; 12:47-51. [PMID: 21171007 PMCID: PMC3193913 DOI: 10.1002/cbic.201000646] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/01/2010] [Indexed: 01/13/2023]
Affiliation(s)
- Michaela Aigner
- Institute of Organic Chemistry, Center for Molecular Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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88
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Ehrenschwender T, Varga BR, Kele P, Wagenknecht HA. New far-red and near-infrared fluorescent probes with large Stokes shifts for dual covalent labeling of DNA. Chem Asian J 2010; 5:1761-4. [PMID: 20589826 DOI: 10.1002/asia.201000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Thomas Ehrenschwender
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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89
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Shaikh KI, Madsen CS, Nielsen LJ, Jørgensen AS, Nielsen H, Petersen M, Nielsen P. Synthesis and Molecular Modelling of Double-Functionalised Nucleosides with Aromatic Moieties in the 5′-(S)-Position and Minor Groove Interactions in DNA Zipper Structures. Chemistry 2010; 16:12904-19. [DOI: 10.1002/chem.201001253] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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90
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Gutsmiedl K, Fazio D, Carell T. High-density DNA functionalization by a combination of Cu-catalyzed and cu-free click chemistry. Chemistry 2010; 16:6877-83. [PMID: 20458711 DOI: 10.1002/chem.201000363] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report the regioselective Cu-free click modification of styrene functionalized DNA with nitrile oxides. A series of modified oligodeoxynucleotides (nine base pairs) was prepared with increasing styrene density. 1,3-Dipolar cycloaddition with nitrile oxides allows the high density functionalization of the styrene modified DNA directly on the DNA solid support and in solution. This click reaction proceeds smoothly even directly in the DNA synthesizer and gives exclusively 3,5-disubstituted isoxazolines. Additionally, PCR products (300 and 900 base pairs) were synthesized with a styrene triphosphate and KOD XL polymerase. The click reaction on the highly modified PCR fragments allows functionalization of hundreds of styrene units on these large DNA fragments simultaneously. Even sequential Cu-free and Cu-catalyzed click reaction of PCR amplicons containing styrene and alkyne carrying nucleobases was achieved. This new approach towards high-density functionalization of DNA is simple, modular, and efficient.
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Affiliation(s)
- Katrin Gutsmiedl
- Department of Chemistry, Center for Integrated Protein Science (CiPSM), Butenandtstrasse 5-13, 81377 Munich, Germany
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91
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Steger J, Graber D, Moroder H, Geiermann AS, Aigner M, Micura R. Efficient Access to Nonhydrolyzable Initiator tRNA Based on the Synthesis of 3′-Azido-3′-Deoxyadenosine RNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003424] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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92
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Steger J, Graber D, Moroder H, Geiermann AS, Aigner M, Micura R. Efficient Access to Nonhydrolyzable Initiator tRNA Based on the Synthesis of 3′-Azido-3′-Deoxyadenosine RNA. Angew Chem Int Ed Engl 2010; 49:7470-2. [DOI: 10.1002/anie.201003424] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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93
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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95
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Raindlová V, Pohl R, Šanda M, Hocek M. Direct Polymerase Synthesis of Reactive Aldehyde-Functionalized DNA and Its Conjugation and Staining with Hydrazines. Angew Chem Int Ed Engl 2010; 49:1064-6. [DOI: 10.1002/anie.200905556] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Raindlová V, Pohl R, Šanda M, Hocek M. Direct Polymerase Synthesis of Reactive Aldehyde-Functionalized DNA and Its Conjugation and Staining with Hydrazines. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905556] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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98
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903251] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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99
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009; 48:7362-5. [DOI: 10.1002/anie.200903251] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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100
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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