Genetic Encoding of a Bicyclo[6.1.0]nonyne‐Charged Amino Acid Enables Fast Cellular Protein Imaging by Metal‐Free Ligation

Borrmann, Annika; Milles, Sigrid; Plass, Tilman; Dommerholt, Jan; Verkade, Jorge M. M.; Wießler, Manfred; Schultz, Carsten; Hest, Jan C. M. van; Delft, Floris L. van; Lemke, Edward A.

doi:10.1002/cbic.201200407

Cited by 163 publications

(149 citation statements)

References 53 publications

(34 reference statements)

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“…This is in line with the fact that BCN undergoes extremely fast IED DielsAlder cycloaddition with 1,2,4,5-tetrazines 20,30,33 , while DIBAC is inert 31 . Fig.…”

Section: Resultssupporting

confidence: 81%

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

Rooijen²,

et al. 2014

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Strain-promoted azide-alkyne cycloaddition (SPAAC) as a conjugation tool has found broad application in material sciences, chemical biology and even in vivo use. However, despite tremendous effort, SPAAC remains fairly slow (0.2-0.5 M À 1 s À 1 ) and efforts to increase reaction rates by tailoring of cyclooctyne structure have suffered from a poor trade-off between cyclooctyne reactivity and stability. We here wish to report tremendous acceleration of strain-promoted cycloaddition of an aliphatic cyclooctyne (bicyclo[6.1.0]non-4-yne, BCN) with electron-deficient aryl azides, with reaction rate constants reaching 2.0-2.9 M À 1 s À 1 . A remarkable difference in rate constants of aliphatic cyclooctynes versus benzoannulated cyclooctynes is noted, enabling a next level of orthogonality by a judicious choice of azidecyclooctyne combinations, which is inter alia applied in one-pot three-component protein labelling. The pivotal role of azide electronegativity is explained by density-functional theory calculations and electronic-structure analyses, which indicates an inverse electron-demand mechanism is operative with an aliphatic cyclooctyne.

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“…This is in line with the fact that BCN undergoes extremely fast IED DielsAlder cycloaddition with 1,2,4,5-tetrazines 20,30,33 , while DIBAC is inert 31 . Fig.…”

Section: Resultssupporting

confidence: 81%

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

Rooijen²,

et al. 2014

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“…For example, Table 1 above displays the reaction rate constants of the known cyclooctynes across these solvents, which in fact makes it difficult to truly compare the usefulness of these probes in a quantifiable manner. Furthermore, it has been noted by several authors that SPAAC proceeds (significantly) faster in more aqueous solvent systems [9,19,24,40,60].…”

Section: Solvent Effectsmentioning

confidence: 99%

“…2) cycloadditions with electron-poor tetrazines [3]. The latter process can be tailored to specific reaction rates with electron-rich cyclooctynes like BCN in organic solvents [15] and was found to proceed at a surprisingly high reaction rates [1000 M -1 s -1 under aqueous conditions when applied for protein labeling [9,34]. We most recently showed that (4 ?…”

Section: Concluding Remarks and Future Prospectsmentioning

confidence: 99%

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides

Dommerholt

Rutjes

Delft

2016

Cycloadditions in Bioorthogonal Chemistry

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A nearly forgotten reaction discovered more than 60 years ago-the cycloaddition of a cyclic alkyne and an organic azide, leading to an aromatic triazole-enjoys a remarkable popularity. Originally discovered out of pure chemical curiosity, and dusted off early this century as an efficient and clean bioconjugation tool, the usefulness of cyclooctyne-azide cycloaddition is now adopted in a wide range of fields of chemical science and beyond. Its ease of operation, broad solvent compatibility, 100 % atom efficiency, and the high stability of the resulting triazole product, just to name a few aspects, have catapulted this so-called strain-promoted azide-alkyne cycloaddition (SPAAC) right into the top-shelf of the toolbox of chemical biologists, material scientists, biotechnologists, medicinal chemists, and more. In this chapter, a brief historic overview of cycloalkynes is provided first, along with the main synthetic strategies to prepare cycloalkynes and their chemical reactivities. Core aspects of the strain-promoted reaction of cycloalkynes with azides are covered, as well as tools to achieve further reaction acceleration by means of modulation of cycloalkyne structure, nature of azide, and choice of solvent.

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“…In a broader context, we have demonstrated the unique combination of reaction efficiency and selectivity of cyclooctyne-based chemistry for the conjugation of sensitive (bio)molecules in aqueous systems, which may be readily extended toward the conjugation of BCN-oligonucleotides to azidecontaining solid surfaces, polymers and large proteins. Finally, we [39] and others [40,41] recently demonstrated that cycloadditions of BCN is not limited to azides, but BCN also undergoes extremely fast strain-promoted inverse-electron-demand Diels-Alder cycloaddition (SPIEDAC) with tetrazines. In contrast, benzofused cyclooctynes DBCO and DIBO are inreactive towards tetrazine [42], which further lifts the potential of BCN-modified oligonucleotides for fast and selective bioconjugations, potentially also in vivo [43].…”

Section: Discussionmentioning

confidence: 90%

Oligonucleotide Tagging for Copper-Free Click Conjugation

Jawalekar

Malik

Verkade³

et al. 2013

Molecules

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Abstract:Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN) into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.

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Genetic Encoding of a Bicyclo[6.1.0]nonyne‐Charged Amino Acid Enables Fast Cellular Protein Imaging by Metal‐Free Ligation

Cited by 163 publications

References 53 publications

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides

Oligonucleotide Tagging for Copper-Free Click Conjugation

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