Bioorthogonal chemistry

Scinto, Samuel L.; Bilodeau, Didier A.; Hincapie, Robert; Lee, Wan-Kyu; Nguyen, Sean S; Xu, Minghao; Ende, Christopher W. am; Finn, M. G.; Lang, Kathrin; Lin, Qing; Pezacki, John Paul; Prescher, Jennifer A.; Robillard, Marc S.; Fox, Joseph M.

doi:10.1038/s43586-021-00028-z

Cited by 229 publications

(223 citation statements)

References 406 publications

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“…[134] Other than using supramolecular interactions, bio-orthogonal chemistry has also emerged as a promising new approach in the biomedical field. [135] The chemistry involved in such reactions avoids the essential biologically active groups, thereby preserving the bioactivity of the materials under consideration. Bio-orthogonal chemistry should be implemented for preparing light-responsive nanocomposite hydrogels to maintain the bioactivity of both the NPs and the polymers.…”

Section: Emerging Approaches and Outlookmentioning

confidence: 99%

Contact‐Free Remote Manipulation of Hydrogel Properties Using Light‐Triggerable Nanoparticles: A Materials Science Perspective for Biomedical Applications

Choi

Chakraborty

Coyle

et al. 2022

Adv Healthcare Materials

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Considerable progress has been made in synthesizing "intelligent", biodegradable hydrogels that undergo rapid changes in physicochemical properties once exposed to external stimuli. These advantageous properties of stimulus-triggered materials make them highly appealing to diverse biomedical applications. Of late, research on the incorporation of light-triggered nanoparticles (NPs) into polymeric hydrogel networks has gained momentum due to their ability to remotely tune hydrogel properties using facile, contact-free approaches, such as adjustment of wavelength and intensity of light source. These multi-functional NPs, in combination with tissue-mimicking hydrogels, are increasingly being used for on-demand drug release, preparing diagnostic kits, and fabricating smart scaffolds. Here, the authors discuss the atomic behavior of different NPs in the presence of light, and critically review the mechanisms by which NPs convert light stimuli into heat energy. Then, they explain how these NPs impact the mechanical properties and rheological behavior of NPs-impregnated hydrogels. Understanding the rheological behavior of nanocomposite hydrogels using different sophisticated strategies, including computer-assisted machine learning, is critical for designing the next generation of drug delivery systems. Next, they highlight the salient strategies that have been used to apply light-induced nanocomposites for diverse biomedical applications and provide an outlook for the further improvement of these NPs-driven light-responsive hydrogels.

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Section: Emerging Approaches and Outlookmentioning

confidence: 99%

Contact‐Free Remote Manipulation of Hydrogel Properties Using Light‐Triggerable Nanoparticles: A Materials Science Perspective for Biomedical Applications

Choi

Chakraborty

Coyle

et al. 2022

Adv Healthcare Materials

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“…3iii ) opens near endless possibilities to site-specifically introduce a desired bio-orthogonal binding capacity. While, traditionally, the highest stability and irreversible coupling was usually pursued [61], DyeCycling asks for the opposite: reversible binding with specific kinetics. Ideally, short dye linkers could be introduced to improve the distance resolution in FRET space [62].…”

Section: Breaking the Photobleaching Limit In Time-resolved Smfret Wi...mentioning

confidence: 99%

Can DyeCycling break the photobleaching limit in single-molecule FRET?

Vermeer

Schmid

2022

Preprint

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Biomolecular systems, such as proteins, crucially rely on dynamic processes at the nanoscale. Detecting biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that control biomolecular systems. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique to observe in real-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural states. Currently, this technique is fundamentally limited by irreversible photobleaching, causing the untimely end of the experiment and thus, a prohibitively narrow temporal bandwidth of ≤ 3 orders of magnitude. Here, we introduce ″DyeCycling″, a measurement scheme with which we aim to break the photobleaching limit in single-molecule FRET. We introduce the concept of spontaneous dye replacement by simulations, and as an experimental proof-of-concept, we demonstrate the intermittent observation of a single biomolecule for one hour with a time resolution of milliseconds. Theoretically, DyeCycling can provide >100-fold more information per single molecule than conventional smFRET. We discuss the experimental implementation of DyeCycling, its current and fundamental limitations, and specific biological use cases. Given its general simplicity and versatility, DyeCycling has the potential to revolutionize the field of time-resolved smFRET, where it may serve to unravel a wealth of biomolecular dynamics by bridging from milliseconds to the hour range.

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“…Yield: 2.16 g (54%); orange powder; R f 0.52 (hexane-EtOAc, 1:1 v/v); R f 0.18 (hexane-EtOAc, 3:1 v/v). 1 H NMR (CDCl 3 , 500 MHz):  = 10.14 (s, 1 H), 8.26 (s, 1 H), 7.41 (d, J = 9.0 Hz, 1 H), 6.64 (dd, J = 9.0, 2.5 Hz, 1 H), 6.49 (d, J = 2.5 Hz, 1 H), 3.48 (q, J = 7.2 Hz, 4 H), 1.26 (t, J = 7.2 Hz, 6 H).…”

Section: -(Diethylamino)coumarin-3-carbaldehyde (17)mentioning

confidence: 99%

“…Yield: 115 mg (47%); off-white sticky solid; R f 0.57 (hexane-EtOAc, 3:1 v/v). 1 H NMR (CDCl 3 , 500 MHz):  = 7.53 (s, 1 H), 7.22 (d,J = 8.8 Hz,1 H),6.64 (dd,J = 17.6,11.3 Hz,1 H),6.54 (dd,J = 8.8,2.5 Hz,1 H),6.44 (d,J = 2.5 Hz,1 H),5.99 (dd,J = 17.6,1.3 Hz,1 H),5.26 (dd,J = 11.3,1.3 Hz, 1 H), 3.37 (q, J = 7.1 Hz, 4 H), 1.17 (t, J = 7.1 Hz, 6 H). 13 C NMR (CDCl 3 , 126 MHz):  = 161.…”

Section: -(Diethylamino)-3-vinyl-coumarin (18)mentioning

confidence: 99%

“…Literature examples describe related reactions of 2-pyrones with electron-deficient alkynes that required long reaction times at higher temperatures; 9 however, no studies under physiological conditions are reported. Therefore, we first set up a pilot experiment using commercially available methyl coumalate (1) with strained cyclooctyne BCN (Scheme 1) in aqueous solution at room temperature. We chose BCN as suitable dienophile because it produces an aromatic system (i.e., a substituted benzene ring) upon IEDDA reaction.…”

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confidence: 99%

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Beyond the Bioorthogonal Inverse-Electron-Demand Diels–Alder Reactions of Tetrazines: 2-Pyrone-Functionalized Fluorogenic Probes

et al. 2022

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The applicability of pyrones as bioorthogonal platform was explored in inverse electron demand Diels-Alder reactions with a strained cyclooctyne. Studies showed that the pyrones are indeed suitable for IEDDA reactions under physiological conditions. Furthermore, the stable pyrone moiety could be utilized to construct easily accessible fluorogenic probes. Mutual orthogonality of the IEDDA reaction of 2-pyrones with SPAAC reactions of azides was also explored.

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Bioorthogonal chemistry

Cited by 229 publications

References 406 publications

Contact‐Free Remote Manipulation of Hydrogel Properties Using Light‐Triggerable Nanoparticles: A Materials Science Perspective for Biomedical Applications

Contact‐Free Remote Manipulation of Hydrogel Properties Using Light‐Triggerable Nanoparticles: A Materials Science Perspective for Biomedical Applications

Can DyeCycling break the photobleaching limit in single-molecule FRET?

Beyond the Bioorthogonal Inverse-Electron-Demand Diels–Alder Reactions of Tetrazines: 2-Pyrone-Functionalized Fluorogenic Probes

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