Strain-promoted Azide-alkyne Cycloaddition Research Articles

Chemically Intractable No More: In Vivo Incorporation of "Click"-Ready Fatty Acids into Poly-[(R)-3-hydroxyalkanoates] in Escherichia coli.

Poly-[(R)-3-hydroxyalkanoate] biopolymers, or PHAs, are biocompatible and biodegradable polyesters that can be produced by diverse microbial strains. PHA polymers have found widespread uses in applications ranging from sustainable replacements of nonbiodegradable bulk-commodity plastics to biomaterials. However, further expansion into other markets and industries has generally been limited by the inability to chemically modify these polymers. Recently, our lab engineered E. coli LSBJ, a microbial strain able to produce PHA copolymers with controlled unit compositions from simple and accessible fatty acid feedstocks. We envisioned meaningfully broadening the application spectrum of these materials via production of chemically tractable PHA biopolymers containing "click"-ready chemical functionalities. With a myriad of applications in mind, in this study we demonstrate the synthesis and biopolymerization of a panel of ω-azido fatty acids and take the first exploratory steps toward demonstrating their conjugation via a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. The convenience of accessing these materials will open the door to new applications for functionalized PHA polymers.

T-shaped and H-shaped polymers constructed from UV-induced strain promoted azide-alkyne cycloaddition reaction

Topological polymers with T-shaped and H-shaped molecular architecture were built on the combination of atom transfer radical polymerization (ATRP) and UV-induced strain promoted azide-alkyne cycloaddition (SPAAC) reaction. In the presence of a cyclopropenone-masked dibenzocyclooctyne functionalized dibromo ATRP initiator, reactive polystyrene (PS) was synthesized to have a cyclopropenone-masked dibenzocyclooctyne group in the middle of polymer chain. After releasing dibenzocyclooctyne from deprotecting cyclopropenone-masked dibenzocyclooctyne under UV irradiation, T-shaped and H-shaped topological polymers were constructed by reacting PS with mono-end and di-end azide functionalized poly(ethylene oxide) (PEO), respectively, based on the SPAAC reaction.

Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and is well-suited for the development of affordable multiplex protein assays, which provides the potential to accelerate proteomics research.

Cooperative capture synthesis: yet another playground for copper-free click chemistry.

Click chemistry describes a family of modular, efficient, versatile and reliable reactions which have acquired a pivotal role as one of the most useful synthetic tools with a potentially broad range of applications. While copper(i)-catalysed alkyne-azide cycloaddition is the most widely adopted click reaction in the family, the fact that it is cytotoxic restricts its practice in certain situations, e.g., bioconjugation. Consequently, researchers have been exploring the development of copper-free click reactions, the most popular example so far being strain-promoted alkyne-azide cycloadditions. An early example of copper-free click reactions that is rarely mentioned in the literature is the cucurbit[6]uril (CB6) catalysed alkyne-azide cycloaddition (CB-AAC). Despite the unique ability of CB-AAC to generate mechanically interlocked molecules (MIMs) - in particular, rotaxanes - its slow reaction rate and narrow substrate acceptance limit its scope. In this Tutorial Review, we describe our efforts of late in developing the fundamental principles and practical applications of a new copper-free click reaction - namely, cooperative capture synthesis, whereby introducing a cyclodextrin (CD) as an accelerator in CB-AAC, hydrogen bonding networks are formed between the rims of CD and CB6 in a manner that is positively cooperative, giving rise to a high level of pre-organisation during efficient and quick rotaxane formation. For example, [4]rotaxanes can be prepared nearly quantitatively within a minute in water. Furthermore, we have demonstrated that CB-AAC can accommodate a wider substrate tolerance by introducing pillararenes as promoters. To date, we have put cooperative capture synthesis into practice by (i) preparing polyrotaxanes containing up to 200 rings in nearly quantitative yields, (ii) trapping conformational isomers of polymacrocycles as rings in rotaxanes, (iii) demonstrating solid-state fluorescence and Förster resonance energy transfer (FRET) processes by fixing the fluorophores in a rotaxane and (iv) establishing the principle of supramolecular encryption in the preparation of dynamically and reversibly tunable fluorescent security inks.

Hydrolytically degradable, dendritic polyglycerol sulfate based injectable hydrogels using strain promoted azide–alkyne cycloaddition reaction

An anionic degradable hydrogel based on a heparin mimetic polymer was prepared using PEG-PCL-DIC as a crosslinker.

An injectable PEG-based hydrogel synthesized by strain-promoted alkyne–azide cycloaddition for use as an embolic agent

Cyclooctyne and azide functionalized PEGs are prepared by ring-opening polymerization. They form a biodegradable hydrogel in situ to temporarily block rabbit ear vessels.

Strain-promoted azide-alkyne cycloaddition for protein-protein coupling in the formation of a bis-hemoglobin as a copper-free oxygen carrier.

Conventional chemical approaches to protein-protein coupling present challenges due to the intrinsic competition between the desired interactions of reagents with groups of the protein as well as reactions with water. Biorthogonal Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC)-processes provide a basis to direct reactivity without functional group interference. However, the requirement for Cu(i) in CuAAC leads to complications that result from the metal ion's interactions with the protein. In principle, a similar but metal-free alternative approach to coupling could employ the reaction of an alkyne that is strained in combination with an azide (strain-promoted azide-alkyne cycloaddition, SPAAC). The method is exemplified by the combination of a cyclooctyne derivative of hemoglobin with an azide-modified hemoglobin. The bis-hemoglobin tetramer that is produced has properties consistent with those sought for use as a hemoglobin-based oxygen carrier (HBOC).

A simple method for enhancing the bioorthogonality of cyclooctyne reagent.

The cross-reactivity between some cyclooctynes and thiols limits the bioorthogonality of the strain-promoted azide-alkyne cycloaddition reaction. We show that a low concentration of β-mercaptoethanol significantly reduces the undesirable side reaction between bicyclononyne (BCN) and cysteine and while preserving free cysteines. We site-specifically label a genetically-encoded azido group in the visual photoreceptor rhodopsin to demonstrate the utility of the strategy.

Cycloadditions for Studying Nucleic Acids.

Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.

Click Functionalization of a Dibenzocyclooctyne-Containing Conjugated Polyimine.

A conjugated poly(phenyl-co-dibenzocyclooctyne) Schiff-base polymer, prepared through polycondensation of dibenzocyclooctyne bisamine (DIBO-(NH2)2) with bis(hexadecyloxy)phenyldialdehyde, is reported. The resulting polymer, which has a high molecular weight (M(n)>30 kDa, M(w)>60 kDa), undergoes efficient strain-promoted alkyne-azide cycloaddition reactions with a series of azides. This enables quantitative modification of each repeat unit within the polymer backbone and the rapid synthesis of a conjugated polymer library with widely different substituents but a consistent degree of polymerization (DP). Kinetic studies show a second-order reaction rate constant that is consistent with monomeric dibenzocyclooctynes. Grafting with azide-terminated polystyrene and polyethylene glycol monomethyl ether chains of varying molecular weight resulted in the efficient syntheses of a series of graft copolymers with a conjugated backbone and maximal graft density.

High-Density PEO-b-DNA Brushes on Polymer Particles for Colloidal Superstructures

We demonstrate a method to create high-density DNA coatings on colloidal particles that can be used for DNA-mediated self-assembly of single- and multiple-component colloidal crystals. First, we modify an amphiphilic diblock copolymer consisting of a hydrophobic polystyrene (PS) block and a hydrophilic poly(ethylene oxide) (PEO) block with azide functional groups at the end (poly(ethylene oxide)-N3). Then, we introduce the diblock copolymers into an aqueous suspension of colloidal polymer particles swollen with a solvent. The hydrophobic PS anchoring block is incorporated into the swollen polymer spheres and physically trapped when the solvent is removed, resulting in a dense PEO polymer brush with azide functional end groups. Finally, single-stranded DNA strands with sticky ends are attached to the azide groups using strain-promoted azide–alkyne cycloaddition (SPAAC, a copper-free click chemistry). This procedure results in a high areal coverage of up to 225 000 DNA strands on 1-μm-diameter particles. Th...

Synthesis and In Vivo PET Imaging of Hyaluronan Conjugates of Oligonucleotides.

Synthesis for (68)Ga-labeled 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA)-chelated oligonucleotide hyaluronan (HA) tetra- and hexasaccharide conjugates is described. A solid-supported technique is used to introduce NOTA-chelator into the 3'-terminus of oligonucleotides and a copper-free strain promoted azide alkyne cycloaddition (SPAAC) to HA/oligonucleotide conjugation. Protecting group manipulation, required for the HA-moieties, is carried out after the SPAAC-conjugation. Positron emission tomography (PET) is used (1) in the whole-body distribution kinetic studies of the conjugates in healthy rats and (2) to show the potential of hyaluronan-induced targeting of oligonucleotides into the infarcted area of rats with myocardial infarction.

Labeling of Enveloped Virus via Metabolic Incorporation of Azido Sugars.

Modification of an enveloped measles virus was achieved by metabolic incorporation of azido sugars in host cells through the protein glycosylation process. Based on this, the resulting measles virus particles could be modified with azido groups on the surface glycoproteins, which could be further labeled with fluorescence dyes using a strain-promoted azide-alkyne cycloaddition reaction. We envision this metabolic labeling approach to be applicable to a wide variety of enveloped viruses, allowing the facile conjugation and surface modification.

Systematic Evaluation of Bioorthogonal Reactions in Live Cells with Clickable HaloTag Ligands: Implications for Intracellular Imaging.

Bioorthogonal reactions, including the strain-promoted azide–alkyne cycloaddition (SPAAC) and inverse electron demand Diels–Alder (iEDDA) reactions, have become increasingly popular for live-cell imaging applications. However, the stability and reactivity of reagents has never been systematically explored in the context of a living cell. Here we report a universal, organelle-targetable system based on HaloTag protein technology for directly comparing bioorthogonal reagent reactivity, specificity, and stability using clickable HaloTag ligands in various subcellular compartments. This system enabled a detailed comparison of the bioorthogonal reactions in live cells and informed the selection of optimal reagents and conditions for live-cell imaging studies. We found that the reaction of sTCO with monosubstituted tetrazines is the fastest reaction in cells; however, both reagents have stability issues. To address this, we introduced a new variant of sTCO, Ag-sTCO, which has much improved stability and can be used directly in cells for rapid bioorthogonal reactions with tetrazines. Utilization of Ag complexes of conformationally strained trans-cyclooctenes should greatly expand their usefulness especially when paired with less reactive, more stable tetrazines.

Synthetic Strategies Toward DNA-Coated Colloids that Crystallize.

We report on synthetic strategies to fabricate DNA-coated micrometer-sized colloids that, upon thermal annealing, self-assemble into various crystal structures. Colloids of a wide range of chemical compositions, including poly(styrene), poly(methyl methacrylate), titania, silica, and a silica-methacrylate hybrid material, are fabricated with smooth particle surfaces and a dense layer of surface functional anchors. Single-stranded oligonucleotides with a short sticky end are covalently grafted onto particle surfaces employing a strain-promoted alkyne-azide cycloaddition reaction resulting in DNA coatings with areal densities an order of magnitude higher than previously reported. Our approach allows the DNA-coated colloids not only to aggregate upon cooling but also to anneal and rearrange while still bound together, leading to the formation of colloidal crystal compounds when particles of different sizes or different materials are combined.

ChemInform Abstract: Hyperbranched Polymers: Advances from Synthesis to Applications

AbstractReview: 347 refs.

Branched Polyhedral Oligomeric Silsesquioxane Nanoparticles Prepared via Strain-Promoted 1,3-Dipolar Cycloadditions.

Conjugation of small organic molecules and polymers to polyhedral oligosilsesquioxane (POSS) cores results in novel hybrid materials with unique physical characteristics. We report here an approach in which star-shaped organic-inorganic scaffolds bearing eight cyclooctyne moieties can be rapidly functionalized via strain-promoted azide-alkyne cycloaddition (SPAAC) to synthesize a series of nearly monodisperse branched core-shell nanoparticles with hydrophobic POSS cores and hydrophilic arms. We established that SPAAC is a robust method for POSS core octafunctionalization with the reaction rate constant of 1.9 × 10(-2) M(-1) s(-1). Functionalization with poly(ethylene glycol) (PEG) azide, fluorescein azide, and unprotected lactose azide gave conjugates which represent different classes of compounds: polymer conjugates, fluorescent dots, and bioconjugates. These resulting hybrid compounds were preliminarily tested for their ability to self-assemble in solution and at the air-water interface. We observed the formation of robust smooth Langmuir monolayers with diverse morphologies. We found that polar lactose moieties are completely submerged into the subphase whereas the relatively hydrophobic fluorescein arms had extended conformation at the interface, and PEG arms were partially submerged. Finally, we observed the formation of stable micelles with sizes between 70 and 160 nm in aqueous solutions with size and morphology of the structures dependent on the molecular weight and the type of the peripheral hydrophilic moieties.

Photodegradable Gelatin-Based Hydrogels Prepared by Bioorthogonal Click Chemistry for Cell Encapsulation and Release.

In this study, we present a method for the fabrication of in situ forming gelatin and poly(ethylene glycol)-based hydrogels utilizing bioorthogonal, strain-promoted alkyne-azide cycloaddition as the cross-linking reaction. By incorporating nitrobenzyl moieties within the network structure, these hydrogels can be designed to be degradable upon irradiation with low intensity UV light, allowing precise photopatterning. Fibroblast cells encapsulated within these hydrogels were viable at 14 days and could be readily harvested using a light trigger. Potential applications of this new class of injectable hydrogel include its use as a 3D culturing platform that allows the capture and release of cells, as well as light-triggered cell delivery in regenerative medicine.

Accelerating Strain-Promoted Azide–Alkyne Cycloaddition Using Micellar Catalysis

Bioorthogonal conjugation reactions such as strain-promoted azide-alkyne cycloaddition (SPAAC) have become increasingly popular in recent years, as they enable site-specific labeling of complex biomolecules. However, despite a number of improvements to cyclooctyne design, reaction rates for SPAAC remain significantly lower than those of the related copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Here we explore micellar catalysis as a means to increase reaction rate between a cyclooctyne and hydrophobic azide. We find that anionic and cationic surfactants provide the most efficient catalysis, with rate enhancements of up to 179-fold for reaction of benzyl azide with DIBAC cyclooctyne. Additionally, we find that the presence of surfactant can provide up to 51-fold selectivity for reaction with a hydrophobic over hydrophilic azide. A more modest, but still substantial, 11-fold rate enhancement is observed for micellar catalysis of the reaction between benzyl azide and a DIBAC-functionalized DNA sequence, demonstrating that micellar catalysis can be successfully applied to hydrophilic biomolecules. Together, these results demonstrate that micellar catalysis can provide higher conjugation yields in reduced time when using hydrophobic SPAAC reagents.

Bioorthogonal Labeling, Bioimaging, and Photocytotoxicity Studies of Phosphorescent Ruthenium(II) Polypyridine Dibenzocyclooctyne Complexes.

The synthesis, characterization, photophysics, lipophilicity, and cellular properties of new phosphorescent ruthenium(II) polypyridine complexes functionalized with a dibenzocyclooctyne (DIBO) or amine moiety [Ru(N^N)2 (L)](PF6 )2 are reported (L=4-(13-N-(3,4:7,8-dibenzocyclooctyne-5-oxycarbonyl) amino-4,7,10-trioxa-tridecanyl-aminocarbonyl-oxy-methyl)-4'-methyl-2,2'-bipyridine bpy-DIBO, N^N=2,2'-bipyridine bpy (1 a), 1,10-phenanthroline phen (2 a); L=4-(13-amino-4,7,10-trioxa-tridecanylaminocarbonyl-oxy-methyl)-4'-methyl-2,2'-bipyridine bpy-NH2 , N^N=bpy (1 b), phen (2 b)). The strain-promoted alkyne-azide cycloaddition (SPAAC) reaction of the DIBO complexes 1 a and 2 a with benzyl azide were studied. Also, the DIBO complexes 1 a and 2 a can selectively label N-azidoglycans located on the surface of CHO-K1 and A549 cells that were pretreated with 1,3,4,6-tetra-O-acetyl-N-azidoacetyl-D-mannosamine (Ac4 ManNAz). Additionally, the intracellular trafficking and localization of these biomolecules were monitored using laser-scanning confocal microscopy. Interestingly, the biolabeling and cellular uptake efficiency of the DIBO complexes 1 a and 2 a were cell-line dependent, as revealed by flow cytometry and ICP-MS. Furthermore, the complexes showed good biocompatibility toward the Ac4 ManNAz-pretreated cells in the dark, but exhibited photoinduced cytotoxicity due to the generation of singlet oxygen.