Chemists figure out a way to force apart click chemistry bonds

 Normally when chemists think of methods to urge chemical reactions, brute force is not really very high on the list; while such techniques might be useful for breaking apart materials, i.e. bashing cement to get smaller pieces of cement; it’s generally not been a useful way to tear apart the molecules that actually comprise the compound itself. At least till now. Christopher Bielawski and colleagues at the University of Texas, as described in their paper in Science, have figured out a way to unbind triazole to get back its original components azide and alkyne, using nothing but force.

Triazole is a ring shaped chemical compound that is formed during the reaction that occurs between azide and alkyne when mixed with copper. Its formation is considered to be a type of “click” or snap-together chemistry reaction due to the fact that the components click together in a very tight formation; sort of like wooden floor panels that click together to keep from sliding apart under constant abuse from foot traffic. Such bonds once formed have traditionally been very difficult to force apart, even under intense heat. Now however, Bielawski and his team have figured out a way to do it using brute force.

To pull the components of triazole apart, the team attached polymer chains to either side of the individual molecules, then immersed them in a solution and applied ultrasound. Doing so caused tiny bubbles to form of a certain size that soon collapsed, leaving a vacuum behind. The vacuum force then pulled the components of the molecule apart by yanking on the polymer chains. The end result is azide and alkyne, the original components in their original forms.

The experiment is the first of its kind, showing that such compounds can be torn apart by force, opening the door to all kinds of other possibilities where researchers wish to be able to take compounds apart piece by piece without impacting anything else in the surrounding environment.

In their paper the team points out that such types of forced reactions might already be taking place in nature leading to failures of materials in previously unexplainable ways; or worse in pharmaceuticals that break down in the body leading to perhaps dangerous consequences.

Looking towards the future, this new method of tearing apart chemical bonds might lead to new types of sensors that can detect stress or be used as a type of “bodyguard” for other compounds that can be taken apart and removed when its usefulness has run its course.

More information: Unclicking the Click: Mechanically Facilitated 1,3-Dipolar Cycloreversions, Science 16 September 2011: Vol. 333 no. 6049 pp. 1606-1609. DOI: 10.1126/science.1207934

ABSTRACT
The specific targeting of covalent bonds in a local, anisotropic fashion using mechanical methods offers useful opportunities to direct chemical reactivity down otherwise prohibitive pathways. Here, we report that embedding the highly inert 1,2,3-triazole moiety (which is often prepared using the canonical “click” coupling of azides and alkynes) within a poly(methyl acrylate) chain renders it susceptible to ultrasound-induced cycloreversion, as confirmed by comprehensive spectroscopic and chemical analyses. Such reactivity offers the opportunity to develop triazoles as mechanically labile protecting groups or for use in readily accessible materials that respond to mechanical force.

 

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Click chemistry with copper -- a biocompatible version

Berkeley Lab researchers have found a way to make copper-catalyzed click chemistry biocompatible. By adding a ligand that minimizes the toxicity of copper but still allows it to catalyze the click chemistry reaction, the researchers can safely use their reaction in living cells.

Biomolecular imaging can reveal a great deal of information about the inner workings of cells and one of the most attractive targets for imaging are glycans – sugars that are ubiquitous to living organisms and abundant on cell surfaces. Imaging a glycan requires that it be tagged or labeled. One of the best techniques for doing this is a technique called click chemistry. The original version of click chemistry could only be used on cells in vitro, not in living organisms, because the technique involved catalysis with copper, which is toxic at high micromolar concentrations. A copper-free version of click chemistry that can safely be used in living organisms is available, but it is not always optimal in terms of reaction kinetics and target specificity. Now, a variation of click chemistry has been introduced that retains the copper catalyst of the original reaction - along with its speed and specificity – but is safe for cells in vivo.

Researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab), in collaboration with researchers at the Albert Einstein College of Medicine at Yeshiva University in New York, have found a way to make copper-catalyzed click chemistry biocompatible. By adding a ligand that minimizes the toxicity of copper but still allows it to catalyze the click chemistry reaction, the researchers can safely use their reaction in living organisms. Compared to the copper-free click chemistry reaction, which can take up to an hour, the ligand-accelerated copper-catalyzed click chemistry reaction can achieve effective labeling within 3-5 minutes. The presence of the copper catalyst also enables this new formulation of click chemistry to be more target-specific with fewer background side reactions.

"The discovery of this new accelerating ligand for copper-catalyzed click chemistry should provide an effective complimentary tool to copper-free click chemistry," says Yi Liu, a chemist with Berkeley Lab's Molecular Foundry and the co-leader of this research with Peng Wu, of the Albert Einstein College of Medicine.

"While copper-free click chemistry may have advantages for whole animal imaging experiments such as imaging in mice," Liu says, "our ligand-accelerated copper reaction is better suited for enriching glycoproteins for their identification."

The ligand-accelerated copper-catalyzed reaction was used to label glycans in recombinant glycoproteins, glycoproteins in cell lysates, glycoproteins on live cell surfaces, and glycoconjugates in live zebrafish embryos. Because a zebrafish embryo is transparent in the first 24 hours of its development, it allows labeled glycans to be detected via molecular imaging techniques, making it a highly useful model for developmental biology studies.

"Based on our results," says Peng Wu, "we believe that ligand-accelerated copper-catalyzed click chemistry represents a powerful and highly adaptive bioconjugation tool that holds great promise for further improvement with the discovery of more versatile catalyst systems."

Click chemistry, which was introduced in 2002 by the Nobel laureate chemist Barry Sharpless of the Scripps Research Institute, utilizes a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction that makes it possible for certain chemical building blocks to "click" together in an irreversible linkage, analogous to the snapping together of Lego blocks. While the technique immediately proved valuable for attaching small molecular probes to various biomolecules in a test tube or on fixed cells, it could not be used for biomolecule labeling in live cells or organisms because of the copper catalyst.

In 2007, Carolyn Bertozzi, a chemist who holds joint appointments with Berkeley Lab, the University of California (UC) Berkeley, and the Howard Hughes Medical Institute, led a research effort that produced a copper-free version of click chemistry. In this version, glycans were metabolically labeled with azides - a functional group featuring three nitrogen atoms - via reactions that were carried out through the use of cyclooctyne reagents that required no copper catalyst. With their latest reagent, biarylazacyclooctynone (BARAC), Bertozzi and her group have provided a copper-free click chemistry technique that delivers relatively fast reaction kinetics and the bioorthogonality needed for biomolecule labeling. However, the technique can only be used on biomolecules that can be tagged with azides.

"Our bio-benign ligand-accelerated copper-catalyzed click chemistry reaction liberates bioconjugation from the limitation where ligations could only be accomplished with azide-tagged biomolecules," Liu says. "Now terminal alkyne residues can also be incorporated into biomolecules and detected in vivo."

Provided by Lawrence Berkeley National Laboratory (news : web)

Click chemistry with copper: A biocompatible version

Biomolecular imaging can reveal a great deal of information about the inner workings of cells and one of the most attractive targets for imaging are glycans -- sugars that are ubiquitous to living organisms and abundant on cell surfaces. Imaging a glycan requires that it be tagged or labeled. One of the best techniques for doing this is a technique called click chemistry. The original version of click chemistry could only be used on cells in vitro, not in living organisms, because the technique involved catalysis with copper, which is toxic at high micromolar concentrations.

A copper-free version of click chemistry that can safely be used in living organisms is available, but it is not always optimal in terms of reaction kinetics and target specificity. Now, a variation of click chemistry has been introduced that retains the copper catalyst of the original reaction -- along with its speed and specificity -- but is safe for cells in vivo.

Researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab), in collaboration with researchers at the Albert Einstein College of Medicine at Yeshiva University in New York, have found a way to make copper-catalyzed click chemistry biocompatible. By adding a ligand that minimizes the toxicity of copper but still allows it to catalyze the click chemistry reaction, the researchers can safely use their reaction in living organisms. Compared to the copper-free click chemistry reaction, which can take up to an hour, the ligand-accelerated copper-catalyzed click chemistry reaction can achieve effective labeling within 3-5 minutes. The presence of the copper catalyst also enables this new formulation of click chemistry to be more target-specific with fewer background side reactions.

"The discovery of this new accelerating ligand for copper-catalyzed click chemistry should provide an effective complimentary tool to copper-free click chemistry," says Yi Liu, a chemist with Berkeley Lab's Molecular Foundry and the co-leader of this research with Peng Wu, of the Albert Einstein College of Medicine.

"While copper-free click chemistry may have advantages for whole animal imaging experiments such as imaging in mice," Liu says, "our ligand-accelerated copper reaction is better suited for enriching glycoproteins for their identification."

The ligand-accelerated copper-catalyzed reaction was used to label glycans in recombinant glycoproteins, glycoproteins in cell lysates, glycoproteins on live cell surfaces, and glycoconjugates in live zebrafish embryos. Because a zebrafish embryo is transparent in the first 24 hours of its development, it allows labeled glycans to be detected via molecular imaging techniques, making it a highly useful model for developmental biology studies.

"Based on our results," says Peng Wu, "we believe that ligand-accelerated copper-catalyzed click chemistry represents a powerful and highly adaptive bioconjugation tool that holds great promise for further improvement with the discovery of more versatile catalyst systems."

Click chemistry, which was introduced in 2002 by the Nobel laureate chemist Barry Sharpless of the Scripps Research Institute, utilizes a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction that makes it possible for certain chemical building blocks to "click" together in an irreversible linkage, analogous to the snapping together of Lego blocks. While the technique immediately proved valuable for attaching small molecular probes to various biomolecules in a test tube or on fixed cells, it could not be used for biomolecule labeling in live cells or organisms because of the copper catalyst.

In 2007, Carolyn Bertozzi, a chemist who holds joint appointments with Berkeley Lab, the University of California (UC) Berkeley, and the Howard Hughes Medical Institute, led a research effort that produced a copper-free version of click chemistry. In this version, glycans were metabolically labeled with azides -- a functional group featuring three nitrogen atoms -- via reactions that were carried out through the use of cyclooctyne reagents that required no copper catalyst. With their latest reagent, biarylazacyclooctynone (BARAC), Bertozzi and her group have provided a copper-free click chemistry technique that delivers relatively fast reaction kinetics and the bioorthogonality needed for biomolecule labeling. However, the technique can only be used on biomolecules that can be tagged with azides.

"Our bio-benign ligand-accelerated copper-catalyzed click chemistry reaction liberates bioconjugation from the limitation where ligations could only be accomplished with azide-tagged biomolecules," Liu says. "Now terminal alkyne residues can also be incorporated into biomolecules and detected in vivo."

This work was supported by a grant from the National Institutes of Health, and in part as a User Project at the Molecular Foundry, which is funded through DOE's Office of Science.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by DOE/Lawrence Berkeley National Laboratory.

Journal Reference:

Christen Besanceney-Webler, Hao Jiang, Tianqing Zheng, Lei Feng, David Soriano del Amo, Wei Wang, Liana M. Klivansky, Florence L. Marlow, Yi Liu, Peng Wu. Increasing the Efficacy of Bioorthogonal Click Reactions for Bioconjugation: A Comparative Study. Angewandte Chemie International Edition, 2011; DOI: 10.1002/anie.201101817

Click chemistry creates new 'stealth' DNA links

Scientists at the University of Southampton have pioneered a chemical method of linking DNA strands that is tolerated by living organisms.

The researchers have developed an artificial DNA "stealth" linkage using click chemistry, a highly-efficient chemical reaction, to join together DNA strands without disrupting the genetic code.

The breakthrough, published online in the journal PNAS this week (27 June), means long sections of DNA can be created quickly and efficiently by chemical methods.

DNA strands are widely used in biological and medical research, and clean and effective methods of making longer sections are of great value. Current techniques rely on the use of enzymes as biological catalysts. Joining DNA chemically is particularly interesting as it does not depend on enzymes so can be carried out on a large scale under a variety of conditions.

Co-author of the paper Tom Brown, Professor of Chemical Biology at the University of Southampton, says: "We believe this is the first example of a chemical method of joining together longer strands of DNA that works well.

"Typically, synthesised DNA strands will be up to 150 bases; beyond that they are very difficult to make. We have doubled that to 300 and we can go further. We can also join together heavily modified DNA strands, used in medical research for example, which normal enzymes might not want to couple together."

The Southampton team investigated whether the artificial links would be tolerated biologically within the bacteria E.coli.

"The genetic code could still be correctly read," says co-investigator Dr Ali Tavassoli.

"The artificial linkages act in stealth as they go undetected by the organism; the gene was functional despite containing 'scars' in its backbone. This opens up all sorts of possibilities."

The team is now hoping to secure funding to explore potential applications of the technology.

More information: The paper "Biocompatible artificial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli" by Afaf H. El-Sagheer, A. Pia Sanzone, Rachel Gao, Ali Tavassoli and Tom Brown, of the University of Southampton, is published online by PNAS, 27 June 2011.

Provided by University of Southampton (news : web)

Copper ions as morphogens for the formation of polymer films by click chemistry

Scientists are envious of nature because of its ability to build up highly complex structures like organs and tissues in an ordered fashion without any problem; it takes a great deal of effort for scientists to produce defined microscale structures. Pierre Schaaf and a team of scientists from Strasbourg have now imitated a few of nature’s tricks in order to get a polymer film to "grow" onto a surface. As the researchers report in the journal Angewandte Chemie, they used morphogens as nature does. These signal molecules show a reaction which way it should go.

The growth of our bones, seashells, or the complicated forms of diatoms, requires the processes involved in biomineralization to occur along precisely controlled tracks. Molecules cannot simply be allowed to react in an uncontrolled fashion as soon as they encounter each other. In order for a complex organism to develop, every individual cell must know where it is located within a growing organ. Special signal molecules called morphogens inform the cell. They are formed in a specific location and then spread out into the surrounding tissue. This results in concentration gradients, which the cells can use to "orient" themselves.

Schaaf and his co-workers chose a similar strategy to form thin films on a substrate. They also used a sort of morphogen to steer the process. The reactants involved were polymers, one containing azide groups (–N3) and the other with alkyne groups (–C?CH) as side chains. In the presence of positively charged copper ions (CuI), these groups react with each other to form a carbon- and nitrogen-containing five-membered ring, crosslinking the polymers. This type of reaction is called “click chemistry”, because the reaction partners simply snap together.

In a solution containing both click partner and CuI ions, the reaction would immediately proceed at random. This would not result in a thin polymer film. The scientists’ idea was thus to place the CuI ions as a morphogen only on the surface to be coated. Their approach was to place CuII ions in the solution. They then applied an electric voltage to the surface. When CuII ions come into contact with this surface, they take an electron to become CuI. These are thus primarily to be found on the surface. Where there are CuI ions, the click reaction can proceed; the polymers only crosslink into a continuous film on the surface. The magnitude of the applied voltage can be used to control the number of CuI ions and thus the thickness of the film.

More information: Pierre Schaaf, Electrochemically Triggered Film Formation by Click Chemistry, Angewandte Chemie International Edition 2011, 50, No. 19, 4374–4377, http://dx.doi.org/ … ie.201007436

Provided by Wiley (news : web)