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Core Technology

baseclick GmbH

Baseclick Technology

Efficient nucleic acid labeling is at the heart of the baseclick technology. This is achieved by using optimized click reaction conditions in nucleic acid applications and we have created an entire portfolio of products around this principle.

The strength of the technology becomes crucial when it is performed in complex mixtures, e.g. for the detection of cell proliferation. But also reactions with pure and isolated compounds can benefit from the superior labeling performance.

Click Chemistry on Nucleic Acids – Simple, Efficient and Diverse

Click chemistry is a concept that was developed by Sharpless, Kolb and Finn in 2001.1 The idea was to join small modular compounds by a few very good reactions to generate chemical diversity instead of using a plethora of reactions that would need extensive optimization for each transformation. The copper-catalyzed version of the Huisgen cycloaddition (CuAAC) between a terminal alkyne and an azide is arguably one of the most popular click reactions.2,3 The reaction proceeds in the presence of many functional groups in good to excellent yields in aqueous solvent (mixtures) and has resulted in more than 1000 research articles based on the reaction within the first decade after its discovery.4 Apart from the efficiency and the modularity of the reaction, several other properties render the CuAAC superior to many other click reactions.

The required functional groups can be introduced by rather simple chemical transformations, they have good long-term stability and they have a relatively low sterical demand. The latter property is one major reason for acceptance of click-ready building blocks by many enzymes, like e.g. polymerases, glycosyl transferases and many others.

Adaption of the reaction conditions to oligonucleotides has been particularly rewarding.5,6 When faced with the challenge to densely label oligonucleotides with more than one label, scientists from the Ludwig-Maximilians University Munich realized that click chemistry can do it. In order to put this into practice they prepared DNA building blocks containing alkyne functional groups for preparation of oligonucleotides and equipped the desired labels with azides. The efficiency and robustness of the click procedures convinced many scientists, which started to request the building blocks from the discoverer.

The increasing demand for click-ready DNA building blocks has fueled the establishment of baseclick in 2008. Since then, we and researchers worldwide continuously increase the diversity of click-chemistry based applications.

Cell Proliferation Analysis

Cell division is of fundamental importance to all living organisms as it is the basis for growth and regeneration. In eukaryotes, like e.g. humans, cell division is preceded by DNA replication. The ability to replicate its own DNA, i.e. to proliferate, is a crucial property of a cell as it is an indicator for a plethora of cellular processes and is studied among others in cancer therapy and for cytotoxicity evaluation of compounds.

Baseclick has developed a best-in-class kit system to study cell proliferation that is superior to alternative methods. The kit is based on an astonishing principle: 5-ethynyl-2’-deoxyuridine (EdU), an alkyne modified nucleoside analogue of thymidine is taken up by eukaryotic cells. Inside the cell the host enzymes generate the triphosphate of the artificial nucleoside, which is then incorporated into de novo synthesized DNA by the DNA polymerase. The resulting alkyne-modified DNA is then detected by specifically clicking fluorescent dyes.

Aptamers – Nucleic Acid Antibodies

Antibodies help our body to repel pathogens and have become valuable therapeutics against diseases like e.g. cancer. Aptamers are DNA or RNA oligonucleotides which possess specific binding activities similar to antibodies. Since aptamers are smaller, are evolved in vitro and can be prepared by synthetic methods, they have some interesting advantages compared to antibodies from mammalian cell culture production. For example, it was demonstrated that aptamers have superior detection properties compared to antibodies, when they are applied in cellular imaging.7

Scientists and companies worldwide are currently developing methods for efficient production and testing of aptamers. In contrast to antibodies, many of the handling steps can be automated and thus save ressources (including animal models). As DNA and RNA are mostly composed of four building blocks, the chemical diversity of the resulting polymers is decreased compared to the 20 (21) amino acids in proteins. This has drastically limited the number and properties of the targets that aptamers can normally bind.

The invention of the so-called click-SELEX procedure has at least partly overcome this bottleneck for the aptamer technology. In click-SELEX an alkyne-modified nucleotide is used for enzymatic incorporation during PCR and the resulting oligonucleotide is subsequently clicked with functionalized azides in order to increase the chemical diversity of the nucleic acid.8 Thereby the success rate to find a good target binder is increased and the physico-chemical properties of the oligonucleotides can be modulated.

RNA Conjugates

In the recent years RNA therapeutics are on their track to become a novel class of drugs which should enable transient gene therapies against diseases that have no cure so far.9 The first FDA approved siRNA drug, Patisiran, from Alnylam marks an important cornerstone for all RNA therapeutics technologies. Key to this landmark achievement was conjugation of the siRNA with N-acetylgalactosamin for receptor-mediated uptake, which enables targeted delivery of the oligonucleotide drug. Due to the small size of the siRNA molecule, production by chemical synthesis was possible and enabled a medicinal chemistry approach for lead structure optimization.10

As mRNA therapeutics are at the advent of becoming drugs, they face even greater challenges compared to siRNAs. Due to their much larger size, chemical preparation is not an option and therefore mRNA is produced via in vitro transcription from a DNA template. So far, chemical modification of the resulting mRNA is mostly limited to the nucleotides that are accepted by the RNA polymerase during transcription. Therefore, targeted delivery of mRNA is much more complex and is achieved by modifying transfection agents instead of the mRNA.

Baseclick is currently pursuing a program to develop and establish methods for chemical modification of mRNAs. We are convinced that click chemistry could become an important option to overcome the remaining challenges in mRNA drug development.

DNA and RNA Sequencing

Sequencing technologies for nucleic acids have evolved at a tremendous pace and are considered as a key technology for diagnostics and might represent the analytical basis for personalized medicine. Despite enormous technological improvements, there is an ongoing need to increase efficiency, throughput and thus cost. This is achieved by decreasing the size of individual sequencing reactions and by massive parallel setups.

Already today, some methods sequence a single DNA molecule in real-time. In order to achieve this, reagents which are required for the sequencing reaction must meet strict specifications. For some of these reagents, this is only feasible when using click chemistry as it combines high yields in complex mixtures with mild reaction conditions and be used to simply create chemical diversity.

Moreover, click chemistry is being studied for improved sample preparation, chip- or microarray loading for NGS applications.

References

1. Kolb, H. C., Finn, M. G. & Sharpless, K. B. Click Chemistry: Diverse Chemical Function from a Few Good Reactions. Angew. Chemie – Int. Ed. 40, 2004–2021 (2001).
2. Rostovtsev, V. V., Green, L. G., Fokin, V. V. & Sharpless, K. B. A stepwise huisgen cycloaddition process: Copper(I)-catalyzed regioselective ‘ligation’ of azides and terminal alkynes. Angew. Chemie – Int. Ed. 41, 2596–2599 (2002).
3. Tornøe, C. W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase:-triazoles by regiospecific copper (I)-catalyzed 1, 3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057–64 (2002).
4. Liang, L. & Astruc, D. The copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) “click” reaction and its applications. An overview. Coord. Chem. Rev. 255, 2933–2945 (2011).
5. Gierlich, J., Burley, G. A., Gramlich, P. M. E., Hammond, D. M. & Carell, T. Click Chemistry as a Reliable Method for the High-Density Postsynthetic Functionalization of Alkyne-Modified DNA. Org. Lett. 8, 3639–3642 (2006).
6. Burley, G. A. et al. Directed DNA metallization. J. Am. Chem. Soc. 128, 1398–1399 (2006).
7. Strauss, S. et al. Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging. Nat. Methods 15, (2018).
8. Pfeiffer, F. et al. Identification and characterization of nucleobase- modified aptamers by click-SELEX. 13, 1153–1180 (2018).
9. Lieberman, J. Tapping the RNA world for therapeutics. Nat. Struct. Mol. Biol. 25, 357–364 (2018).
10. Adams, D. et al. Patisiran, an RNAi Therapeutic, for Hereditary Transthyretin Amyloidosis. N. Engl. J. Med. 379, 11–21 (2018).

Literature

Click Chemistry

  • Discovery of the copper-catalyzed click conditions[1,2]
  • The role and effect of copper(I)-stabilizing ligands[3–5]
  • The first click chemistry on DNA publication [6][7]
  • Click chemistry applications on RNA molecules[8]
  • Some clickable artificial nucleotides are accepted by DNA polymerases as good as natural nucleotides[9]
  • Click chemistry on oligonucleotides for labeling[6,10]
  • Click chemistry compounds as tools for biological applications[11]

Selected references

[1] V. V. Rostovtsev, L. G. Green, V. V. Fokin, K. B. Sharpless, Angew. Chemie – Int. Ed. 2002, 41, 2596–2599.
[2] C. W. Tornøe, C. Christensen, M. Meldal, J. Org. Chem. 2002, 67, 3057–64.
[3] Q. Wang, T. R. Chan, R. Hilgraf, V. V. Fokin, K. B. Sharpless, M. G. Finn, J. Am. Chem. Soc. 2003, 125, 3192–3193.
[4] T. R. Chan, R. Hilgraf, K. B. Sharpless, V. V Fokin, Org. Lett. 2004, 6, 2853–2855.
[5] C. Besanceney-Webler, H. Jiang, T. Zheng, L. Feng, D. Soriano Del Amo, W. Wang, L. M. Klivansky, F. L. Marlow, Y. Liu, P. Wu, Angew. Chemie – Int. Ed. 2011, 50, 8051–8056.
[6] J. Gierlich, G. a. Burley, P. M. E. Gramlich, D. M. Hammond, T. Carell, Org. Lett. 2006, 8, 3639–3642.
[7] G. A. Burley, J. Gierlich, M. R. Mofid, H. Nir, S. Tal, Y. Eichen, T. Carell, J. Am. Chem. Soc. 2006, 128, 1398–1399.
[8] E. Paredes, S. R. Das, ChemBioChem 2011, 12, 125–131.
[9] H. Cahova, A. Panattoni, P. Kielkowski, M. Hocek, 2016, DOI 10.1021/acschembio.6b00714.
[10] J. Gierlich, K. Gutsmiedl, P. M. E. E. Gramlich, A. Schmidt, G. A. Burley, T. Carell, Chem. – A Eur. J. 2007, 13, 9486–9494.
[11] M. Grammel, H. C. Hang, Nat. Chem. Biol. 2013, 9, 475–484.

FAQs

  • What kind of labels can be clicked?

    As it is the nature of click reactions, various groups can be attached to nucleic acids, not constricted to dyes. The only requirement is that you are using high quality reagents for your reactions and each reaction partner is soluble. Baseclick therefore provides a wide range of clickable groups, linkers and fluorescent dyes, fatty acids, etc. all tested in click reactions.

  • I have heard that copper could negatively influence my biological system.

    Free copper species in solution at high concentration can generate reactive oxygen species that might damage biomolecules. This can be completely avoided by using our copper-chelating ligands like TBTA, THPTA and BTTAA. They lower the effective free copper concentration (for oxidative side reactions) in solution and at the same time reaction kinetics are drastically improved. This means incubation times, reaction temperature and concentration of each reaction partner can be decreased and still good yields are obtained. We suggest using a ligand to copper ratio of 5:1 to 3:1 in your reaction.

    For some applications usage of strain-promoted click reactions could be an alternative.

    Please check our protocol section for some standard procedures.

  • Are there standard protocols for the different click reactions?

    Yes. We provide protocols for different applications. Please find them here (“link”).

  • Are there reagents to avoid in a copper-catalyzed click reaction?

    Some common biochemical buffer components can interfere with the progress of copper-catalyzed click reactions (CuAAC) and therefore should be avoided. For example, TE and TAE buffer contain EDTA which chelates the catalytic copper ions and thus decreases reaction kinetic and yield.

    Moreover, free thiols, like dithiothreitol (DTT) and -mercapto ethanol, can deteriorate or completely stop click reactions.

  • What is the best catalyst for my reaction?

    The optimal catalyst depends on your application and the solvents used. In general, there are three major catalyst systems for copper-catalyzed click reactions that apply the required Cu(I) source:

    1) You are working in aqueous media: Then we recommend using a CuSO4 (BCMI-004) based system. To generate the catalytic Cu(I) species, please do not forget to add the necessary sodium ascorbate (BCMI-005) and our water soluble THPTA ligand (BCMI-006). As the sodium ascorbate has restricted stability when dissolved, please prepare this solution always fresh.

    2) When your medium is of organic nature (mostly DMSO or click solution) then use CuBr and our TBTA ligand (BCMI-002) for labeling reactions. We would like to note, that CuBr is sensitive to air. Therefore, we take precautions when aliquoting and sealing this compound. Once opened, please use the solution fast (within a few hours maximum).

    3) For small sample amounts from e.g. enzymatic reactions in aqueous solvents we recommend using our reactor system that is part of our Oligo Click kits. As this catalyst will not dissolve during the reaction and can also be applied in organic media, its handling is very simple as you will see in the kits user manual. Additionally, the long-term storage is superior compared to the other catalyst systems.

  • Can I upscale the click reaction?

    Upscaling of click reactions is possible depending on the catalyst system you are using. Homogenous catalyst systems (copper bromide and copper sulfate) can be upscaled by increasing the amount of the reagents. Anyhow, please avoid to dilute your mixture too much. The baseclick reactor, a heterogenous catalyst, which is provided in the oligo-click kits is limited due to the surface activity and thus much harder for upscaling.

  • What is the difference between strain-promoted and copper catalyzed click reactions?

    Copper-catalyzed click reactions (CuAAC) require the presence of a Cu(I) catalyst for efficient reaction and thus the reaction between a terminal alkyne and an azide can be controlled through external catalyst supply. In very versatile applications this highly efficient reaction yields a single regioisomer product. Due to the low sterical demand of each reaction partner, biomolecules equipped with azides or terminal alkynes can be accepted by a range of enzymes.

    Strain promoted click reactions require a strained alkyne (e.g. DBCO) for reaction with an azide and need no external catalyst for reaction. The reaction kinetics are a bit slower compared to CuAAC, but if each reaction partner is provided in sufficient concentration (>50 µM) good yields can be achieved in reasonable time. In some cases, they have a limited shelf-life and they produce mixtures of regioisomers, but they can be valuable options for very sensitive applications, e.g. in vivo labeling.

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