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DNA Applications

baseclick GmbH

Reliable and simple click labeling of DNA

Do you need to prepare labeled DNA with many labels? Or are you looking for DNA with properties beyond the natural 5 bases? We have your solutions for simple and reliable labeling of DNA. We offer ready-to-use custom oligonucleotides, but also provide corresponding building blocks to prepare click-ready DNA by chemical or enzymatic synthesis. In addition, kits for click reactions and purification enable DNA labeling for everyone.

The key attributes of baseclick’s DNA application products are:

  • Tested phosphoramidites for reliable solid-phase synthesis performance
  • High-purity custom oligos for meaningful experiments help you save time
  • Triphosphates for chemoenzymatic labeling, e.g. in vitro aptamer generation in click-SELEX, enable innovative technologies
  • High quality nucleosides for cell proliferation experiments, for reliable performance
  • Simple kits for click labeling and purification enable click reactions for everyone

Applications

Baseclick offers all components to prepare labeled short and long DNA oligonucleotides to allow full flexibility for your experiments. They should be considered whenever the standard nucleobases and functionalities are not enough or when detection in complex mixtures is required, e.g. for chemical synthesis of probe oligos, for metabolic labeling or for aptamer generation.

Which kit or reagent is the right for me?

Our phosphoramidites are ideal for researchers or professional oligo production facilities that need to prepare highly labeled oligonucleotides of up to 100mer length. For longer oligonucleotides, chemoenzymatic approaches involving modified triphosphates can be applied or even modified nucleosides can be an option. For click reactions with alkyne- or azide-modified oligonucleotides oligo² labeling click kits can be used and purified with the baseclean kits.

You are not sure what you are looking for or you need a quote? Just contact us.

Literature

DNA Applications

  • The first click chemistry on DNA publications[1][2]
  • DNA nanostructures stabilized by click reaction[3][4]
  • Immunoproliferative response analysis using EdU[5]
  • A detailed protocol how to generate and select click-modified aptamers by “click-SELEX”[6]
  • Some clickable artificial nucleotides are accepted by DNA polymerases as good as natural nucleotides[7]

Selected references

[1] J. Gierlich, G. a. Burley, P. M. E. Gramlich, D. M. Hammond, T. Carell, Org. Lett. 2006, 8, 3639–3642.
[2] G. A. Burley, J. Gierlich, M. R. Mofid, H. Nir, S. Tal, Y. Eichen, T. Carell, J. Am. Chem. Soc. 2006, 128, 1398–1399.
[3] V. Cassinelli, B. Oberleitner, J. Sobotta, P. Nickels, G. Grossi, S. Kempter, T. Frischmuth, T. Liedl, A. Manetto, Angew. Chemie – Int. Ed. 2015, 54, 7795–7798.
[4] S. Raniolo, S. Croce, R. P. Thomsen, A. H. Okholm, V. Unida, F. Iacovelli, A. Manetto, J. Kjems, A. Desideri, S. Biocca, Nanoscale 2019, 11, 10808–10818.
[5] Y. Kitazawa, H. Ueta, T. Hünig, Y. Sawanobori, K. Matsuno, Histochem. Cell Biol. 2015, 144, 195–208.
[6] F. Pfeiffer, F. Tolle, M. Rosenthal, G. M. Brändle, J. Ewers, G. Mayer, 2018, 13, 1153–1180.
[7] H. Cahova, A. Panattoni, P. Kielkowski, M. Hocek, 2016, DOI 10.1021/acschembio.6b00714.

FAQs

  • What kind of oligonucleotides are available at baseclick?

    We are offering modified and unmodified synthetic DNA, RNA, LNA and PNA oligonucleotides. Our online request oligo formula gives you an overview of the most standard configurations and prices thereof.

  • What is the maximum length for the oligo synthesis?

    We routinely provide synthetic oligonucleotides of up to 100 bases length in high-purity. For longer oligonucleotides please send us a request as we will then check feasibility as such syntheses are much more challenging.

  • Can I also link 2 oligos and not just oligo-dyes by click chemistry?

    For conjugating 2 oligos, some precautions (protocol and reaction composition) have to be taken as otherwise the charged molecules would repel each other and provide low yields. We have worked some time to find optimal conditions and are glad to offer you our solution for such efficient linkages in our Oligo² Labeling kits.

    But herein, please note: Oligonucleotides can have folded structures, which hinder accessibility of the functional groups that are needed for the reaction. By adding some DMSO (5-10% (v/v) final) these folded structures are destabilized and improved reaction progress can be observed.

  • I have low or no recovery of DNA after purification using the BaseClean Kits. What can I do?

    Elution of DNA can be inefficient when the pH of the buffer for elution is not between 7.0 -8.0. Please make sure to use the provided baseclick solution or check your buffer. Also, the elution solution must have time to be completely absorbed by the BaseClean column membrane before centrifugation. It is not recommended to decrease the incubation time for this step.

    In case the size of your DNA fragment is larger than 5 Kb it could be still bound to the BaseClean column. Preheat the elution solution to 60 °C before usage for stronger elution.