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Modified Oligonucleotides for
Innovative Applications

baseclick GmbH

Special oligonucleotides for outstanding applications

Are you looking for oligonucleotides with several modifications or modifications which are hardly available?

We have developed compounds for a labeling technology that allows preparation of oligonucleotides which contain even several modifications. These modifications augment the usual DNA and RNA oligonucleotides with functional groups e.g. for detection as aptamers, but can even change the physicochemical properties of the biopolymer. Chemical synthesis of alkyne modified oligonucleotides of up to 100mer length is a routine. Due to our patented click technology several differently modified oligonucleotides can be prepared from the same alkyne modified oligo.

The key attributes of baseclick´s custom oligonucleotides are:

  • High-purity oligos for meaningful experiments help you save time
  • Efficient post-synthetic labeling enables to introduce sensitive modifications, which are out of reach for conventional methods
  • The wishes and ideas of our customers are our guideline, we will try the impossible
  • Modified DNA, RNA, PNA and LNA oligos for full flexibility
  • Preparation of oligo libraries for aptamer generation

Modified Oligonucleotides for Innovative Applications


Baseclick´s custom oligonucleotides offer full labeling flexibility for your experiment. They should be considered whenever a single-label might not be enough, e.g. for sensitive fluorescence in situ hybridization (FISH) or for aptamer generation.

Which modification is the right for me?

Alkyne modified oligonucleotides are ideal for post-synthetic modifications with azide-modified labels. We also offer a range of other modifications for custom oligonucleotides. Please check here for an overview.

You want to order an oligo? Here is the order form.


Oligos to aptamers

  • A detailed protocol how to generate and select click-modified aptamers by “click-SELEX”[1]
  • Click ligation mediated gene-synthesis[2,3]
  • DNA nanostructures stabilized by click reaction[4][5]
  • Aptamers for high-resolution bioimaging[6]

Selected references

[1] F. Pfeiffer, F. Tolle, M. Rosenthal, G. M. Brändle, J. Ewers, G. Mayer, 2018, 13, 1153–1180.
[2] I. Manuguerra, S. Croce, A. H. El-Sagheer, A. Krissanaprasit, T. Brown, K. V. Gothelf, A. Manetto, Chem. Commun. 2018, 54, 4529–4532.
[3] M. Kukwikila, N. Gale, A. H. El-Sagheer, T. Brown, A. Tavassoli, Nat. Chem. 2017, DOI 10.1038/nchem.2850.
[4] 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.
[5] 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.
[6] S. Strauss, P. C. Nickels, M. T. Strauss, V. J. Sabinina, J. Ellenberg, J. D. Carter, S. Gupta, N. Janjic, R. Jungmann, Nat. Methods 2018, 15, DOI 10.1038/s41592-018-0105-0.


  • What kind of oligonucleotides are available at baseclick?

    We are offering modified and unmodified synthetic DNA, RNA and LNA oligonucleotides with a clear focus on modified oligonucleotides. Our online request oligo sheet gives you an overview of the most standard configurations and prices thereof.

  • What is the difference between a scale and a yield synthesis?

    In a scale synthesis we start with a definite amount of solid support and the customer will get the outcome.
    In a yield synthesis the customer defines the required amount and the synthesis setup will be adjusted as needed to ensure these requirements are met. As this yield synthesis is more challenging and might require repeated synthesis or higher starting amounts, this option is more expensive than the scale synthesis.

  • 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.

  • Are multiple modifications possible?

    Oligonucleotides containing multiple modifications are at the heart of our technology. Please be aware that increased modification numbers can lower the synthesis yield, especially when the modifications are positioned at the beginning of the sequence. It could be that some combinations of modifications are excluded.

    Please contact us and we will support you with more information.

  • Is it possible to order oligos with modifications not listed?

    Yes. Please use our online request formula and we will check feasibility. We can offer a wide range of modifications, also for non-click-chemistry applications.

  • Can you prepare aptamers (libraries)?

    Yes, we can prepare aptamers and aptamer libraries for click SELEX protocols. If you have questions, please do not hesitate to contact us.

  • Is it possible to use click chemistry modified oligonucleotides as a backbone mimic accepted by polymerases?

    Yes, this is possible and depends on the structure of the modification and the type of DNA polymerase.1 (Shivalingam, A., Tyburn, A. E. S., El-Sagheer, A. H. & Brown, T. Molecular requirements of high-fidelity replication-competent DNA backbones for orthogonal chemical ligation. J. Am. Chem. Soc. 139, 1575–1583 (2017)). If you are interested in the corresponding building blocks, we would be glad to assist you. Read also our white paper on this topic.