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baseclick GmbH

Simple click labeling of RNA and transfection into cells

Do you want to learn how to modify and handle RNA efficiently?

We have your solutions for simple and reliable labeling of RNA and transfection. We offer ready-to-use custom oligonucleotides, but also provide corresponding building blocks to prepare click-ready RNA by enzymatic synthesis. Actually, a click-ready nucleoside can be fed to cells to allow de novo RNA detection.

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

  • High-purity custom oligos for meaningful experiments help you save time.
  • High quality nucleotides to be used in various applications e.g. for in vitro transcription provide good mRNA yields and quality.
  • Simple kits for RNA labeling enable click reactions for everyone.


Baseclick offers all components to prepare labeled short and long RNA 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 RNA tracking inside of cells.

Which kit or reagent is the right for me?

Our nucleotides are ideal for researchers to prepare labeled oligonucleotides, applying chemo-enzymatic approaches, e.g. in vitro transcription of RNA. Even the modified nucleoside 5-ethynyluridine can be an option for metabolic labeling. Our kit systems are available for easy preparation of labeled RNAs.

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


RNA Applications

  • Click chemistry applications on RNA molecules[1][2][3]
  • (m)RNA as a therapeutic agent[4][5]

Selected references

[1] E. Paredes, S. R. Das, ChemBioChem 2011, 12, 125–131.

[2] S.Croce, S. Serdjukow, T. Carell, T. Frischmuth, ChemBioChem, 2020, 21, 1-7.

[3] M.L. Winz, E. C. Linder, J. Beckera and A. Jäschke, ChemComm, 2018, 54, 11781-11784.

[4] J. Lieberman, Nat. Struct. Mol. Biol. 2018, 25, 357–364.

[5] U. Sahin, K. Karikó, Ö. Türeci, Nat. Rev. Drug Discov. 2014, 13, 759–780.


  • What is the best way to handle RNA to avoid degradation?

    Due to its chemical structure RNA is less stable than DNA. At high temperatures, under basic conditions (pH>9) and in the presence of high Mg2+ concentrations, chemical reactions that favour hydrolysis of the RNA molecule take place. Additionally, RNases are common contaminations in standard laboratory conditions compared to DNases.

    We recommend to clean the benches and equipment with RNase inhibitors or specific detergent mixtures and to wear fresh gloves when handling the tubes (gloves that have been worn or that e.g. touched door/refrigerator handles are considered contaminated). Moreover, RNase-free H2O and tubes should be used for buffer preparation and to dissolve the samples.

  • What is the best way to store RNA to avoid degradation?

    For storage we recommend to store RNA at –80 °C, which should conserve RNA for one year without significant degradation. Alternatively,
    in our experience, short synthetic RNAs (up to 50mer) are more stable than long single-stranded RNAs from biological samples and therefore can be stored at –20 °C in a dry format.

  • Are you offering RNA oligos?

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

  • Can I use 5-ethynyl uridine (EU) for labeling of nascent RNA inside cells?

    EU can be fed to cells and detected using a fluorescent dye via click labeling. Our own experiments indicate that it will be first integrated in de novo RNA, but we have also observed incorporation into DNA after some incubation time. This is most likely via conversion of the EU ribonucleoside into EdU aided by intracellular ribonucleotide reductases.

    Research from several groups demonstrates successful EU cellular labeling for divers applications. (1)(2)

    1. Jao,C.Y. and Salic,A. (2008) Exploring RNA transcription and turnover in vivo by using click chemistry. Proc. Natl. Acad. Sci. U. S. A., 105, 15779–84.

    2. Bao,X., Guo,X., Yin,M., Tariq,M., Lai,Y., Kanwal,S., Zhou,J., Li,N., Lv,Y., Pulido-quetglas,C., et al. (2018) Capturing the interactome of newly transcribed RNA. 15.

  • What kits are available from Baseclick for RNA modification?

    We offer several kits to prepare labelled RNAs that are based on enzymatic incorporation of alkyne- or azide-modified nucleotides and subsequent click labelling.

    The RNA Labeling Kit allows you to introduce several alkyne groups randomly in your RNA through the incorporation of the 5-ethynyl-UTP (EUTP) by the T7 RNA polymerase during in vitro transcription.

  • How does the DNA template influence in vitro transcription performance?

    DNA template quality directly influences yield and quality of transcription reactions. Linearized plasmid DNA needs to be fully digested and should be free of contaminating RNase, protein and salts. We recommend selecting restriction enzymes that generate blunt ends or 5´-overhangs and purification after the enzymatic restriction (e.g. via silica-membrane based purification columns).

    Alternatively, a PCR mixture can be used directly, but better yields will usually be obtained with purified PCR products (e.g. via silica-membrane based purification columns).

  • What do I need to consider when planning my transcription experiments?

    Promotor choice: Different RNA polymerase promoters such as T7, T3 and SP6, are commonly used for the in vitro production of RNA.

    mRNA production: For the production of functional mRNA please ensure that the DNA template encodes the required structural features e.g. 3’-UTR, 5’-UTR, correctly orientated target sequence and ideally a poly A-tail. Alternatively, polyA-tailing can be introduced post-transcriptionally using a Poly(A) polymerase.

  • What is the promoter sequence of T7 RNA Polymerase?


    T7 RNA polymerase starts transcription at the underlined G in the promoter sequence. The polymerase then transcribes using the opposite strand as a template from 5’->3’. The first base in the transcript will be a G.