Labeling chemistries

There are different possibilities for labeling an oligonucleotide:

  • All of our dyes can be attached post-synthetically to the 5'- terminus of an oligonucleotide via an amino- or thiol-linker with a 6-Carbon spacer arm.
  • Another possibility for labeling an oligonucleotide at the 5'- terminus is to couple the dye directly during synthesis via its phosphoramidite. This method is available for Cy3TM, Cy3.5TM, Cy5TM, Cy5.5TM, Fluorescein, HEX, TET and Dabcyl.
  • Postsynthetic labeling of oligonucleotides at internal sites of the sequence is possible by substituting any thymidine with 5-C6-Amino-2'-deoxythymidine. In addition, all other bases can be substituted if required. All dyes available for 5'- labeling can also be attached internally.
  • It is also possible to label the 3'- end of oligonucleotides post-synthetically via an amino link. This method is available for all dyes. For the 3'- labeling with Fluorescein and Dabcyl IBA has special solid supports [CPGs] with the dyes already attached. This is very useful for high quality production of double labeled probes.
Possible dye combinations

IBA offers a great variety of oligonucleotides with different labels and their combinations. For example: 5'-Fluorescein, 5'-HEX, 5'- Cyanine 3, 5'- Cyanine 3.5, 5'- Cyanine 5, 5'- Cyanine 5.5, 5'-TET, 3'-Dabcyl, and 3'-Fluorescein can be combined with any of the available dyes in varied positions. For double labelings with dyes that are not available as amidites labeling via thiol-reactive compounds is possible.

NEW! Custom oligonucleotides labeled via Click-Chemistry

Click chemistry for oligonucleotide labeling

A new oligonucleotide labeling philosophy allows

  • completely new dye combinations previously not available
  • flexible dual and multiple labeling with so far unreachable labeling densities
  • very reliable labeling
  • high yield of completely labeled product
  • combination with existing labeling techniques for greater diversity

The Click-Chemistry is not a specific chemical reaction, it’s a "plug-and play" philosophy

Inspired by the fact that nature generates also new molecule classes by joining small modular units (e.g. exon shuffling etc.), Click-Chemistry describes the quick and reliable generation of new entities by joining small building blocks.

With the Click-Chemistry, new labeling densities can be achieved, which are unreached by conventional DNA labeling techniques. It also overcomes other weaknesses of current protocols such as poor incorporation rates of the label and instable intermediate products. This enables completely new lab protocols and the development of new diagnostic products.

Dyes presently available for the Click-Chemistry are e.g. the new ultra-photostable Eterneon™ dyes, as well as several dyes from Luminartis, Dyomics, Abberior and Atto-Tec. Please refer to the overview of dyes available for olidonucleotide labeling. Biotin can also be coupled using Click-Chemistry.

In addition, the combination of the Click-Chemistry with conventional labeling procedures offers completely new possibilities for dye combinations.

For further information on the Click-Chemistry please refer to Kolb et al. (2001) Click chemistry: diverse chemical function from a few good reactions. Angew. Chem. Int. Ed. 40 (11):2004. A comprehensive list for publications related to the Click-Chemistry can be found at

Take advantage of the new diversity!