Currently, labeled and dual-labeled oligonucleotide probes are mainly manufactured using either dye-labeled amidites or activated esters. Both of these methods have their limitations.

For companies and departments involved in custom oligonucleotide synthesis, we offer a click chemistry-based solution for oligo labeling.

Just as in the case of NHS esters, click chemistry labeling is a two-step protocol. First, an alkyne moiety is introduced into the oligonucleotide using an alkyne amidite. Second, the deblocked oligo is labeled with a dye azide under appropriate conditions. The labeled oligo is then precipitated with acetone and purified (HPLC is the most appropriate method).

Compared to amidite-based labeling, click chemistry yields more pure probes, with a higher yield, requiring less purifying effort. The sensitive and expensive dye is not subjected to reactive deblocking reagents and won’t be wasted. There is no need to use ultra-mild protective groups.

Compared to the activated ester method, click chemistry is more scalable and requires less dye. The probes are purified more easily. The excess of the dye (about 0.2 to 0.5 eq. above the required amount) is nearly completely removed during acetone precipitation. It differs from activated ester labeling, where multiple precipitations are sometimes required to remove the excessive dye. Click chemistry allows efficient labeling of hundreds of OD₂₆₀ oligonucleotide units in a single centrifuge tube.

The cost-efficiency of the labeling method is comparable to amidite and NHS ester labeling.

We provide all necessary reagents for oligo labeling: alkyne amidites (5'-terminal and Dmt-protected for 3'-labeling on universal CPG), alkyne CPG, dye azides, and click chemistry catalyst. Use our recommended protocol for oligonucleotide labeling for optimal results!

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