Oligo Modifications
Support and Educational Content

Attach modifications after oligo synthesis using Azide (NHS Ester)

Quick facts

Availability: DNA and RNA

Location: 5', internal, 3'

Scales: 100 nmol to large scale

Purification: HPLC

IDT ordering symbol: /5AzideN/, /iAzideN/, /3AzideN/

A standard oligonucleotide modification available from IDT, Azide (NHS Ester) provides a reactive site for attachment of alkyne groups to an oligo (Figure 1) through a copper-catalyzed, click chemistry reaction (Figure 2; see the sidebar, Definition: Click chemistry reactions, below). Several types of modifications are commercially available for conjugation to an azide-modified oligo; these include ferrocene and 5/6 TAMRA. Alternatively, you can add a strained alkyne modification, such as DBCO (dibenzocyclooctyl), DIBO (dibenzocyclooctyne), or BCN (bicyclo[6.1.0]nonyne), to the azide modified oligo using a copper-free click reaction.

Definition: Click chemistry reactions

Click chemistry is used to join small chemical subunits in a modular fashion, yielding a single reaction product that is typically physiologically stable and stereospecific. Most commonly, azide and alkyne groups are coupled in a copper-catalyzed reaction, forming a 1,2,3-triazole. This irreversible reaction is thermodynamically favorable and has no side products. There are also click chemistry reactions that do not require copper. For more information about lick chemistry reactions, see the DECODED articles, Click chemistry-generated, internal dye-labeled oligonucleotides and Oligo modification—post-synthesis conjugation explained, for more information about click chemistry reactions.

Figure 1. Azide (NHS Ester)

Figure 1. Azide (NHS Ester).

At IDT, we incorporate azides into oligos after synthesis, using NHS ester chemistry. An amino modification, added during oligo synthesis, is used in the NHS ester reaction. For example, a 5' azide is attached to the oligo sequence through a 5' Amino Modifier C6, while a 3' azide is attached through a 3’ Amino Modifier. An internal azide is attached through the Amino Modifier C6 dT, which results in the incorporation of a dT base at that location in the oligo sequence.When you order, you need only specify the Azide (NHS Ester) modification in your sequence; we will automatically add the necessary amino modifier.


Figure 2. Azide click chemistry reaction.

Figure 2. Azide click chemistry reaction. This copper catalyzed reaction between an azide group and an alkyne group produces a 1,2,3-triazole. IDT attaches a variety of modifications post-synthesis using this click chemistry reaction.


To order, enter your sequence using the IDT ordering symbol for azide (see Quick facts, above) in the desired location within your sequence. Oligonucleotides with Azide (NHS Ester) require HPLC purification.


Product focus—oligos, modifications, dsDNA fragments

Custom oligonucleotides and primers

Order up to 1 µmol desalted, custom synthesized DNA oligonucleotides for shipment to you the next business day (larger scales are shipped within 5 business days). You can specify whether to receive them dried down or hydrated, and whether you want them already annealed. Every IDT oligonucleotide you order is deprotected and desalted to remove small molecule impurities. Your oligos are quantified twice by UV spectrophotometry to provide an accurate measure of yield. Standard oligos are also assessed by mass spectrometry for quality you can rely on.

Learn more or order now.


Oligo modifications

Review a list of the common modifications IDT can add to oligonucleotides here. Not finding a modification you need on our website? We will consider any modification you need. In addition to our standard modifications, we offer over 90 modifications that are not listed in our online catalog. Just send your request to noncat@idtdna.com.


Further reading

Click chemistry-generated, internal dye-labeled oligonucleotides—Learn about "click chemistry" reactions used to join small chemical subunits in a modular fashion, yielding singular reaction products that are typically physiologically stable and stereospecific.

Oligo modification—post-synthesis conjugation explained—Addition of NHS esters, and of amino and alkene mods through click chemistry. Common questions regarding post-synthesis conjugation are also answered.

Need a non-standard modification?—Not finding the modifications you need? IDT will consider any modification you have in mind. In addition to our standard modifications, we offer 89 modifications that are not listed in our online catalog. A few of the more popular ones are described along with information on how to order them. Contact us with any inquiries at noncat@idtdna.com.

Review other DECODED Online newsletter articles on oligo handling and analysis, and oligo modifications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.


Author: Stephanie Youtsey is the Non-Catalog Coordinator in the Specialty & Manufacturing Services group at Integrated DNA Technologies.

© 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.


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