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Ordering modified oligonucleotides

Standard IDT oligonucleotide modifications

Learn about the many oligo modifications IDT can provide, both as online selections and through special requests. IDT will consider any modification you need. Find out how to request and order them here.

IDT offers a variety of modifications that can be incorporated into both DNA and RNA oligonucleotides during synthesis. You can find a list of over 200 standard modifications we can incorporate onto oligonucleotides on the Modifications page of our online catalog. These include modifications of the following types:




Iowa Black® Dark Quenchers

Dark Quenchers

Attachment Chemistry / Linkers

Modified Bases

Phosphorothioate Bonds

Click Chemistry

How to order modified oligos

To include catalog modifications in your oligo sequence, simply go to the Custom DNA Oligos or Custom RNA Oligos ordering page and begin typing your oligonucleotide sequence into the Sequence section (Figure 1, red arrow). When you reach the desired position in your sequence, select the modification(s) you wish to insert from the 5' Mod, Internal, and 3' Mod pulldown menus above the Sequence box (Figure 1, blue arrow; Figure 2). If you are unable to locate your specific modification, try selecting a higher synthesis scale as many modifications are only available at the 100 nmole scale or higher. Additionally, the modifications are listed by category and alphabetically within that category. Click on the mod code to add that modification to the sequence you are entering. Be sure to review your purification options, as the modification you select may require additional purification.

art155-MH-Ordering Mods-Fig1

Figure 2. Drop down menu of 5′ modifications available for the sequence shown in Figure 1.
Not finding the modification you need?

Need a non-standard modification not listed on the IDT website? No worries. IDT currently offers over 90 modifications that are not listed in our online catalog. We have experience synthesizing these “off-catalog modifications”, but they are not in high demand like our catalog options (listed above).

The main difference between catalog and off-catalog modifications is that off-catalog modifications are not typically kept in stock. Therefore, these special modifications need to be prepared prior to oligonucleotide synthesis. This may increase turnaround time by 2–5 business days.

Some examples of off-catalog modifications include:

  • 5' and internal quenchers, such as Black Hole Quencher® 1 and Black Hole Quencher 2
  • 5' and internal 8-oxo-dG
  • N6-Methyl deoxyAdenosine
  • Trimer 19 and Trimer 20
  • 5' and 3' DBCO
IDT will consider any modification you need. If you don’t see your desired modification on our website, just send your request to

How to order off-catalog modified oligos

The codes used to order off-catalog modifications can be obtained from our Customer Care department (contact them here). Once you receive the modification codes for your off-catalog modifications, you can order them through the website just like standard catalog modifications. Just go to the Custom DNA Oligos or Custom RNA Oligos ordering page, and add in the modification code(s) manually, as you type in your sequence. The minimum synthesis scale for many of these modifications is the 100 nmole scale and may require additional purification. These oligos receive yield guarantees, and pricing will be provided in the website shopping cart.

Published Jan 18, 2013
Revised/updated Dec 22, 2016