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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. A list of over 200 standard modifications that can be incorporated or added onto oligonucleotides is found on the Oligo modifications page of our website. These include modifications of the following types:



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 nmol 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 1. Choose standard modifications as you input your nucleic acid sequence into the ordering tool.
Figure 2. Drop down menu of  available 5′ modifications. 

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 (Figure 2).

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.

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, contact us.


How to order off-catalog modified oligos

The codes used to order off-catalog modifications can be obtained from our Customer Care department (contact us 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 nmol scale and may require additional purification. These oligos receive yield guarantees, and pricing will be provided in the website shopping cart.

For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations. Doc ID: RUO23-1922_001

Published Jan 18, 2013
Revised/updated Apr 28, 2023