Oligo Modifications
Support and Educational Content

Ordering modified oligonucleotides

Standard IDT oligonucleotide modifications

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:

For more details, visit www.idtdna.com/site/Catalog/Modifications.

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.

Figure 1. Chose standard modifications as you input your nucleic acid sequence into the order tool.


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.

Indentifying an off-catalog modification

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 noncat@idtdna.com.

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 via web chat, phone (800-328-2661), or email (custcare@idtdna.com). 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.

Product focus—Oligos, modifications, dsDNA fragments

Custom oligonucleotides and primers

You can order up to 1 µmol of desalted, custom synthesized DNA oligonucleotides and they will be shipped to you the next business day (larger scales are shipped within 5 business days, pending final quality control). You can also 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 count 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 on the IDT website? IDT will consider any modification you need. Just send your request to noncat@idtdna.com


Custom dsDNA fragments

Rather than annealing oligonucleotides to obtain dsDNA fragments, when your fragment size is 125 bp or longer, it might make more sense to order gBlocks® Gene Fragments. gBlocks Gene Fragments are double-stranded, sequence-verified, DNA genomic blocks, 125–3000 bp in length, that can be shipped in 2–5 working days for affordable and easy gene construction or modification. These dsDNA fragments have been used in a wide range of applications including CRISPR-mediated genome editing, antibody research, codon optimization, mutagenesis, and aptamer expression. They can also be used for generating qPCR standards.


Learn more about gBlocks Gene Fragments at www.idtdna.com/gblocks.

Related articles

Oligonucleotide modifications: Choosing the right mod for your needs—Learn about our broad family of oligonucleotide modifications, and get suggestions for selecting modifications that can help you in your research.

Oligo modification—post-synthesis conjugation explained—A description of addition of NHS esters and of amino and alkene modifications through use of click chemistry. We also provide answers to common questions regarding post-synthesis conjugation.

Modification highlight: When dT is required for modification attachment—Certain modifications require a dT base in the oligonucleotide sequence in order to be added. Learn which modifications these are, and how to add them to your oligo sequence.

Need a library of related DNA or RNA oligo sequences?—Build variability into your oligo sequences by incorporating Mixed Bases. We offer mixes of multiple base types as well as nonstandard and modified bases.


Review other DECODED Online newsletter articles on handling oligonucleotides and highlighted oligonucleotide modifications.


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


Author: Heather Schumann is the non-catalog advocate in Platinum Services at IDT.

© 2015, 2016 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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