Oligo Modifications
Support and Educational Content

Need a non-standard modification?

Not finding the modification you need on the IDT website? No worries. IDT currently offers 89 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 209 catalog options (see the sidebar, Standard IDT Oligonucleotide Modifications, for a summary of those listed on our oligo modification catalog page).

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 1–3 business days.

Standard IDT oligonucleotide modifications

You can find a list of 209 standard modifications we make to oligonucleotides on the Modifications page of our online catalog. These include modifications of the following types:

Off-catalog modifications we can synthesize for you

Here are a few examples of the off-catalog modifications we can provide:

Internal NHS ester modifications. We can provide several internal NHS ester modifications as off-catalog orders (Table 1). All internal NHS ester modifications are attached post synthesis to an amino modifier, C6 dT. Thus, such modifications will require a dT base at the position modified in your final oligo (for further explanation, see the article, Modification Highlight: When dT is Required For Modification Attachment).

Off-Catalog Modification Modification Code
DIG NHS ester /iDigN/
Cy® 5 NHS ester /iCy5N/
Cy® 3 NHS ester /iCy3N/
Most Alexa Fluor® Dye NHS esters Varies*

* For Alexa Dye mod codes, contact IDT Customer Care via web chat, phone (800-328-2661), or email (custcare@idtdna.com).

Representative internal NHS Ester modifications.

Figure 1. Internal DIG NHS Ester.

Dibenzocyclooctyl (DBCO). DBCO (Figure 2A) is used for copper-free click reactions. We can place this modification on the 5′ or 3′ ends of an oligo. To order, use the 5′ modification code /5DBCON/, and the 3′ modification code /3DBCON/. DBCO-TEG (Figure 2B) offers a longer linker arm and is available for modification of the 5′ end of oligos; to order, use the 5′ modification code /5DBCOTEG/.


Figure 2A. DBCO.

Figure 2B. DBCO-TEG.

Figure 2. Dibenzocyclooctyl (DBCO) Modifications.

Puromycin. We can synthesize oligos with puromycin on the 3′ end (Figure 3). This modification is an antibiotic that mimics transfer RNA (tRNA). It is commonly added to the end of RNA oligos to facilitate binding in the ribosome’s A site. From there, it can attach to the growing peptide to ultimately stop elongation. Order this modification using the code /3Puro/.

Figure 3. Puromycin.

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. These oligos receive yield guarantees, and pricing will be provided in the website shopping cart.

IDT will consider any modification you have in mind. Please make such inquiries to noncat@idtdna.com.

Additional reading

DNA Oligonucleotide Resuspension and Storage
Upon receiving newly synthesized oligonucleotides, researchers must decide how to resuspend and store the product. Here are some guidelines and recommendations.

Oligonucleotide Modifications: Choosing the Right Mod for Your Needs
Guidelines on selecting oligonucleotide modifications and a discussion of how they 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.

Which Biotin Modification to Use?
A discussion of the applications for each of the different biotins available through IDT.

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: Stephanie Youtsey is a Scientific Applications Support Representative II at IDT.

© 2016, 2015 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.

IDT web tools for oligo properties

Free, online tools for oligo design, secondary structure, dilution, and resuspension.

Try them now ≫

Related Articles

DNA Oligonucleotide Resuspension and Storage

Guidelines and recommendations for how to resuspend and store newly synthesized oligonucleotides.

Read more ≫

Calculation Tips for Resuspending and Diluting Nucleic Acids

Easy guidelines for making a 100 µM solution; calculating nmoles, µg, copy number, and concentration; and determining concentration equivalencies.

Read more ≫

Understanding Melting Temperature

Advice on considerations for better oligo design: oligo concentration, salt, and SNPs.

Read more ≫

Oligonucleotide Modifications: Choosing the Right Mod for Your Needs

Guidelines on selecting specific oligonucleotide modifications and how they can help you in your research.

Read more ≫

Which Biotin Modification to Use?

Applications of each of the different biotins available from IDT.

Read more ≫