Oligo Modifications
Support and Educational Content

Inverted bases

How to add 5'-end restricted modifications to the 3' end of an oligo


Quick facts

Availability: DNA

Location: 5', internal, and 3'

Scales: 250 nmol to large scale

Purification Standard desalt or HPLC

Ordering: By email to noncat@idtdna.com

In addition to our catalog 3′ Inverted dT and 5′ Inverted Dideoxy-T modifications, we offer inverted DNA bases as a non-catalog option (on request). Inverted bases (A, C, G, and T) allow you to design an oligo with a 3′–3′ or 5′–5′ reversed linkage (Figure 1). For example, with a reverse linkage, you can start a sequence in the 3′ → 5′ orientation, incorporate a 5′–5′ linkage in the middle, and finish in the 5′ → 3′ orientation.

MH-Inverted Bases

Figure 1. Structure of 3′–3′ or 5′–5′ reversed linkages.

Inverted bases also allow you to add to the 3' end of an oligo modifications that are normally restricted to the 5' end. Popular 5'-end modifications requested for addition to the 3' end are: Acrydite, HEX, and dideoxy-modified bases (other than dideoxy-C, which is regularly available through IDT). Dideoxy-modified bases are often used to block 3' extension.

To order, email noncat@idtdna.com, providing  your name, organization, and sequence designs. Oligos containing inverted bases can be ordered as standard desalted or with HPLC purification. Standard desalt is only available if other modifications in the sequence do not require the oligo to be HPLC purified.

Author: Stephanie Youtsey is the Non-Catalog Coordinator in the Specialty and Manufacturing Services group at IDT.

© 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 ≫