Inverted bases

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

Learn how inverted bases allow you to reverse the orientation of part of your oligo sequence or add a 5′-end restricted modification to the 3′ end of your sequence.

Nov 30, 2015

Quick facts

Availability: DNA
Location: 5′, internal, and 3′
Scales: 250 nmol to large scale
Purification: Standard desalt or HPLC
Ordering: By email to

Insert 3′–3′ or 5′–5′ linkages

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.

art108-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, 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.