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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.

Quick facts

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

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 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, contact us. Oligos containing inverted bases can be ordered as standard desalted oligos or with HPLC purification. Standard desalt is only available if other modifications in the sequence do not require the oligo to be HPLC purified.

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: RUO23-1920_001


Published Nov 30, 2015
Revised/updated Apr 25, 2023