Oligo Modifications
Support and Educational Content

Insert an abasic site into your sequence

dSpacer, rSpacer, and Abasic II modifications add a single nucleotide space into an oligo sequence

Quick facts:

Availability: DNA and RNA

Location: 5', internal, and 3'

Scales: 100 nmol to large scale

Purification: Standard desalt or HPLC

Ordering: /5dSp/, /idSp/, /3dSp/

DNA abasic sites

The dSpacer (1,2'-Dideoxyribose) modification (Figure 1A) can be used to insert a single base space into a DNA oligonucleotide sequence. It replicates the loss of base pairing ability by a nucleotide, which can occur naturally through depurination or other mechanisms [1]. This modification can be useful when examining DNA damage and repair.

dSpacer is also referred to as an abasic site, tetrahydrofuran (THF), or apurinic/apyrimidinic (AP) site. It can be incorporated into an oligonucleotide sequence internally, or at the 5' or 3' end of a sequence.

Spacer Structures

Figure 1. Structures of dSpacer, rSpacer, and Abasic II modified bases.

To order a dSpacer modified oligonucleotide, go to the Custom DNA Oligos ordering page and enter your sequence using the IDT ordering symbol shown in the blue Quick facts box above to place this abasic site into the desired location within your sequence. You can request dSpacer modified oligonucleotides with standard desalt or HPLC purification.

RNA abasic sites and “unstable” DNA abasic II sites

Additionally, RNA abasic (rSpacer) and the unstable Abasic II modifications are available as non-catalog offerings from IDT. The rSpacer modification (Figure 1B) creates an RNA abasic site with an RNA backbone. Such sequences are much less common in nature than those with DNA abasic sites.

The Abasic II modification contains a hydroxyl group at the 1' position (Figure 1C). The hydroxyl makes this DNA modification more reactive than the dSpacer. We provide oligos with the Abasic II modification in the protected form; therefore, such modified oligos require a deprotection step before use. A deprotection protocol is provided by Glen Research at http://www.glenresearch.com/Technical/TB_Abasic%20II-1.pdf, beginning at the Abasic Formation section.

To order oligos containing rSpacer (RNA abasic) or abasic II modifications, email us at noncat@idtdna.com with your name, organization, and sequence designs. Oligos containing RNA abasic sites or abasic II sites can be ordered with HPLC purification. They can also be ordered with standard desalt, providing other modifications in the sequence do not require HPLC.


  1. http://www.glenresearch.com/GlenReports/GR21-14.html. [Accessed 19 Mar, 2016].

Additional reading

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.

Increase the Tm of short, AT-rich primers and probes—Add this modified base to increase the melting temperature (Tm) of primers and probes. It is especially useful when you need to work with short, A-T rich sequences.

Inverted bases—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.

Oligonucleotide modifications: Choosing the right mod for your needs—Review these guidelines on selecting oligonucleotide modifications to learn how they can help you in your research.

Need a non-standard modification?—Did you know that IDT offers 89 modifications that are not listed in our online catalog? A few of the more popular ones are described along with information on how to order them. IDT will consider any modification you require. Please make such inquiries to noncat@idtdna.com.

Author: Stephanie Youtsey is the Non-Catalogue Coordinator in the Specialty and Manufacturing Services group at Integrated DNA Technologies.

© 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.

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 ≫