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Insert an abasic site into your sequence

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

Use the dSpacer, rSpacer, and Abasic II modifications to introduce abasic sites into DNA or RNA oligonucleotides. These modifications create a single base space that replicates the loss of base pairing ability by a nucleotide.

Feb 26, 2016

Revised/updated Feb 3, 2017

Quick facts

Availability: DNA and RNA
Location:
5', internal, and 3'
Scales:
100 nmol to large scale
Purification:
Standard desalt or HPLC
Ordering (modification codes):
/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.

art109-MH-abasic-Fig1

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 here, 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.

References

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

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