{"id":823,"date":"2016-02-26T20:51:00","date_gmt":"2016-02-26T20:51:00","guid":{"rendered":"https:\/\/www.idtdna.com\/page\/insert-an-abasic-site-into-your-sequence"},"modified":"2025-08-22T16:07:38","modified_gmt":"2025-08-22T16:07:38","slug":"insert-an-abasic-site-into-your-sequence","status":"publish","type":"post","link":"https:\/\/www.idtdna.com\/page\/support-and-education\/decoded-plus\/insert-an-abasic-site-into-your-sequence\/","title":{"rendered":"Insert an abasic site into your sequence"},"content":{"rendered":"<h3>Quick facts<\/h3>\n<p><strong>Availability:<\/strong> DNA and RNA<strong> Location:<\/strong> 5', internal, and 3'<strong> Scales:<\/strong> 100 nmol to large scale<strong> Purification:<\/strong> Standard desalt or HPLC<strong> Ordering (modification codes):&nbsp;<\/strong><a href=\"\/site\/Catalog\/Modifications\/Product\/1682\">\/5dSp\/<\/a>,&nbsp;<a href=\"\/site\/catalog\/modifications\/product\/1202\">\/idSp\/<\/a>,&nbsp;<a href=\"\/site\/catalog\/modifications\/product\/3480\">\/3dSp\/<\/a> <\/p>\n<h3>DNA abasic sites<\/h3>\n<p>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 any base pairing ability by a nucleotide, which can occur naturally through depurination or other mechanisms [<a href=\"#references\">1<\/a>]. This modification can be useful when examining DNA damage and repair.<\/p>\n<p>dSpacer can also be referred to as an abasic site, tetrahydrofuran (THF), or apurinic\/apyrimidinic (AP) site. It may be incorporated into an oligonucleotide sequence internally, or at the 5' or 3' end of a sequence.<\/p>\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/www.idtdna.com\/page\/wp-content\/uploads\/idt-images\/5b885a15-3279-6e2e-aa53-ff00001c1b3c-art109-mh-abasic-fig1.png\" data-displaymode=\"Original\" alt=\"art109-MH-abasic-Fig1\" title=\"D-OLI16PS-abasic-F1\" \/><figcaption class=\"image-caption\">Figure 1. Structures of dSpacer, rSpacer, and Abasic II modified bases.<\/figcaption><\/figure>\n<\/p>\n<p>To order a dSpacer modified oligonucleotide, go to the <a href=\"\/pages\/products\/custom-dna-rna\/dna-oligos\/custom-dna-oligos\"> Custom DNA Oligos ordering page<\/a>&nbsp;and enter your sequence using the <strong>IDT ordering symbol<\/strong> shown in the blue <strong>Quick facts<\/strong> 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.<\/p>\n<h3>RNA abasic sites and &ldquo;unstable&rdquo; DNA abasic II sites<\/h3>\n<p> 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. <\/p>\n<p>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 [<a href=\"#references\">2<\/a>]. 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 <a href=\"https:\/\/www.glenresearch.com\/catalogsearch\/result\/index\/?index=8&amp;q=Preparation+of+Oligonucleotides+Containing+Abasic+Sites\" target=\"_blank\">here<\/a>, on the second page of their published technical bulletin.<\/p>\n<p>To order oligos containing rSpacer (RNA abasic) or abasic II modifications, <a href=\"\/pages\/about\/contact-us\">contact us<\/a>&nbsp;with your name, organization, and sequence designs. Oligos containing RNA abasic sites, or abasic II sites, can be ordered with HPLC purification. Alternatively, they can be ordered with standard desalt, providing other modifications in the sequence do not require HPLC.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>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):&nbsp;\/5dSp\/,&nbsp;\/idSp\/,&nbsp;\/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 any base [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"ct_builder_shortcodes":"","ct_template_type":"","ct_parent_template":0,"inline_featured_image":false,"footnotes":""},"class_list":["post-823","post","type-post","status-publish","format-standard","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Insert an abasic site into your sequence | IDT<\/title>\n<meta name=\"description\" content=\"Use the dSpacer, rSpacer, and Abasic II modifications to introduce abasic sites into DNA or RNA oligos.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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