Oligo Modifications
Support and Educational Content

DeoxyInosine: Don’t call me a universal base!

DeoxyInosine, a naturally occurring base, was considered the first “universal” base—meaning that it could base pair with the other natural bases, A, C, G, and T. However, this terminology has encountered some criticism, notably from Michael Smith, winner of the Nobel Prize for Chemistry in 1993 for developing site-directed mutagenesis, who mentioned deoxyInosine in his Nobel Prize acceptance speech [1]: “I have always been puzzled by the widespread acceptance of the idea that deoxyInosine is precocious in base pairing because Inosine behaves in a precocious manner in t-RNA duplex interactions. Studies on deoxyInosine, in fact, indicate that it functions as a specific analog of deoxyGuanosine, although it does not self-aggregate as does deoxyGuanosine.” Subsequent studies have shown that Dr Smith was correct: deoxyInosine binds preferably to dC [2]. So go ahead and use it in experiments, just don’t call it universal!


  1. www.nobelprize.org [Accessed 5, Jul, 2017].
  2. Watkins Jr NE, SantaLucia Jr, J (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucl Acids Res 33(19):6258–6267.

Product focus—oligos, modifications, dsDNA fragments

Custom oligonucleotides and primers

You can order up to 1 µmol desalted, custom synthesized DNA oligonucleotides and they will be shipped to you the next business day (larger scales are shipped within 5 business days). You can also specify whether to receive them dried down or hydrated, and whether you want them already annealed. Every IDT oligonucleotide you order is deprotected and desalted to remove small molecule impurities. Your oligos are quantified twice by UV spectrophotometry to provide an accurate measure of yield. Standard oligos are also assessed by mass spectrometry for quality you can count on.

Learn more or order now.

Oligo modifications

Review a list of the common modifications IDT can add to oligonucleotides here. Not finding a modification you need on the IDT website? IDT will consider any modification you need. Just send your request to noncat@idtdna.com.

Custom dsDNA fragments

Rather than annealing oligonucleotides to obtain dsDNA fragments, when your fragment size is 125 bp or longer, it might make more sense to order gBlocks® Gene Fragments. gBlocks Gene Fragments are double-stranded, sequence-verified, DNA genomic blocks, 125–3000 bp in length, that can be shipped in 2–5 working days for affordable and easy gene construction or modification. These dsDNA fragments have been used in a wide range of applications including CRISPR-mediated genome editing, antibody research, codon optimization, mutagenesis, and aptamer expression. They can also be used for generating qPCR standards.

Learn more about gBlocks Gene Fragments at www.idtdna.com/gblocks.

Additional reading

Generate codon balanced libraries for mutagenesis with trimer modifications—Incorporating oligo codon trimers into oligo libraries results in balanced encoding of amino acids and eliminates unwanted stop codons. Such oligo libraries are useful for mutagenesis experiments to prepare proteins for screening for potential improvements in biological function. 

Towards real-time imaging in single, living cells—Read about new oligonucleotide technologies for detection and quantification of specific RNA transcripts in live cells.

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

Review other DECODED Online newsletter articles on oligo handling and analysis, and oligo modifications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.

Author: Martin Whitman is a Technical Support Representative at IDT.

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IDT web tools for oligo properties

Free, online tools for oligo design, secondary structure, dilution, and resuspension.

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