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Did You Know?

Why are oligos synthesized 3′−5′?

In nature, DNA is formed in the 5′–3′ direction. Early efforts in DNA synthesis were based on biological synthesis, and thus the first synthetic oligonucleotides were produced in the 5′–3′ direction. Har Gobind Khorana, a University of Wisconsin biochemist who won the 1968 Nobel Prize in Physiology or Medicine, led the group that developed the early 5′–3′ synthesis technique using a polystyrene solid support and three different protecting groups. Though this technique led to important breakthroughs, it was eventually replaced in the 1980s by much a more efficient synthesis method using phosphoramidite monomers (phosphoramidites are nucleotides with protection groups which are removed after synthesis). The growing oligonucleotide is connected to the solid support, a controlled pore glass bead via the 3′ carbon, and thus synthesis proceeds in the 3′–5′ direction.

Additional resources

  1. Beaucage SL and Caruthers MH (1981) Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters 22: 1859–1862.


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

Oligo synthesis: Why IDT leads the oligo industry—Read about the phosphoramidite method of oligonucleotide synthesis that IDT uses in its manufacturing processes. We also highlight the additional measures we take to ensure our customers receive the highest quality oligos and nucleic acid products in the shortest time possible. 

ESI mass spectrometry—why we use it for oligonucleotide quality control—IDT has been, and still is, a pioneer in using mass spectrometry for quality control in oligonucleotide synthesis. Learn about why a particular method, electrospray ionization (ESI), is used ubiquitously in our manufacturing processes.

SameDay™ Oligos—Need oligos fast? SameDay™ Oligo orders placed online by 3:00 pm ET in the United States can be shipped priority for delivery by 10:30 am the next business day. Expedited shipping from our European and Singapore manufacturing facilities as well.

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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