Oligo Handling, Analysis, and Applications
Support and Educational Content

Getting enough full-length oligo?

Coupling efficiency matters!

The coupling efficiency achieved by an oligonucleotide manufacturer has a direct effect on the quality of the oligonucleotides produced. When the coupling efficiency is high, there are fewer truncated products and deletions, resulting in a higher percentage of the desired sequence. In an industry where the standard coupling efficiency is 98.5%, IDT consistently exceeds that. The coupling efficiency for standard oligos from IDT is 99.2% and even higher—99.5%—for Ultramer® Oligonucleotides. This allows us to synthesize 70-base Ultramer oligos and achieve up to 70% full-length product; the same oligo synthesized at an average coupling efficiency of 98.5% by a competing manufacturer might only garner 35% full-length product at most (Figure 1). Thus what may appear as small differences in percentage translates to a dramatic difference in amount of full-length product.

A higher coupling efficiency means better performance

Why should coupling efficiency be important to you? Because there are more full length sequences present, you will likely see better and more consistent results in experiments when using an oligonucleotide manufactured with a higher coupling efficiency. This consistency also extends across multiple syntheses of an oligonucleotide. Thus, when re-ordering, you can be confident that the new oligonucleotide will function the same as an oligo from a previous synthesis, contributing to the consistency of your reactions and decreasing efforts needed to troubleshoot anomalous results.

The high coupling efficiency attained by IDT facilitates synthesis of sufficient full-length yields of high quality, long oligos, such as the IDT Ultramer® Oligonucleotides. This is one of the reasons IDT is unique in its field, as it is a feat our competitors struggle to accomplish. At the industry standard of 98.5% coupling efficiency, a 150mer is not commercially viable, as only 10% would be full-length.

IDT proprietary synthesis platforms yield the highest quality modified and unmodified oligonucleotides across various lengths. Even when these oligos are ordered without additional purification, the large percentage of full-length product can provide a substantial improvement in the data you collect. Effects of variance in oligonucleotide quality can influence many common molecular techniques, including cloning, mutagenesis, sequencing, and qPCR. While the industry standard is 98.5%, IDT recognizes that even modest gains in coupling efficiency lead to higher quality oligonucleotides and, therefore, improved sensitivity and consistency in experiments.

Product focus—Oligonucleotides and primers, 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.

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, 125–2000 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.

Related articles

My oligos have arrived: Now what?—Get these recommendations for resuspension and storage of newly received oligonucleotides.

Oligo Quantification—Getting it right—Learn why a supplier's yield readings can differ from what the researcher calculates after resuspension, and the importance of using the [right] molar extinction coefficient in calculations of oligonucleotide concentration.

Which type of oligo purification should I choose?—Review this advice for oligonucleotide purification based on oligo length, application, yield required, and presence of modifications.

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.

Author: Stephanie Youtsey, BA is a Technical Support Representative at IDT.

© 2013, 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.

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