Affinity Plus™ DNA & RNA Oligonucleotides

There are no structural differences between the locked nucleic acids used in Affinity Plus and PrimeTime LNA* qPCR Probes. Functional performance data can be found on the Affinity Plus qPCR Probes page. While these modified probes provide identical performance, Affinity Plus qPCR Probes provide a better value.

Learn more about Affinity Plus qPCR Probes.

*LNA is a registered trademark of Qiagen,

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Yes, locked nucleic acids are available as Affinity Plus DNA & RNA Oligonucleotides, which can be designed to contain 1 to 20 locked nucleic acid bases.

To include an Affinity Plus base in your sequence, simply place “+” in front of the base, e.g., +A+C+G+T.

Learn more about Affinity Plus DNA & RNA Oligonucleotides.

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For most applications, it is best to purify PCR products by gel electrophoresis.

This simple method not only purifies the final PCR product but can be a valuable troubleshooting tool as well since nonspecific PCR products, primer-dimer products, negative amplification, and other elements can easily be identified by gel analysis.

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Partial shipping means that we are shipping the oligos you ordered to you as they are completed, rather than our default method of waiting to ship until the entire order is complete, with all of the oligos shipping at the same time. We make every effort to synthesize and ship your oligos as quickly as possible because we know that they are time sensitive.

On occasion, one or more oligos may become delayed, e.g., because they did not pass one of our quality control checks or their processing took longer than anticipated. In these cases, we can ship you a partial order at your request. You can also choose to have your order ship partial if you know some of your oligos will take longer than others (because of purification, etc.)—such requests will incur an extra shipping charge.

If you would like to set an order to ship partial, you can request it at the time of checkout or  contact us.

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Standard desalted oligos can be used in routine PCR, qPCR, and DNA sequencing applications.

Through improvements to the traditional phosphoramidite chemistry and advances in instrumentation, IDT has obtained a coupling efficiency that allows standard desalt oligos to work well for these applications.

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We do not do post-synthesis sequencing of oligonucleotides. However, the oligos are checked by mass spectrometry to check that the oligos have the correct molecular weight.

The products we perform post-synthesis sequencing on are the double-stranded gBlocks™ Gene Fragments, and the Gene and Mini Gene™ synthetic genes.

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Yes, IDT can synthesize oligonucleotides for customers using trimer phosphoroamidites. You can order Trimer 19 using modification code /iTriMix19/, or Trimer 20 using modification code /iTriMix20/.

To order a Custom Trimer Mix, contact us.

Oligos containing Custom Trimer Mixes can be ordered with standard desalt (recommended for oligos containing mixes), provided that other modifications included in the sequence do not require HPLC.

For more information about trimer mixes, contact us.

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Although it may be possible to anneal oligos at room temperature, heating to denature the oligos and then cooling slowly to anneal the two oligos will help to ensure more efficient annealing and favor the stable duplex formation.

If you choose not to heat the oligos, it would be prudent to carefully screen the oligos for secondary structures which could interfere with the annealing reaction.

More information on how to anneal oligos can be found in the Annealing Oligos DECODED™ article.

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Though the majority of product will be the desired sequence, standard desalt oligos will contain a heterogeneous population of sequences, and this heterogeneity will increase with increasing length of the oligo. Oligos are synthesized 3'->5', base by base, through a series of chemical reactions. Chemical reactions are rarely, if ever, 100% efficient; the coupling reaction itself is approximately 99.6% efficient. With each base addition, less than 1% of the growing oligonucleotide chains will not undergo base extension.

After base coupling, we perform a capping step to prevent any truncated molecules from participating in further base addition. Because the capping reaction is slightly less than 100% efficient, a very small percentage of the truncated mutants will remain uncapped and can react during subsequent couplings steps. This leads to the formation of deletion mutants. The resulting oligonucleotide preparation, while comprised mostly of the ordered sequence, is a mixture of the full length oligos, truncated sequences, and sequences with internal deletions.

For exceptionally long oligos, such as our Ultramer™ Oligonucleotides and xGen™ Hyb Panels, IDT uses a proprietary IDT Ultramer synthesis process, which has been designed to give a high coupling efficiency (99.6%). This high coupling rate helps to allow us to synthesize long oligos (xGen Custom Hyb Panels are 60–120 bases long) with a high percentage of full-length product.

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For long term oligo storage, temperature is the most important factor to consider. For long term storage, whether oligos are dried down, or resuspended in non-DEPC treated water or TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA; such as IDTE), we recommend that you store your oligos at –20°C.

For 4°C storage, oligos are stable for at least 60 weeks when stored dry, or resuspended in non-DEPC treated water or TE buffer (10 mM Tris pH 8.0, 0.1 mM EDTA; such as IDTE).

It is also important to note that for DNA oligos, an acidic pH can induce depurination, therefore maintaining a neutral pH is important. For RNA oligos a neutral pH is also important, as basic pH buffers can induce RNA breakdown.

Please see the DECODED, Storing oligos: 7 things you should know, for data on oligonucleotide storage and a more thorough explanation.

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Oligonucleotides provided by IDT are desalted—free of added salt. First, no inorganic salts, such as sodium or magnesium, are used when DNA is synthesized chemically. Our standard desalting step refers to the removal of small organic molecules left over from synthesis.

The desalting process does remove the majority of these organic molecules, though trace amounts can still be present in a shipped oligo.

For the most demanding applications sensitive to even trace amounts of salts, e.g., NMR or crystallography, upon receipt we recommend dialyzing your oligos or using a size exclusion column as a clean-up step.

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All of the custom DNA and RNA oligonucleotides that IDT offers are synthesized chemically, not enzymatically. As a result, there should not be DNase or RNase present.

It is worth noting that there are abundant nucleases present in most environments, so good laboratory practice is very important to minimize potential exposure. IDT also offers RNaseAlert® and DNaseAlert™ substrates to help identify nuclease degradation.

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