oPools™ Oligo Pools

Calculate the appropriate resuspension volume for your oPools product with the  IDT Resuspension Calculator.

First, convert the oPool scale—provided in pmol—to a nmol quantity.

If your desired final concentration is µM per oligo, use this equation to determine your quantity:

pmol per oligo / 1000 = # nmol per oligo

Example 1. Final concentration of 1 µM per oligo.
Scenario: 50 pmol oPools Oligo Pool
Quantity: 50 pmol oPools Oligo Pool / 1000 = 0.05 nmol 
Final concentration: 1 µM

Resuspension calculator (Figure 1):

• Enter the quantity that you calculated
• Enter your final concentration
• Select Sgl-Stranded DNA (single-stranded DNA)
• Click Calculate

Figure 1. 50 pmol oPools Oligo Pool resuspended to 1 µM per oligo.

If your desired final concentration is nM per oligo, you can convert using this equation: 

nM concentration / 1000 = # µM

Example 2. Final concentration of 100 nM per oligo.
Scenario: 50 pmol oPools Oligo Pool
Quantity: 50 pmol oPools Oligo Pool / 1000 = 0.05 nmol 
Final concentration in µM: 100 nM  / 1000 = 0.1 µM
Resuspension calculator (Figure 2):

• Enter the quantity that you calculated 
• Enter your final concentration per oligo that you calculated
• Select Sgl-Stranded DNA (single-stranded DNA) 
• Click Calculate

Figure 2. 50 pmol oPools Oligo Pool resuspended to 100 nM per oligo.

If your desired final concentration is per pool, use this equation: 

(pmol per oligo x # of oligos in pool) / 1000 = # nmol per pool

Example 3. Final concentration of 1 µM per pool.
Scenario: 50 pmol oPools Oligo Pool containing 100 oligos
Quantity: (50 pmol x 100 oligos) / 1000 = 5 nmol
Final concentration: 1 µM
Resuspension calculator (Figure 3):

• Enter the quantity that you calculated
• Enter your final concentration
• Select Sgl-Stranded DNA (single-stranded DNA)
• Click Calculate

Figure 3. 50 pmol oPools Oligo Pool containing 100 oligos resuspended to 1 µM per pool.

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Yes, all oligos that go into  oPools Oligo Pools  are synthesized separately. The oligos are pooled before shipment.

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oPools Oligo Pools go through the standard desalting process.

We do not offer additional purification as the manufacturing process is designed to be as efficient as possible.

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The individual oligos in oPools Oligo Pools are pooled based on an assumed average yield. This average yield was generated using historical data from previously synthesized IDT Ultramer™ oligos.

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As there are no QC checks performed on oPools Oligo Pools, there are no guarantees in terms of sequence identity or individual oligo purity.

While we expect that the vast majority of sequences ordered in the pool will be present, we cannot guarantee that any individual oligo is present in the pool.

Historical data has shown the percentage of oligos missing from the pool to be less than 1%.

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The oPools Oligo Pools manufacturing process is designed to be as efficient as possible.

Therefore, there are no quality control checks or quantification.

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The oPools Oligo Pools manufacturing process is designed to be as efficient as possible. Therefore, we do not offer any formulation services on oPools Oligo Pools. All oPools Oligo Pools are delivered dry.

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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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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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