Processing
Ultramer™ DNA Oligonucleotides
Long, high-quality oligos for demanding applications such as cloning, ddRNAi, homology-directed repair, and gene construction
Ultramer DNA Oligonucleotides are generated by proprietary synthesis methods that deliver high-quality oligos up to 200 bases. They are available single- or double-stranded and can be delivered in tubes or plates.
Ordering
- Available single- or double-stranded and can be delivered in tubes or plates
- Unrivalled control of oligo specifications with custom formulation and mixing options
NEW! Try our Alt-R™ HDR Donor Oligos; single-stranded DNA oligos specifically built for your homology-directed repair (HDR) experiments. Designed and optimized through extensive wet-bench testing, Alt-R HDR Donor Oligos are ideal for introducing point mutations and short insertions.
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Ultramer DNA Oligos
Formulated to 4 nmol or 20 nmol guaranteed yield. Shipped dry or resuspended to 100 µM in IDTE buffer, pH 8.0.
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Duplexed Ultramer DNA Oligos
2 oligos, annealed and delivered in a single tube. Formulated to 4 nmol or 20 nmol guaranteed yield. Shipped dry.
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The following annealing fees will be applied to each duplex ordered:
4 nmol:
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20 nmol:
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Ultramer DNA Oligos
Shipped dry or resuspended to your specifications. Minimum 24 and 96 oligos required for 96- and 384-well plates, respectively. 200 pmol scale requires a minimum of 96 oligos.
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Duplexed Ultramer DNA Oligos
1 oligo pair per well, annealed. Shipped dry or resuspended in duplex buffer. Minimum of 24 and 96 oligos required for 96- and 384-well plates, respectively.
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The following annealing fee will be applied to each plate of duplexes:
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For ordering inquiries, please contact us.
Product details
Ultramer DNA Oligos are long, single- and double-stranded synthetic DNA sequences. They are manufactured with an synthesis platform that consistently results in coupling efficiencies over 99.5%. Ultramer DNA Oligos can be used in a variety of molecular biology applications, including (but not limited to):
- Site directed mutagenesis—used to efficiently and quickly generate large insertions, deletions or change stretches of sequence identity
- In vitro transcription—templates for the synthesis of RNA
- DNA-directed RNAi (ddRNAi)—hairpins are cloned into an expression vector, such as the GeneClip™ U1 Hairpin Cloning System (Promega)
- qPCR—as DNA standards
- CRISPR genome editing—as HOR templates
Every Ultramer DNA Oligo you receive will be deprotected and desalted to remove small molecule impurities. In addition, your oligos will be checked via electrospray ionization mass spectrometry (ESI-MS)* and quantitated by UV spectrophotometry.
*With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be evaluated by ESI‑MS.
Available modifications for Ultramer DNA Oligos
| Description | 200 pmol Ultramer DNA Oligo | 4 nmol Ultramer DNA Oligo | 20 nmol Ultramer DNA Oligo | PAGE Ultramer DNA Oligo |
|---|---|---|---|---|
| Availability | Plates | Plates and tubes | Plates and tubes | Tubes |
| 5' Phosphorylation | • | • | • | • |
| 5' Biotin | • | • | • | • |
| 5' Amino Modifier C6 | • | • | • | |
| 5' Amino Modifier C12 | • | • | • | |
| 5' deoxyInosine | • | • | • | • |
| 5' deoxyUridine | • | • | • | • |
| Int deoxyInosine | • | • | • | • |
| Int deoxyUridine | • | • | • | • |
| Phosphorothioate Bond | • | • | • | • |
| 2' O-Methyl RNA bases | • | • | • | • |
| 3' Amino Modifier | • | • | ||
| 5' 5-Methyl dC | • | • | • | |
| Int 5-Methyl dC | • | • | • | |
| Int Spacer 18 | • | • | • | |
| 3' C3 Spacer | • | • | • |
Product data
IDT proprietary DNA synthesis equipment permits rapid, high-quality synthesis of nucleic acids. This platform is adjusted to a lower throughput mode which uses an "extra rich" synthesis cycle for long oligos. Along with this refined synthesis cycle, Ultramer DNA Oligos use a solid support that is specifically designed to synthesize low-yield, high-quality oligos up to 200 bases in length. Overall, these improvements to our already established manufacturing methods allow you to acquire longer, purer oligos for your research. Figure 1 illustrates the quality of Ultramer DNA Oligos.
Figure 1. IDT proprietary platforms have a better coupling efficiency than other suppliers, which provides more full-length oligonucleotides in your order. Small increases in coupling efficiency (≤1%) result in measurable increases in full-length product yield. The curves represent the theoretical yield for different lengths of oligos based on a coupling efficiency of 99.4% (IDT Oligos, n = 126) and 99.1% (other suppliers, n = 134 from three different suppliers) using the formula, percent full length product = (eff )(n-1)*100 where eff = coupling efficiency (for example, 99.4% = 0.994) and (n–1) is the number of coupling reactions needed to make an oligo of length n.
Our proprietary ESl-MS methods allow us to confidently provide quality control documentation for your oligos up to 200 bases in length.* These QC traces, such as the examples shown in Figure 2, are available online free of charge.
*With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be evaluated by ESI-MS.
Figure 2. QC data shows high purity of 185 nt and 189 nt Ultramer DNA Oligos. The measured molecular weight of each oligo is within 0.01% of its expected molecular weight. Data generated from in-house ESI-MS instruments.
Services
Formulation
Diverse laboratory configurations and various individual preferences in the field require oligos that can be delivered in unique formats. With the formulation services listed below, you can have your oligos tailor-made to your specific requirements. Learn more »
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Custom quality control
In addition to the free ESI-MS analysis that comes standard with your oligos,* your project may require one of the analytical services listed below. Learn more »
*With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be evaluated by ESI‑MS.
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GMP and OEM
If you require oligos that are ISO 13485:2016 certified, or if you are interested in our third-party manufacturing services, please click here.
Resources
Frequently asked questions
Optimal Length for Left & Right Homology Arms for CRISPR?
DNA with homology to the sequences flanking a double-stranded break (DSB) can serve as template for error-free homology directed-repair (HDR) of the DSB. The efficiency of HDR is determined by the concentration of donor DNA present at the time of repair, length of the homology arms, cell cycle, and activity of the endogenous repair systems in the particular cell [1]. These factors contribute to the high variability of HDR efficiency observed across different cell lines, and particularly in immortalized cells [2]. Typically, in replicating mammalian cells, donor arms are at least 500 bp in length [3]. However, it is important to determine the optimal HDR conditions for your cell line.
Inserts between the homology arms are frequently in the 1–2 kb range [4]. While longer inserts are possible, the efficiency of recombination decreases as the insert size increases [5]. Finding successfully integrated inserts is likely to be challenging when inserts are greater than 3 kb in most mammalian cells.
Single-stranded oligo DNA (ssODN) has recently been identified as a substrate that is preferred by the HDR mechanism and often achieves good efficiency with homology arms as short as 40 bp [6,7]. The drawback to using ssODNs is that they are limited in length to a few hundred bases, so the insert size is limited. When using Ultramer® oligos as templates for a short insertion, tag, or SNP conversion, we have found arm lengths of 30–60 nt to be sufficient.
References
- Elliott B, Richardson C, et al. (1998) Gene conversion tracts from double-strand break repair in mammalian cells. Mol Cell Biol, 18(1):93–101.
- Lin S, Staahl BT, et al. (2014) Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife. 3:e04766.
- Thomas KR, Folger KR, Capecchi MR (1986) High frequency targeting of genes to specific sites in the mammalian genome. Cell, 44(3):419–428.
- Dickinson DJ, Ward JD, et al. (2013) Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Methods,10(10):1028–1034.
- Li K, Wang G, et al. (2014) Optimization of genome engineering approaches with the CRISPR/Cas9 system. PloS One, 9(8):e105779.
- Chen F, Pruett-Miller SM, et al. (2011) High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods, 8(9):753–755.
- Davis L and Maizels N (2014) Homology-directed repair of DNA nicks via pathways distinct from canonical double-strand break repair. Proc Natl Acad Sci U S A, 111(10):E924–932.
Will you synthesize aptamers?
Yes. If you can provide the aptamer sequence(s), you can order directly from the IDT website. To order online choose “Main Menu” from the “Order” drop-down menu. Click on “Custom DNA Oligos,” or if your sequence contains RNA bases, “Custom RNA Oligos.”
Enter your desired scale, sequence, and purification.
If you are ordering aptamers with a fixed sequence, IDT recommends HPLC or PAGE purification. For aptamer libraries containing random bases, IDT recommends standard desalt.
Enter your desired scale, sequence, and purification.
If you are ordering aptamers with a fixed sequence, IDT recommends HPLC or PAGE purification. For aptamer libraries containing random bases, IDT recommends standard desalt.
Will I lose more oligo when resuspending in polystyrene tubes compared with polypropolyene tubes?
Oligonucleotide can be lost due to adsorption into the tube wall when storing the DNA in polystyrene. We recommend using polypropylene tubes for oligonucleotide storage to minimize such loss.
All IDT oligonucleotides are shipped out in low absorption polypropylene tubes which can be used for long term storage without significant loss of material.
All IDT oligonucleotides are shipped out in low absorption polypropylene tubes which can be used for long term storage without significant loss of material.
Why should I consider purification of my oligos?
Purification removes truncated products and other synthesis impurities. Our experience has shown that purifying an oligonucleotide that will be used in demanding applications saves both time and money in the long run. We recommend considering additional purification for any oligonucleotide that is to be used for an application other than routine PCR or DNA sequencing.
As a general rule, IDT also recommends that any oligonucleotide longer than 40 bases should receive further purification.
As a general rule, IDT also recommends that any oligonucleotide longer than 40 bases should receive further purification.
Why is your ordering system not recognizing the universal IUB codes I am using to specify mixed (degenerate, random, wobble) bases?
Be sure to use upper case letters (e.g., R, N, S) to denote mixed (degenerate, random, wobble) bases. Lower case letters are not recognized as they are used to denote certain modifications and RNA bases.
The codes are provided here:
The codes are provided here:
Why is freezing in TE buffer recommended over storing oligos dry?
It is important to remember that ‘dry’ oligos always have some level of moisture present, and are never actually completely dry. This is one of the contributing reasons for why resuspension in TE buffer (10 mM Tris, 0.1 mM EDTA, pH 7.5–8.0; for example, IDTE) provides a more stable long-term storage method compared to oligos stored dry.
However, oligos stored dry or in non-DEPC treated water, are very stable for the short period of time it takes to ship an oligo. IDT ships its oligos dry to provide the researcher complete control over the reagents they want to use for resuspension.
Please see the Technical Report, Oligonucleotide Stability Study, for data on oligonucleotide storage and a more thorough explanation.
However, oligos stored dry or in non-DEPC treated water, are very stable for the short period of time it takes to ship an oligo. IDT ships its oligos dry to provide the researcher complete control over the reagents they want to use for resuspension.
Please see the Technical Report, Oligonucleotide Stability Study, for data on oligonucleotide storage and a more thorough explanation.
Why does the shipped quantity of product vary even for reorders of the same sequence?
Every IDT custom oligo is synthesized to order through a series of tightly controlled steps, including the coupling of the individual bases, cleaving the oligo from the solid support, desalting, and if requested, purification. Each of these steps will result in a loss of final yield, which varies with each synthesis. Due to this variation, IDT oligos are ordered according to the amount of starting material, also referred to as the scale. All custom oligos are assigned a minimum yield guarantee, but lot-to-lot variability in the final delivered quantity should be expected, even when reordering the same sequence. For further questions about this subject, please contact custcare@idtdna.com.
Why do the scale I order and the amount of oligo I receive differ—I receive less than the requested scale quantity?
The scale you order determines the amount of sequence-initiating base used to begin synthesis of your oligonucleotide. Since oligonucleotide synthesis (or any chemical reaction) is never 100% efficient, the amount of final product recovered after synthesis and purification steps (yield) will always be less than the starting amount used for synthesis. Modifications, secondary structures, and purification services further affect the final yield for a given construct.
IDT offers guaranteed yields based on all of these factors that define the minimum amount of oligonucleotide you will receive for a given construct.
The minimum yield guarantee is listed in the shopping cart and in your confirmation email.
To receive a higher final yield, select a larger synthesis scale. For further discussion on this topic, see the Technical Report, Oligonculdotide Yield, Resuspension, and Storage.
IDT offers guaranteed yields based on all of these factors that define the minimum amount of oligonucleotide you will receive for a given construct.
The minimum yield guarantee is listed in the shopping cart and in your confirmation email.
To receive a higher final yield, select a larger synthesis scale. For further discussion on this topic, see the Technical Report, Oligonculdotide Yield, Resuspension, and Storage.
Why do my primers have deleted 3' bases in the amplified fragment when I use a proofreading enzyme for PCR?
Proofreading polymerases (Pfu, Diamond Taq®, etc) have been shown to remove 3' bases from PCR primers (see Nucl Acids Res 20(14):3551-3554, for more information). If you experience this problem, you can protect your primer from degradation by adding one or more phosphorothioate bonds to the 3' end of your primer. Also make sure to add the enzyme last, after the addition of dNTPs, in your PCR to minimize the risk of this issue taking place.
Why can’t I select a quantity when I order custom oligos?
IDT Custom DNA Oligos are available at several synthesis scales and are usually supplied dried down. Therefore, we do not offer the option for a quantity of tubes. Even with our lowest synthesis scale, the yield delivered is sufficient for thousands of reactions with most standard applications. Due to this excess of product, most researchers resuspend oligos as a concentrated stock solution and, from that, create several tubes of working solution. IDT also offers several options for normalization and preparative services. Please contact Customer Care at custcare@idtdna.com for additional information on custom formulation.
Why are my oligos a yellow/brown color?
Customers who are new to working with large amounts of material are sometimes surprised when they see a yellow or brown discoloration to their oligos. If you have experienced this, do not worry. Color variation is normal in custom synthesis, especially as concentration increases. Importantly, IDT does not expect this to affect oligo function in customer’s experimental applications.
The image above depicts normal color variation, as seen in oligo pools which are formulated to the same concentration (200 nmol oligos in 15 mL solution). In general, modified oligos at larger scales are more likely to display the variation seen above, while small-scale unmodified oligos (e.g., 25 nmol) tend to remain colorless in solution.
The image above depicts normal color variation, as seen in oligo pools which are formulated to the same concentration (200 nmol oligos in 15 mL solution). In general, modified oligos at larger scales are more likely to display the variation seen above, while small-scale unmodified oligos (e.g., 25 nmol) tend to remain colorless in solution.
Where do I find my QC data?
If you placed your IDT order through the web, quality control documents will be uploaded to your web account. These documents can be accessed under Order History, which can be found in the Order dropdown menu on the IDT website.
When searching for old orders, you may need to adjust the date range using the Search link located in the upper right hand corner.
For further help, contact Customer Care at CustCare@idtdna.com.
When searching for old orders, you may need to adjust the date range using the Search link located in the upper right hand corner.
For further help, contact Customer Care at CustCare@idtdna.com.
Where can I find a fax order form or excel template to order DNA oligos?
IDT no longer takes orders by FAX. Instructions for how to order via email can be found by going to the Home drop down menu, and clicking on How to Order. There, you will find an email Order template.
When will my oligos be shipped?
SameDay® oligos ordered online before 3:00 pm ET (US and Canada) or 1:00 pm CET (Europe) will ship the same day the order is received. Standard oligos are shipped using overnight delivery within 24 hours of receipt of your order.
For US and Canada orders, Rapid HPLC and HOTplate™ oligos ordered online before 3:00 pm ET and Express Dual-Labeled Probe orders placed online before 2:00 pm ET are shipped the next business day. HPLC- or PAGE-purified oligos are routinely shipped within 3 to 5 working days.
For EU orders, there is no cut-off time for Rapid HPLC and HOTplate oligos and Express Dual-Labeled Probe orders, which are shipped the following business day.
For turnaround time of standard plate orders, contact Customer Care at custcare@idtdna.com or phone (US and Canada only) 1-800-328-2661.
For US and Canada orders, Rapid HPLC and HOTplate™ oligos ordered online before 3:00 pm ET and Express Dual-Labeled Probe orders placed online before 2:00 pm ET are shipped the next business day. HPLC- or PAGE-purified oligos are routinely shipped within 3 to 5 working days.
For EU orders, there is no cut-off time for Rapid HPLC and HOTplate oligos and Express Dual-Labeled Probe orders, which are shipped the following business day.
For turnaround time of standard plate orders, contact Customer Care at custcare@idtdna.com or phone (US and Canada only) 1-800-328-2661.
When using the IDT online Resuspension calculator (SciTools), is it more accurate to use Extinction Coefficient or MW for single-stranded oligos?
Either value should provide the same results, using the Resupension Calculator.
When calculating the Tm of my oligo, should I only use the bases which are complementary to my target or should I also include any sticky overhangs on the primer?
To determine the relative Tm of primers with non-complementary overhangs, only the complementary region should be taken into account.
You can obtain the Tm using the free, online OligoAnalyzer tool.
You can obtain the Tm using the free, online OligoAnalyzer tool.
What options do you offer for oligos ordered in plates?
We offer both 96- and 384-well plates in the following plate types: Deep Well, V-bottom, and PCR. Matrix plates are also available for an additional fee. Oligos can be normalized to a specific yield, volume, and concentration at no extra charge.
What molar concentrations of oligonucleotide and salts are used to calculate the Tm reported on specification sheets?
The Tm value reported on our spec sheets uses a 25 µM oligonucleotide and a 50 mM salt concentration. It does not take into account dNTP or Mg2+ concentrations.
To get an accurate Tm for your specific application, all of these concentrations should be input and adjusted to match the reaction conditions you plan to use.
The free IDT OligoAnalyzer SciTool® (www.idtdna.com/scitools) calculates Tm for the concentrations you input.
To get an accurate Tm for your specific application, all of these concentrations should be input and adjusted to match the reaction conditions you plan to use.
The free IDT OligoAnalyzer SciTool® (www.idtdna.com/scitools) calculates Tm for the concentrations you input.
What is the standard desalting procedure IDT uses for newly synthesized oligos, and what additional purification options do I have?
IDT uses a proprietary desalting technique that removes some truncation products and small organic contaminants from the synthesized oligonucleotide preparation. Removal of n-1mers produced during synthesis requires additional PAGE or HPLC purification.
PAGE is recommended for unmodified oligos >80-100 bases, while HPLC is the preferred method for oligos modified with either fluorescent dyes or attachment chemistries.
PAGE is recommended for unmodified oligos >80-100 bases, while HPLC is the preferred method for oligos modified with either fluorescent dyes or attachment chemistries.
What is the shelf life of my oligo?
The shelf life of an oligo is dependent on the temperature at which the oligo is stored, and how the oligo is resuspended. Temperature is the more important of the 2 variables. Generally, oligos should be stored at –20°C. At this temperature an oligo has a minimum shelf life of 2 years, whether it is stored dry / lyophilized, in TE buffer, or in (non-DEPC treated) water.
Please see the Technical Report, Oligonucleotide Stability Study, for data on oligonucleotide storage and a more thorough explanation.
Please see the Technical Report, Oligonucleotide Stability Study, for data on oligonucleotide storage and a more thorough explanation.
GMP refers to products manufactured under ISO 13485: 2016 QMS. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations for their legal marketing.
*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.
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