Processing
Ultramer™ RNA Oligonucleotides
Single-stranded RNA oligos up to 120 bases, desalted and delivered dry in tubes
Ultramer RNA Oligonucleotides are manufactured using proprietary synthesis methods that deliver high-quality, long RNA oligos.
Ordering
- Each oligo is quality controlled by electrospray ionization mass spectrometry (ESI-MS)*
- Increase hybridization precision in your experiments using longer RNA oligos (60−120 bases)
- Supports RNA-related applications such as CRISPR and the generation of RNA controls and templates
- Receive guaranteed quantities of 4, 20, or 80 nmol
* With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be evaluated by ESI-MS.
Ultramer RNA Oligos
Formulated to guaranteed quantities of 4, 20, or 80 nmol. Shipped dry, in tubes.
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Product details
IDT has developed proprietary synthesis methods to deliver high-quality, long RNA oligos up to 120 bases. Ultramer RNA Oligos can be used in a variety of RNA-related applications. These include, but are not limited to:
- Single-guide RNAs (sgRNAs) for CRISPR
- Long RNAs for RNA structural studies
- RNA controls for PCR and qPCR
Ultramer RNA Oligos are desalted to remove small molecular impurities and formulated to 4, 20, or 80 nmol.
In addition, your oligos will be verified via 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.
Using the RNA Oligo Entry tool
- To enter individual RNA bases, insert "r" before the base (rA, rU, rC, rG)
- To enter individual 2'-O-Methyl RNA bases, insert "m" before the base (mA, mU, rC, rG)
- To quickly convert an entire oligo to RNA, enter your sequence as DNA using A, T, C, G and then click "Convert to RNA''. All bases in your sequence will be converted to RNA (rA, rU, rC, rG)
Product data
IDT employs proprietary equipment that permits rapid, high-quality synthesis of nucleic acids. However, this platform can be modified to a lower throughput mode that uses an "extra rich" synthesis cycle. Truncated byproducts of synthesis obscures mass spectra, making it difficult to deconvolute and identify the desired species. However, our mass spectrometry methods enable us to confidently QC your Ultramer RNA Oligos up to 120 bases (Figure 1,2). We provide ESI-MS quality documentation for every oligo we synthesize*. Overall, these improvements to our already established manufacturing methods allow you to acquire longer, purer oligos for your research.
* With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be evaluated by ESI-MS.
Figure 1. QC data illustrate the quality of a sample 90mer Ultramer RNA Oligo. The measured molecular weight of the oligo matches its expected molecular weight, which is determined by the specific oligo sequence. Data generated from ESI-MS instruments at IDT.
Figure 2. QC data illustrate the quality of a sample 120mer Ultramer RNA Oligo. The measured molecular weight of the oligo is within 0.01% of its expected molecular weight, which is determined by the specific oligo sequence. Data generated from ESI-MS instruments at IDT.
Services
To provide you with an exceptional experience when using our custom oligos, we offer a range of custom purification, formulation, and quality control services. To learn more about available services for Ultramer RNA Oligos, click here.
Large-scale synthesis
Custom RNA oligos can be ordered in bulk with the same high purity you expect from IDT. For further information about our large-scale synthesis capabilities, click here.
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
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 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.
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 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 stability of RNA vs. DNA?
RNA is inherently less stable than DNA due to its chemical structure. Additionally RNases are more prevalent in standard laboratory conditions than DNases. As even the slightest exposure to RNase can impact RNA stability, IDT has not performed rigorous long term stability studies for RNA.
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.
What is the fidelity of your Ultramer® Oligonucleotide synthesis?
Standard DNA oligos have a coupling efficiency of 99.2%. Ultramer oligos have a 99.5% coupling efficiency. This increase results in higher fidelity synthesis. With both syntheses, purification may be recommended for longer oligos based on your specific application. For further information regarding Ultramer oligos, please see our Ultramer Oligos Catalog Page at www.idtdna.com.
What is the difference between scale and yield, and why don’t I receive that full amount designated by the scale I order?
Oligo synthesis is accomplished through a series of steps, including coupling of individual bases, cleaving the oligo from the solid support, desalting, and if requested, purification of the oligo by HPLC or PAGE. No chemical reaction occurs with 100% efficiency, and, thus, each of these steps will incur a loss of final yield, which varies from specific sequence synthesis to synthesis. Due to this variation, IDT custom oligos are ordered according to the amount of starting material used for the synthesis, referred to as the scale. While we cannot predict the actual final yield, we do guarantee a specific minimum yield for each oligo based on its sequence, starting scale, and the typical yield obtained under those specified conditions. If you would like to know the minimum guaranteed yield for a specific oligo, simply add it to your Shopping Cart. The Shopping Cart provides you with the guaranteed minimum yield. If it is insufficient or excessive for your needs, simply edit the scale. Please contact our Technical Support Department at 1-800-328-2661 or techsupport@idtdna.com if you have any questions about the yield you have received.
What is CE service?
CE, short for capillary electrophoresis, is a purity measurement utilizing a gel filled capillary to assess the proportion of full-length products to truncated products present in the final oligo sample. HPLC or PAGE purified oligos up to 60 bases in length receive a complimentary CE trace to document final purity.
Read more about CE in the Tech Vault document entitled Capillary Electrophoresis of Oligonucleotides.
Read more about CE in the Tech Vault document entitled Capillary Electrophoresis of Oligonucleotides.
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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