RNA Oligonucleotides
All single-stranded and duplexed RNA sequences are produced using proprietary technology that delivers high quality RNA. Our specialized synthesis platforms allow us to produce the custom high-fidelity guides for CRISPR, duplexes for RNAi, template switching oligos for NGS, microRNAs, aptamers, and custom RNA oligos for other applications.
Ordering
Single-stranded RNA
Shipped dry.
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Duplexed RNA
2 oligos, annealed and delivered in a single tube. Shipped dry.
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Annealing fees will be applied to duplexed oligos (per duplex), as follows:
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Single-stranded RNA
Shipped dry or resuspended to your specifications. A minimum of 24 or 96 oligos required for 96- or 384-well plates, respectively.
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Product Details
RNA oligos are short, single- or double-stranded synthetic RNA sequences that can be used in nearly any RNA specific molecular biology application. Using the Oligo Entry ordering tool, you can design your sequences to contain unmodified RNA bases, 2'-O-methyl RNA bases, or chimeric DNA bases. You can select from hundreds of modifications to suit your specific research needs. (2'-O-methyl RNA is a useful RNA analog that is resistant to degradation by single-stranded ribonucleases. Every RNA Oligo you receive is deprotected and desalted to remove small molecule impurities. In addition, your oligos will be quality controlled using ESI mass spectrometry* and quantified by UV spectrophotometry to provide yield measurements.
* With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be accurately evaluated by ESI mass spectrometry.
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, mC, mG)
- 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)
Quality
IDT's reputation as a pioneer in custom oligo manufacturing is largely due to our vertically integrated proprietary synthesis platforms. Nearly every component of our manufacturing process is designed and developed in-house, including specialized synthesizers that can accommodate the most demanding oligo requests, and high-throughput automation. We rarely rely on third-party manufacturers for any of the machines or chemical reagents used for synthesis, allowing us to easily monitor and refine instruments and reagents. Our ability to control these variables allows us to produce high-quality oligos.The inherent structure of RNA makes it more difficult to manufacture than DNA. However, our proprietary nucleic acid synthesis technology allows us to obtain high coupling efficiencies, meaning you will receive RNA oligos with the yield and purity that your project needs.
Services
The following services represent our most common offerings. If your project requires a service not listed here, contact us and we will work with you to accommodate your request.
Purification
For more demanding RNA applications, additional purification by RNase-Free HPLC purification is needed. Most purified oligos up to 60 bases receive a purity guarantee* following quality control by capillary electrophoresis or analytical HPLC. Learn more »
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*Based on sequence characteristics
Formulation
Diverse application requirements and individual researcher preferences necessitate oligos that can be delivered in unique formats. You can have your oligos prepared to your specific requirements. Learn more »
For information on available services, contact us.
Custom quality control
In addition to the free ESI mass spectrometry analysis that is provided for your oligos*, your project may require one of the more advanced analytical services listed below.
* With the exception of mixed base oligos, which could potentially represent multiple sequences and therefore cannot be accurately evaluated by ESI mass spectrometry.
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Large-scale synthesis
Custom RNA oligos can be ordered in bulk with the same high quality, competitive pricing, and fast turnaround times you expect from IDT. To learn more about our large-scale synthesis capabilities, click here.
GMP and OEM
If you require oligos that are ISO 13485 certified, or if you are interested in our third-party manufacturing services, please click here.
Resources
Frequently asked questions
What is MALDI-TOF?
While small compared to nucleic acids from biological sources, synthetic oligonucleotides are nevertheless relatively large molecules, ranging in size from about 6000 daltons for a 20mer to 30,000 daltons for a 100mer. MALDI-TOF is useful for compounds up to ~15,000 daltons, or about a 50mer oligonucleotide. Samples above 15,000 daltons do not ionize and fly effectively and, additionally, are outside the optimal resolution range of these instruments.
Electrospray Ionization-Time of Flight (ESI-TOF) MS can resolve longer oligonucleotides, up to 80 nt. In the underlying MALDI technology the oligonucleotide test sample is mixed with a carrier or matrix (picolinic acid) and is deposited on a grid. The MALDI-TOF instrument uses pulses of laser light to vaporize the oligo/matrix in a process known as desorption. During this process, some molecules become ionized through protonation. The laser pulse can also fragment the molecule into a variety of charged and neutral particles (which can lead to spurious bands or artifacts in the resulting spectrum). In time of flight (TOF) mass spectrometry, ionized oligo molecules are accelerated by an electrostatic field in the mass analyzer to a common kinetic energy. With the same kinetic energy, lighter ions travel faster and heavier ions travel more slowly. The ionized particles enter at one end of the TOF tube, and the number of ions reaching a detector at the other end is recorded in a time-dependent manner. The lightest ions reach the detector first and the heaviest arrive last. The entire mass spectrum is recorded in a fraction of a second as ion flux versus time.
How do I convert my yield from nanomoles to ODs?
Calculating this conversion requires you to know the extinction coefficient for your sequence. With this, you can easily convert from your nanomole amount to ODs. To determine the extinction coefficient, you can analyze your sequence using IDT's free OligoAnalyzer™ Tool. Results from this analysis will also provide you with nmol/OD260 and µg/OD260 values.
Will you synthesize aptamers?
Yes. If you can provide the aptamer sequence(s), you can order directly from the IDT website.
To order online 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.
Will I lose more oligo when resuspending in polystyrene tubes compared with polypropolyene tubes?
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 will be used for an application other than routine PCR, qPCR, or Sanger DNA sequencing.
As a general rule, IDT also recommends that any oligonucleotide longer than 40 bases should receive further purification. For questions, please contact us.
Why is purification not recommended for randomized oligos?
Additional purification for oligonucleotides incorporating randomized bases can result in a bias in the degeneracy of the randomized bases.
Oligos with degenerate/randomized bases do not migrate in a tight distribution. Purification by either method (PAGE or HPLC) may purify out some of the randomized sequences. This results in the reduction of sequence diversity.
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, contact us.
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 our customers' 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.
When will my oligos be shipped?
IDT oligos have various estimated ship dates depending on product type and composition. Oligos added to the shopping cart will show an estimated ship date for each line item.
Once the order is placed, this estimated ship date can be found on the order confirmation email as well as in the order history of your web account. You can find the order history at idtdna.com/site/orderstatus/orderstatus.
Select the order number you wish to review, and the status and estimated ship date of each line item will be shown.
IDT will email you a confirmation when your order has been shipped. This shipping confirmation will include the tracking number of the package, which you can use to monitor the status of your shipment. If you have additional questions about your order, please contact us.
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.
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 entered and adjusted to match the reaction conditions you plan to use.
The free IDT OligoAnalyzer™ 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.
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 sodium salt exchange that is done after HPLC purification?
The sodium salt exchange we perform post-HPLC purification is a sodium acetate precipitation. It helps remove any remaining TEAA in the oligo preparation after HPLC purification.
It is important to make sure oligos used in in vivo assays are TEAA-free because it can be toxic to cells.
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 our DECODED™ article, Storing oligos: 7 things you should know, for data on oligonucleotide storage and a more thorough explanation.
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 us if you have any questions about the yield you have received.
What is the best way to purify PCR products?
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.
What is CE service?
What does OD260 stand for?
The heterocyclic ring structures in DNA and RNA absorb light with a maximum absorbance near 260 nanometers (nm). An OD260, or optical density 260, is defined as the amount of light at a 260 nm wavelength which will be absorbed by an oligo resuspended in 1 mL water and the concentration is read in a 1 cm quartz cuvette.
This method of measurement is considered the most accurate means of assessing the amount of oligonucleotide present following synthesis. The relationship between measured OD260, molar extinction coefficient (ε260), and oligonucleotide concentration is given as: OD260 = ε260 x concentration.
What conditions should I use to HPLC purify my oligos?
IDT uses our own proprietary HPLC method to purify oligos in-house. A published set of conditions for an RP-HPLC protocol is:
- Hamilton PRP-1 Reverse Phase column 250 x 10 mm
- Buffer A = 100% ACN (acetonitrile)
- Buffer B = ACN/0.1 M TEAA pH 7.3
- Run at 4 mL/min over 30 min from 95–60% A
- Monitor at 260/297 nm