TechVault
  • 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.
  • 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.

  • Is my oligo still good after X amount of time?

    This will depend on how the oligo has been stored.  Our on-going stability study addresses oligos stored dry, in TE and in water, at –20°C, 4°C, and 37°C.  Please see the Technical Report, Oligonucleotide Stability Study, for data and a more thorough explanation.

  • Do modifications affect the stability or shelf life of oligos?

    For the modifications tested at this point, the pattern of degradation seen for modified oligos is similar to that for standard oligos.  Those are:

    For optimal stability, oligos that are to be stored long term should be stored frozen, at –20°C.  If the oligos are going to be resuspended, storage in a TE buffer (10 mM Tris, 0.1 mM EDTA, pH 7.5–8.0; such as IDTE) is better than using water (non-DEPC treated). The impact from the type of storage medium used is marginal at -20°C, but becomes more important at higher temperatures. It is ideal to store oligos in the dark. Exposure to UV light should be avoided, and ambient lab light should be minimized, particularly for some types of modified oligos.

    Please see the Technical Report, Oligonucleotide Stability Study for data on oligonucleotide storage and a more thorough explanation.

    Studies are currently in progress with selected modifications and further specific information will be available in the future.

  • What is the shelf life and stability for other IDT products that aren't included in the IDT Oligonucleotide Stability Study?

    Our stability studies have been performed with sequences designed to represent a practical range of the oligos we produce. It is important to remember that sequence variations may impact stability. The only way to know the precise stability of a specific oligo is to perform functional stability studies on that specific oligo.

    A summary of the results from the IDT Oligonucleotide Stability Study (as of May 1, 2014) can be found in the Technical Report, Oligonucleotide Stability Study.

  • Can an expiration date be printed on the oligonucleotide tube label?

    Yes, IDT can provide custom labels that include the oligo expiration date. Please contact customquotes@idtdna.com for more information regarding the quotation process for this service.

  • Do freeze / thaw cycles affect oligo stability?

    IDT has functionally tested oligo stability after up to 30 freeze/thaw cycles. These oligos were stored in both water and TE buffer. We have not found a significant impact on oligo function over the course of these 30 freeze/thaw cycles. Please see the Technical Report, Oligonucleotide Stability Study, for this data.

  • 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 should I be concerned about when designing multiplex qPCR assays?
    The most important aspect of multiplex qPCR to consider is potential negative interactions between PCR components, specifically the primers. Primer dimer formation can significantly decrease amplification efficiency. Therefore, you should analyze heterodimer potential between all of the primers included in your reaction to ensure that any structures predicted to form will not be strong enough to significantly affect the reaction. As with primer design for a singleplex reaction, strive for a ΔG value more positive than -9 kcal/mole for all predicted heterodimers. The IDT SciTools® OligoAnalyzer® application is ideal for this purpose.
  • 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.
  • I’ve been using Tsug’s Rule to calculate the Tm of my oligonucleotide. Is that still the best method to calculate Tm?
    While these rules of thumb offer a general approximation of Tm, there are better algorithms available that are free and easy to use, and that will provide an extremely accurate Tm estimation. We offer one such algorithm for free use in our SciTools® OligoAnalyzer® application (see http://www.idtdna.com). This detailed equation takes into account the effects of sodium and magnesium on Tm calculations. These cations have a significant impact on the functional Tm of an oligonucleotide in solution due to their charge. For the most accurate Tm estimation we recommend entering your sequence and adjusting the ionic concentrations in the OligoAnalyzer tool so that they match your reaction conditions. You can view the exact algorithm used for our Tm calculations by clicking on the Definitions link in the OligoAnalyzer program.
  • How can I determine if a hairpin in my oligo is too strong to allow hybridization?
    Using free OligoAnalyzer® software, part of the IDT SciTools programs, enter your oligonucleotide sequence and choose “Hairpin.” The software will generate a series of possible hairpin structures. You can arrange these structures in order of decreasing melting temperature (Tm). If the highest hairpin Tm is at or above your annealing temperature, that hairpin is likely to impede hybridization.
  • How do I resuspend my PrimeTime® qPCR Assay?
    PrimeTime qPCR Assays can be re-suspended as 40X, 20X, or 10X stocks. Different concentrations may be preferred depending on the size of the assay and desired final reaction volume. Resuspend the assay in IDTE Buffer (10 mM Tris, 0.1 mM EDTA pH 8.0—available from IDT) at the volumes indicated in the chart below. After adding the volume indicated, pipette the solution up and down the sides of the tube to ensure maximal product recovery. Following resuspension, store at –20°C.

  • Can I email an order to IDT?
    IDT offers two convenient ways to order: via our website and by email. Templates for email orders can be found by going to www.idtdna.com > Home > How to Order. Once completed, simply email the template to orders@idtdna.com. If you are unable to use the Excel template, your email order should include the following information in the body of your email: your name, address, and phone number; the name of your institution; payment information for the order; the name of your Principal Investigator (PI); the synthesis scale and sequence of the oligos you want to order. Entering sequences one oligonucleotide per line will ensure the sequences are communicated correctly.
  • How can I review my order history, and how do I update it if I move?
    To review your order history, go to the “Order” tab on the IDT website (www.idtdna.com) and select “Order History”. If you move to a new institution, you will need to create a new web account. If you retain access to your old account, you will still be able to see your old order history when logged into that account.
  • Why are some of the items in my order history not available for re-order?
    IDT occasionally makes updates to our catalog, resulting in changes to or discontinuation of previously offered products. To know specifically why a product is unavailable for re-order through your order history, and to discuss options, please contact IDT Customer Care.
  • Will IDT synthesize aptamers for me?

    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.

  • Does IDT allow base modifications with their gene products?
    IDT requires both strands of Genes and MiniGenes products to be 100% complementary. Therefore, mixed bases and modifications are not available for this product type—Genes and MiniGenes sequences may only be composed of A/C/G/T bases. Genes and MiniGenes products are delivered double-stranded in a vector. Ultramer™ Oligonucleotides, which allow mixed bases, can be used for gene synthesis if your method allows.
  • How can I check my order status?
    Checking the status of your order is as easy as logging into your account at our website and checking your order history via www.idtdna.com > Order > Order History. Alternatively, you can contact IDT Customer Care by phone or through our Web Chat feature, also located on our website in the upper right hand corner of the homepage (see the article Your Questions Answered by a Live Expert: IDT Web Chat Service for more information on using Web Chat).
  • Why should I sequence multiple colonies when cloning?
    Sometimes researchers will pick just a colony or two for sequencing. If they find problems with their clone, they may conclude something must be wrong with their primers when they simply have picked a bad colony. IDT recommends sequencing at least 8–10 separate colonies to get a realistic representation of the clonal population and to provide a good chance of finding the correct sequence if one exists.