TechVault
  • Are N and K the only mixed bases are allowed for gBlocks Gene Fragments?
    Only N and K are available at this time. We are working on adding other mixed bases such as – R, Y, M, S, W, H, B, V, D. By letting us know what you need for your research on libraries@idtdna.com, you can influence how we prioritize our development efforts. In many cases, we can already offer suitable solutions, that are not offered online.
  • What are DNA/RNA hybrid oligos used for, and can IDT synthesize them?
    DNA/RNA hybrids are most commonly used in RNA silencing applications where DNA bases are placed on the ends of an siRNA molecule to decrease degradation within the cell. Other uses include RNase H based applications for genotyping and SNP detection.

    DNA/RNA hybrid oligos are available from IDT. Oligos that contain RNA bases are ordered under “Custom RNA Oligos” from the main menu order page on the IDT website. The RNA bases should be represented with a lower case r in front of them, with DNA bases represented by the base letter alone. For example: ACGTrArCrGrU.
  • How does what I order affect turnaround time (TAT)?
    TAT is affected by scale, sequence composition, and complexity (modifications or type of product), and purification. Estimated TAT for some general product types:

  • Should I avoid purification for sequences containing mixed bases (degenerate or randomized oligos)?
    The decision to order purified oligos will vary by your research needs. Purification involves collecting fractions of the total product synthesized and will inherently reduce variability in the oligos, possibly skewing the random base ratios, resulting in less overall randomness. Taking this into consideration, there are some cases where purification may still be warranted, especially with very long or highly modified oligos. If you have additional questions regarding purification of your mixed base oligos, contact customer service at custcare@idtdna.com.
  • What is the difference between universal and standard blocking oligos (used in NGS experiments)?
    Complimentary sequences within adapter sequences cause a daisy chaining effect during hybrid capture pull-down which results in off-target capture.

    Generally speaking, blocking oligos will bind to these adapter sequences:

     However, the challenge that many researchers face is when multiplexing many libraries. There are typically two options - do singleplex capture, normalize and pool, then capture. The second option, which most researchers prefer, is to normalize and pool samples, and then perform hybrid capture. For both options, each unique barcoded library requires its own unique blocking oligo.


    So if you were to perform capture on 96 libraries, you will need 96 blocking oligos in addition to the 96 adapters. In the past, some researchers would use inosine or degenerate bases in the index region in order to create a blocking oligo that will block all indexed adapters. Unfortunately, because these products are not perfect matches, there is typically a % on-target hit of 15-20% (so if on-target was previously 50% with base-specific blocking, the on-target rate would drop to 40% with non-specific indexed blocking oligos).

    xGen Universal Blocking Oligos essentially overcomes the performance degradation that is observed with other universal variants, and actually provides an on-target boost when conducting multiplexed capture when compared to standard, base-specific blocking oligos. We have stocked a 6nt and 8nt index.




    The following is a 6-plex experiment on a MiSeq with our recently launched AML panel and our 4-hour hybridization protocol:






    And this is the %-on target normalized against standard blocking oligo performance:

    We observed a 28% performance boost in % on-target for our Universal Blocking Oligos compared to our Standard Blocking Oligos. 

  • Can you make xGen® Lockdown® Probes based on our design results from another vendor?
    Generally speaking, all IDT needs are the capture probe sequences to synthesize Lockdown Probes. For custom designs, it is important to note that other vendors may use different databases for target sequence extraction. For reference, IDT uses NCBI databases (at the end of 2013 we were using RefSeq Build 58).
  • Can I combine my recently placed orders to save on shipping costs?

    Unfortunately, IDT is not able to combine orders once production commences. Production starts almost immediately after the order is placed, thus helping us to expedite getting your products to you.

  • What is the length of synthetic/custom genes that IDT can synthesize?

    gBlocks™ Gene Fragments—sequence verified double-stranded DNA—are available from 125 to 2000 bp, MiniGene™ Synthetic Genes are available from 25 to 500 bp, and Genes, start at 501 bp. MiniGene and Genes products are supplied cloned into IDT vectors. For additional information on synthetic biology products, email genes@idtdna.com.

  • What is the LabLinker® tool and how can it help my lab to place orders?
    The LabLinker platform, available through the IDT website, lets researchers consolidate orders, customize the lab ordering process, and share ideas and experimental findings. To set up a LabLinker account, log into your IDT web account, select the LabLinker tool for the Order tab at the top of the screen, and click “Create new Group”. For more information, see the article, Personalized Group Ordering for Your Lab, in the WebTools column of the DECODED 2.1 issue (Decoded 2.1).
  • What is the difference in specificity when using an intercalating dye (e.g., SYBR Green) vs. a 5’ nuclease assay probe (e.g., PrimeTime® qPCR Assays) to detect PCR product?

    Intercalation dyes such as SYBR® Green intercalate into any double-stranded DNA in the sample. They will detect the amplicon of interest but also additional nonspecific products and primer dimers. Thus, use of intercalation dyes can result in a false positive signal and loss of sensitivity when examining products with low copy numbers. Along with the primer set, PrimeTime® qPCR Assays include a probe that is specific to the target product. Therefore, signal will only result when the actual product of interest is amplified and will not result from nonspecific products or primer dimers. This provides greater specificity in the assay.

  • What is the difference in sensitivity when using an intercalating dye (e.g., SYBR® Green) vs. a 5’ nuclease assay probe (e.g., PrimeTime® qPCR Assays) to detect PCR product?

    Probe-based assays and SYBR assays both have the potential to detect a single copy of target, and thus, can be equally sensitive. However, it is important to remember that SYBR assay fluorescent signal can be generated as a sum of fluorescence due to dimers and other nonspecific products in addition to the desired target. Hence, when using SYBR assays, it is necessary to determine whether or not the fluorescent signal comes entirely from detection of the desired product. Find out more about probe- and intercalating dye assays by visiting our PrimeTime qPCR Assays webpage.

  • What dyes should I select for my qPCR assay?

    The most important thing is to select dyes that are compatible with your machine. FAM is generally compatible with all machines. If you would like suggestions about which dye to use, contact Customer Care at custcare@idtdna.com with the name of your machine and we can make a recommendation. IDT also offers a free PrimeTime® qPCR Applications Guide that contains additional information on available dyes, and instrument compatibility.

  • What is the cutoff for ordering expedited products online?
    IDT expedited products have a deadline of 3:00 pm ET, and include our SameDay™ Oligos for individual tube orders as well as our HOTPlates™ expedited service for rush 96-well plates. In addition to this deadline, HOTPlates service and SameDay Oligo orders must fall within our 15−60 base length restrictions.
  • 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.

  • Why don’t your cloning vectors contain multiple cloning sites?

    IDT has mutated their in-house vectors to remove MCS regions to allow for greater customer flexibility when choosing restriction enzymes. When placing your order for genes online, you can either select the restriction sites from the drop down menus provided OR include the sites directly in your sequence.

  • For what applications is it OK to use standard desalted oligos?

    Standard desalted oligos can be used in routine PCR, qPCR, and DNA sequencing applications. Through improvements to the traditional tert-butyldimethylsilyl (tBDMS) chemistry and advances in instrumentation, IDT has achieved the highest coupling efficiency in the industry allowing standard desalt oligos to perform extremely well for these applications.

  • 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.

  • With which sequencing protocols are xGen® Lockdown® Probes compatible?
    xGen® Lockdown® Probes are compatible with the NimbleGen® SeqCap® EZ Reagent Kit (Roche) and the SureSelect® Reagent Kit* (Agilent). A target enrichment protocol, which contains recipes for all of the reagents required, is available on the IDT website at www.idtdna.com/xGen (Support tab). Alternatively, you can contact xGen@idtdna.com to obtain the protocol or enquire about kit compatibility.
    * SureSelect reagents are not recommended for targeting genomic regions with >70% A/T.
  • What are aptamers and why are they growing in popularity?
    Aptamers are RNA or DNA oligonucleotides (or peptides) that, through their 3-dimensional structures, bind to specific target molecules with high affinity and specificity. They are often identified using a technique such as SELEX (Systematic Evolution of Ligands by EXponential enrichment), where oligos with increased affinity and specificity to the target molecules are isolated from the sequence pool after several rounds of selection. These molecules can serve as a substitute for antibodies used to identify a specific target. They have similar affinities as antibodies for their targets (Ahmad KM, Oh SS, et al. (2011) PLos ONE, 6(11):e27051), and provide several advantages, including greater stability, easier (large-scale) production, low immunogenicity, and the ability to target molecules with low antigenicity (Jayasena SD (1999) Clin Chem 45(9):1628– 1650).

    Like antibodies, aptamers have a broad range of applications, serving as drugs, diagnostic and therapeutic tools, analytic reagents, and bio-imaging molecules. The sequences are often modified to enhance stability during in vitro and in vivo use. Read more about aptamer applications by visiting the IDT publications list under the Support tab at www.idtdna.com.
  • What are AMOs (miRNA inhibitors) and how are they used?
    Anti-microRNA Oligonucleotides (AMOs), or microRNA inhibitors, are steric blocking antisense reagents that inhibit microRNA (miRNA) function by hybridizing to and repressing the activity of a mature miRNA. The miRNA regulatory networks exert some level of control in the majority of cellular biological processes, including cell differentiation, apoptosis, and proliferation. AMOs/microRNA inhibitors can be used to inhibit miRNA function, both to investigate that function and for therapeutic purposes to correct diseases associated with miRNA dysregulation. You can read more about as well as order IDT® miRNA Inhibitors at miRNA Inhibitor product page.