Ask Alex
Your Questions For Our Resident Expert






































What types of sequence motifs should be avoided when ordering gBlocks® Gene Fragments?

Sequence motifs to avoid when ordering gBlocks™ Gene Fragments.

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

Applications for which standard desalt oligos are sufficient.

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Why should I consider purification?

Reasons to have your oligo purified.

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

Why IDT has removed the MCS from their vectors.

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What is the cutoff for ordering expedited products online?

Ordering deadlnes for SameDay® and HOTPlates™expedited services.

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

Synthetic Genes are available from 25 to 400 bp, while Genes start at 401 bp up.

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How can I order oligos in a plate format?

Order plate format oligos online or by email from the ordering tab.

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Can I combine my recently placed orders to save on shipping costs?

IDT is not able to combine orders once production commences.

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How does what I order affect turnaround time (TAT)?

Turnaround time is affected by scale, sequence composition, complexity, and purification.

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Why are there no catalog numbers for IDT products?

Because most IDT products are custom-made, IDT has no catalog numbers.

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Do modified oligos require special storage and resuspension?

Only oligos with photocleavable or photolabile modifications require special storage. Amine-modified oligos that will be used in NHS ester reactions should not be resuspended in TRIS buffers.

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Why do the scale I order and the amount of oligo I receive differ?

IDT uses a starting scale, referred to as just “scale”, for the amount of initiating nucleotide used to begin synthesis. However, processing steps such as cleavage and deprotection of the oligonucleotide will reduce the final delivery amount (yield).

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What is the difference between 27-mer siRNAs and traditional 21-mer siRNAs?

Traditional 21-mer siRNAs mimic the products of Dicer processing and therefore, when used in RNA interference experiments, bypass interaction with the Dicer enzyme.

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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.

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When should I choose PAGE vs HPLC purification?

IDT recommends PAGE purification for long unmodified oligos and oligos used in cloning, gel shift, and mutagenesis protocols.

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How do I reorder an oligo?

For IDT orders placed through the web, reorder items via Order History.

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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.

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When do researchers use random (mixed) base oligos? Can I get custom ratios of the random bases incorporated?

Mixed bases are used in primers to bind to templates that contain variability or a mixture of sequences at the primer binding sites.

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What does sequence-verified mean for gBlocks® Gene Fragments?

gBlocks Gene Fragments are double-stranded DNA fragments that are ideal for use in synthetic biology, gene construction and traditional cloning applications.

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Why does the Tm on my spec sheet differ from that generated by the IDT SciTools® programs (e.g., RealTime PCR, OligoAnalyzer® tools)?

The IDT RealTime PCR design tool calculates Tm under real-time PCR conditions different from those on the spec sheet.

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Why should I sequence multiple colonies when cloning?

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.

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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”.

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How do I resuspend my PrimeTime® qPCR Assay?

PrimeTime qPCR Assays can be re-suspended as 40X, 20X, or 10X stocks.

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How do I order an oligonucleotide with a modification?

When ordering, select the Custom DNA Oligos option, and then the type of oligo product you desire.

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What should I be concerned about when designing multiplex qPCR assays?

The most important aspect of multiplex PCR to consider is potential negative interactions between PCR components, specifically the primers.

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Do fluorescently modified oligonucleotides need to be protected from light?

The main cause of oligonucleotide damage from light comes from the UV radiation in natural light.

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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.

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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.”

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Does IDT allow base modifications with their gene products?

IDT requires both strands of Genes and MiniGenes products to be 100% complementary.

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Will IDT synthesize aptamers for me?

Yes. If you can provide the aptamer sequence(s), you can order directly from the IDT website.

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Can I email an order to IDT?

IDT offers three convenient ways to order: via our website, by email, or by fax.

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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.

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Why do my OD measurements never match the values reported by IDT?

Comparing oligo OD values reported by IDT and those calculated by the end-user.

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What is the best way to purify PCR products?

For most applications, it is best to purify PCR products by gel electrophoresis.

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Why do I receive less than the requested scale quantity for a synthesized oligonucleotide?

The scale of the oligonucleotide synthesis reaction is based solely on the starting material. As no chemical reaction is 100% efficient, the final deliverable amount is never equal to the starting amount for synthesis.

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Are there any special requirements for the handling and storage of my labeled probes?

Labeled probes should, for the most part, be handled in the same fashion as other custom oligonucleotide sequences. We recommend resuspending probes in TE buffer.

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How do I enter RNA sequences online?

Oligonucleotides containing at least one RNA base must be ordered under “Custom RNA Oligos” from the order main menu page.

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When is it important to get HPLC purification?

HPLC purification helps remove truncated synthesis products and enrich purity. Purification is recommended for oligos greater than 40 bases in length and for many modified oligos.

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What is your protocol for annealing oligos?

It is sometimes necessary to make double-stranded DNA from single-stranded oligos. While the annealing procedure is simple, attention to a few details can greatly reduce the presence of undesired single-stranded material.

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What is the minimum number of bases that can be annealed?

You can anneal an oligo of any size to its target, but longer sequences lead to more stable duplexes.

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Do synthetic oligonucleotides contain a 5’ phosphate?

The 5’ end of an unmodified synthetic oligo terminates in a hydroxyl group.

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How do I order modified oligos online?

Modified oligos can be ordered from our Custom DNA Synthesis or Custom RNA Synthesis page.

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What are OligoCard payment cards?

OligoCard payment cards are prepaid cards that can be used to purchase IDT products.

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Where can oligo invoices, quality control documents, and specification sheets be found online?

For orders placed via the web, all of these documents are uploaded to your Order History.

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How many reactions will I be able to do with 25 nmole PCR primers?

Most PCR reactions use 0.1−0.5 μM primer. Assuming a maximum concentration of 0.5 μM and a reaction volume of 20 μL, each reaction will require 10 pmoles of oligonucleotide primer.

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What secondary structure considerations need to be included when designing primers for PCR?

When designing primers for PCR, two types of secondary structures should be analyzed: dimers and hairpins. For dimers, both self- and hetero-dimers should be reviewed.

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How can I determine the guaranteed yield for a specific construct?

The best way to determine the guaranteed yield for a specific oligonucleotide is to add that construct to the shopping cart on the website.

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