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Primer design and other tools you should know about

IDT offers a free suite of software applications—the SciTools™ Web Tools—which are available on IDT’s website. These tools give you the opportunity to determine the properties of any oligo sequence and facilitate the design and conditions of your experimental set-up.

With our expertise in oligonucleotide production, IDT offers a variety of high-quality predesigned and custom oligonucleotides suitable for PCR, cloning, next generation sequencing, CRISPR, and other applications. In addition to manufacturing high-quality components for your experiments, IDT also provides a free suite of software applications that gives you the opportunity to determine the properties of any oligo sequence and to facilitate the design and conditions of your custom experiments. This post will give you a brief overview of some of the SciTools™ Web Tools available on the IDT’s website.

The OligoAnalyzer™ Tool

To determine physical characteristics of your oligonucleotide sequences, including length, GC content, melting temperature (Tm), molecular weight, extinction coefficient, and optical density, IDT offers a powerful analytical tool called the OligoAnalyzer™ Tool. By simply entering your nucleotide sequence, including DNA, RNA, mixed bases, and several modifications, the tool will produce the complementary sequence, GC content, Tm, molecular weight, and extinction coefficient as an output. Refer to this page for more information on how to use the tool for the best results.

The resuspension and dilution calculators

To help you take full advantage of our high-quality oligo products, IDT provides you with two online calculators that give you the opportunity to easily formulate the correct working concentration for your oligos. The Resuspension Calculator assists in determining the volume needed to resuspend a dry, lyophilized oligo to a desired concentration. The Dilution Calculator takes an oligo stock solution of higher concentration and determines how much volume to dilute down to final working concentration.

The PrimerQuest™ Tool

Even though you have access to IDT’s PrimeTime Predesigned qPCR Sequence Database, that contains predesigned qPCR sequences for human, mouse, and rat targets, we understand that sometimes a full customization of your PCR primers is needed. This is when the PrimerQuest™ Tool comes in play. It gives you the opportunity to use your own nucleic acid sequences to generate a list of primers that can be used in your custom designed experiments. The PrimerQuest™ Tool offers you the option to customize almost 50 different parameters that will lead to the most efficient primer design for your experiment. These customizable parameters let you select primer, probe, and amplicon criteria to target regions. Refer to this article for more information on the PrimerQuest™ Tool.

Alt-R™ CRISPR-Cas9 guide RNA

As part of its CRISPR portfolio, IDT offers chemically synthesized and modified custom guide RNAs (gRNAs) for common as well as specialized research applications. You can select from predesigned Alt-R CRISPR-Cas9 guide RNAs (e.g., crRNA and sgRNA) targeting human, mouse, rat, zebrafish, or C. elegans genes. You can also generate CRISPR-Cas9 gRNAs targeting any sequence from any species using IDT’s Custom Alt-R™ CRISPR-Cas9 guide RNA tool. To assess on- and off-targeting potential of your own protospacer designs, you can use IDT’s CRISPR-Cas9 guide RNA design checker.

Need further assistance?

If you need help with these software applications, you can follow step-by-step instructions on how to use them via a link on each tool’s webpage. For further assistance, you can always contact an IDT Customer Care Representative.

Doc ID: RUO232245_001

Published Sep 5, 2023