Oligo Handling, Analysis, and Applications
Support and Educational Content

LISH method enables highly multiplexed, sensitive gene expression in FFPE samples, without RT

Ligation in situ Hybridization (LISH) enables sensitive, multiplex detection of mRNA expression in archival FFPE samples, without RNA isolation or reverse transcription. The authors show that LISH can be used to detect expression in archived FFPE specimens up to 10 years old and that it can be highly multiplexed (>100 target sequences). Review the mechanism of this technique, and learn about its many applications.

Read More>


16S rRNA indexed primers amplify phylogenic markers for microbiome sequencing analysis

The 16S rRNA gene is frequently used in microbiome studies to identify the subset of microbes present in biological samples. Researchers amplify short hypervariable regions from this gene, tag the amplified products with unique barcodes, perform highly multiplexed sequencing runs, and compare the sequences to the known bacterial genome database. However, primer design for such analyses can be challenging given the massive sequence variability in sampled lifeforms. Read about the development and design of these primers, and how you can obtain your own custom, high fidelity versions of these sequences.

Read More>


Storing oligos: 7 things you should know

Lab tips: Researchers often have questions about the stability of their oligos and how best to store them. Review these important considerations and supporting data, which were generated from an ongoing, multi-year, longitudinal stability study.

Read More>


SameDay® Oligos

Need oligos fast? SameDay™ Oligo orders placed online by 3:00 pm ET in the United States can be shipped priority for delivery by 10:30 am the next business day. Expedited shipping from our European and Singapore manufacturing facilities as well.

Read More>


Tips for resuspending and diluting your oligonucleotides

You have received your custom oligonucleotides, and now it is time to resuspend and dilute them. Here are a few tips from our scientists that will help facilitate use of the oligos in your experiments.

Read More>


Long, custom RNA oligos—Ultramer® RNA Oligonucleotides

Product spotlight: Use Ultramer® RNA Oligonucleotides to increase specificity and improve performance in a variety of RNA-related applications. Learn more about these high-quality, single-stranded custom oligos, made up to 120 bases.

Read More>


ESI mass spectrometry—why we use it for oligonucleotide quality control

IDT has been, and still is, a pioneer in using mass spectrometry for quality control in oligonucleotide synthesis. Learn about why a particular method, electrospray ionization (ESI), is used ubiquitously in our manufacturing processes.

Read More>


Zika virus: Advances in disease modeling and detection

IDT is supporting global research aimed at reducing the widespread effects of Zika. Learn about the virus, and read a summary of the latest developments.

Read More>


Valuable support for genomics research

Product Spotlight: Take advantage of the full list of products, services, and support IDT provides for genomics research. Whether you are performing sequencing, gene expression, genome editing, or synthetic biology experiments, IDT has cost-effective, rapid, high quality, and high throughput solutions.

Read More>


3D polyhedral meshes—simplifying nanoscale DNA structure designs

Research profile: Learn how the Högberg Lab designed a simplified DNA scaffolding method, including software that quickly determines the “oligonucleotide staples” required to fold a ssDNA sequence into any desired shape.

Read More>


Planning to work with aptamers?

We are often asked whether IDT manufactures aptamers. The answer is, yes! IDT does synthesize aptamers and aptamer libraries, and there are already 100s of published research papers describing the successful use of such sequences manufactured by IDT. Learn about aptamers, SELEX, and how IDT can assist you with reagents for your aptamer applications.

Read More>


Oligo synthesis: Why IDT leads the oligo industry

Read about the phosphoramidite method of oligonucleotide synthesis that IDT uses in its manufacturing processes. We also highlight the additional measures we take to ensure our customers receive the highest quality oligos and nucleic acid products in the shortest time possible.

Read More>


Methane-oxidizing bacteria for a reduced carbon footprint

In 2015, IDT awarded Dr Patricia Tavormina with the inaugural ISO 14001 Sustainability Award for her innovative research on methane-oxidizing bacteria. Learn about Dr Tavormina’s work, and how her findings could someday guide methane mitigation strategies for a more sustainable future.

Read More>


Don’t lose expiring grant funds

OligoCard® payment cards let you use current grant money towards future purchases. Order the oligos you want to order, when you want to order them, and don't lose expiring grant money!

Read More>


A novel non-enzymatic assay for SNP detection in cancer DNA

Citation summary: Learn how scientists use a long, biotinylated Ultramer® Oligo to capture specific gene fragments for the identification of SNPs with single-molecule resolution. Their method is not only cost-effective, but avoids enzyme-based technologies, such as PCR and NGS, that vary in fidelity and increase risk of introducing amplification bias.

Read More>


Assessing formulas that calculate Tm—do nearest-neighbor parameters matter?

Should programs that predict Tm include nearest neighbor parameters? Learn which factors are critical for Tm calculation accuracy, and which online software takes them into account.

Read More>


DRONE delivers oligos for promoter oligonucleotide pull-down assay

An IDT customer who is using IDT oligos for a transcription factor pull-down assay and qPCR assays for expression analysis, wins an April Fools' Day drone prize.

Read More>


Troubleshooting polyacrylamide gel electrophoresis (PAGE)

Review this extensive troubleshooting guide for the PAGE issues our gel electrophoresis team has encountered during their work.

Read More>


RxnReady Oligos—premixed oligos for PCR and more

Would getting your oligos premixed help speed up your research? Have 2 standard desalted DNA oligonucleotides premixed in a single tube according to your specifications. This can be useful when performing PCR, fluorescent dye RT-PCR, or when generating sets of insertions or deletions through site-directed mutagenesis.

Read More>


My oligos have arrived: Now what?

Review these recommendations for resuspension and storage of newly received oligonucleotides.

Read More>


Understanding melting temperature (Tm)

Read this advice from our own thermodynamics specialist, Dr Richard Owczarzy, on the effects of melting temperature (Tm) on hybridization. He provides considerations for better oligo and PCR/qPCR assay design, including oligo concentration, salt, and base pairing mismatch positioning.

Read More>


Calculations: Converting from nanograms to copy number

Here is a calculation often used when creating a qPCR standard curve. Link to a free, online tool that will do it for you.

Read More>


3D DNA canvas—synthetic DNA learns new tricks

Research profile: These scientists assemble DNA bricks (32mers) to create complex, nanostructure shapes. Read how they use DNA bricks to design 3D structures.

Read More>


Oligopaints—visualizing the three-dimensional organization of the genome

Research profile: See how this research group used modified oligos as probes for chromosomal mapping of specific sequence elements. The location of these sequence elements correlates with the 3D organization of the genome.

Read More>


Your DNA as Personalized Art

Learn how molecular biologist at DNA11 introduce the idea of DNA as art. The scientists turn DNA fingerprint images into colorful art pieces printed on canvas for display.

Read More>


Which type of oligo purification should I choose?

Do your oligos need purification for your intended application? Use these recommendations based on oligo length, application, yield required, and presence of modifications to determine which oligonucleotide purification method to select.

Read More>


Oligo quantification—getting it right

Did you know that a supplier's yield readings can differ from what the researcher calculates after resuspension? Learn the importance of using the [right] molar extinction coefficient in calculations of oligonucleotide concentration.

Read More>


Scale and yield—are they the same?

When you order a certain amount of oligo, how much are you going to recieve? Review the distinction between the amount of starting material used for synthesis vs the amount of final product recovered.

Read More>


G repeats—structural challenges for oligo design

G-quadruplexes are formed from the stacking of two or more G-tetrads, which occur naturally in sequences with short G base repeats. Find out more about G-quadruplexes and how they can affect oligonucleotide synthesis and applications.

Read More>


Getting enough full-length oligo?

The coupling efficiency achieved by an oligonucleotide manufacturer has a direct effect on the quality of the oligonucleotides produced. Find out why coupling efficiency should be important to you.

Read More>


DNA Oligonucleotide Resuspension and Storage

You just received your newly synthesized oligonucleotides. Now what? Here are some guidelines and recommendations on how to resuspend and store your oligos.

Read More>


Easy resuspension and dilution of oligonucleotides

Save time by using these free resuspension and dilution calculators. A variety of units can be used as input values. Review the screen shots that show how these calculation tools can help you move on with your research.

Read More>


Single nucleotide resolution of RNA structure

Research profile: Shape chemical reagents differentially modify accessible nucleotides in an RNA molecule. Read how Dr Weeks and his team used SHAPE to elucidate the 3D structure of even very large RNAs.

Read More>


Annealing oligonucleotides

Use this quick protocol for making double-stranded DNA from single-stranded, complementary oligonucleotides. Also review some considerations for making and using annealed oligos.

Read More>


Determining the physical characteristics of your oligos—the OligoAnalyzer Tool

Use this free web tool to determine many of the physical characteristics of your oligonucleotides. By simply inputting your sequence, you can find out its length, GC content, melting temperature range, molecular weight, extinction coefficient, and optical density.

Read More>


The importance of Tm in molecular biology applications

Learn how to predict and select appropriate Tms for oligo hybridization steps, including PCR.

Read More>


Calculation tips for resuspending and diluting nucleic acids

Use these simple guidelines for making a 100 µM solution; calculating nanomoles, micrograms, copy number, and concentration; and determining concentration equivalencies.

Read More>


Why are oligos synthesized 3′−5′?

The cell may synthesize DNA from 5′−3′, but synthetic oligos are made much more efficiently in the 3′−5′ direction. Learn why in a brief history on in vitro synthesis of oligos.

Read More>


Running agarose and polyacrylamide gels

One of the most widely used tools in molecular biology, electrophoresis provides a simple, low-cost way to separate nucleic acids based on size for quantification and purification. Get some tips on running your gels.

Read More>


Understanding mass spectrometry of oligonucleotides

IDT pioneered the use of mass spectrometry (MS) analysis for assessing oligonucleotide identity and monitoring quality during oligo synthesis. Read this review on mass spectrometry that includes examples of MS data and advice on data interpretation. Our follow-up article, ESI mass spectrometry, provides an introduction to ESI technology and why it is now our preferred method of MS quality control.

Read More>


Unraveling RNA—the importance of a 2' hydroxyl

On paper, the small structural differences between RNA and DNA may not look substantial but, in practice, these small differences have major significance for the biological role of RNA. Find out how.

Read More>



The OligoAnalyzer® Tool

Learn everything you need to know about your primers—Tm, hairpins, mismatches, and more.

Try it now ≫


Related Articles

DNA Oligonucleotide Resuspension and Storage

Guidelines and recommendations for how to resuspend and store newly synthesized oligonucleotides.

Read more ≫

Annealing Oligonucleotides

Tips on making double-stranded DNA from single-stranded, complementary oligonucleotides.

Read more ≫

Calculation Tips for Resuspending and Diluting Nucleic Acids

Easy guidelines for making a 100 µM solution; calculating nmoles, µg, copy number, and concentration; and determining concentration equivalencies.

Read more ≫

Calculations: Converting from Nanograms to Copy Number

Link to a free, online tool that will help you do this calculation often used when creating a qPCR standard curve.

Read more ≫

Understanding Melting Temperature

Advice on considerations for better oligo design: oligo concentration, salt, and SNPs.

Read more ≫