Oligo Modifications
Support and Educational Content

Use thiol modifications to prepare synthetic oligos for attachment chemistry

Thiol modifiers are a common type of chemical modification for synthetic oligos. They are designed to react with a broad array of activated accepting groups, such as maleimide and gold microspheres. Use them to prepare synthetic oligos for subsequent attachment chemistry.

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Attach modifications after oligo synthesis using Azide (NHS Ester)

Need to perform a click chemistry reaction? Start with an azide-modified oligo from IDT, to which you can add alkyne modifications, post-synthesis, in either copper-mediated or copper-free click reactions. Order Azide NHS (Ester) and other modifications from IDT. We will consider any requests.

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Aptamer-based electrochemical biosensors using methylene blue as a redox reporter

Modification highlight: Did you know that methylene blue, one of the stains commonly used in cytology, can also function as a reporter molecule in non-colorimetric assays? Learn about the novel use of methylene blue in aptamer-based, electrochemical biosensors for both diagnostics and basic research applications.

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Synthetic CpG ODNs activate immune cells through the Toll-like receptor (TLR) pathway

Did you know that synthetic CpG oligodeoxynucleotides (ODNs) can serve as an adjuvant to enhance the immune response of vaccines by mimicking the immune-stimulatory effects of unmethylated bacterial or viral sequences? Read about the 3 classes of CpG ODNs and how their distinct structures are tied to their varied functions. Order these modified oligos from IDT.

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Use of template switching oligos (TS oligos, TSOs) for efficient cDNA library construction

Conventional cDNA construction strategies usually result in an underrepresentation of the 5' ends of cDNA. However, use of a template switching chimeric DNA:RNA oligo and MMLV reverse transcriptase can improve on this. See how this approach, dubbed SMART, makes it possible to efficiently amplify the entire full-length transcript pool, in a completely sequence-independent manner.

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Ordering modified oligonucleotides

Learn about the many oligo modifications IDT can provide, both as online selections and through special requests. IDT will consider any modification you need. Find out how to request and order them here.

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Generate codon balanced libraries for mutagenesis with trimer modifications

Incorporating oligo codon trimers into oligo libraries results in balanced encoding of amino acids and eliminates unwanted stop codons. Such oligo libraries are useful for mutagenesis experiments to prepare proteins for screening for potential improvements in biological function.

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N6-methyladenosine (m6A)—modulating RNA localization, structure, stability, splicing, and translation

Modification Highlight: Read about the mechanism of methylation and functions of N6-methyladenosine (m6A) modifications in the cell. N6-methyladenosine is available as a popular non-catalog modification from IDT, providing a substrate for studying the role of this natural, reversible, post-translational modification.

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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.

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Insert an abasic site into your sequence

Use the dSpacer, rSpacer, and Abasic II modifications to introduce abasic sites into DNA or RNA oligonucleotides. These modifications create a single base space that replicates the loss of base pairing ability by a nucleotide.

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Need a library of related DNA or RNA oligo sequences?

Build variability into your oligo sequences by incorporating Mixed Bases. We offer mixes of multiple base types as well as nonstandard and modified bases.

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Increase the Tm of short, AT-rich primers and probes

Modification highlight: Add this modified base to increase the melting temperature (Tm) of primers and probes. It is especially useful when you need to work with short A-T rich sequences.

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Inverted bases

Learn how inverted bases allow you to reverse the orientation of part of your oligo sequence or add a 5-end restricted modification to the 3 end of your sequence.

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Antisense Oligonucleotides (ASOs)

Modification Highlight: Antisense oligos are the first oligonucleotide-based approach for disrupting gene expression. Learn about new applications for antisense oligos, including the study of lncRNA function.

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HRP for sensitive hybridization probes

Modification Highlight: HRP can be directly conjugated to hybridization probes to increase signal amplification in CARD-FISH protocols. Also use this oligo modification in nonradioactive immunoassays, northern/Southern blot analysis, and other in situ hybridization applications.

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Design functional oligos with poly G runs

Modification Highlight: Insert this modification in a run of G residues to increase oligo yield and purity, eliminate secondary structure, improve probe-based qPCR signal, and increase duplex stability and mismatch discrimination.

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N6-Methyl deoxyAdenosine (N6-Me-dA)

Modification Highlight: Do you know about this competitive antagonist specific to P2Y1 receptors? N6-Methyl deoxyAdenosine (N6-Me-dA) modifications are useful in pharmacologic and research applications examining the effects of selective inhibition of P2Y1 receptors, which appear to play a role in blood clotting.

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Improving immuno-PCR by optimizing antibody-oligo conjugation

Immuno-PCR, a modified antigen detection method, uses antibodies coupled to DNA, followed by real-time PCR. Using IDT amino-modified oligos, see how this method can increase the sensitivity of antibody-target detection by 100–10,000X over standard ELISA assays. An Innova Biosciences kit and service include IDT oligos to generate the antibody-oligonucleotide conjugates. Innova affirms that the high quality of IDT oligos provides optimal conjugation.

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Need a non-standard modification?

Need a modification you don’t find on our website? IDT offers 89 modifications that are not listed in our online catalog. A few of the more popular ones are described along with information on how to order them. IDT will consider any modification you have in mind. Just make a request at noncat@idtdna.com.

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Fluorescent dyes with no licensing restrictions—a growing portfolio

Need fluorescent dyes suitable for commercial and diagnostic applications? These have no patent licensing restrictions. Review this table of Freedom Dye alternatives for commonly used proprietary dyes.

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Oligonucleotide modifications that block nuclease degradation

Modification Highlight: Are you working with your oligos in cells culture or in vivo? Find out which modifications can be added to an oligo to limit nuclease degradation.

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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.

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When dT is required for modification attachment

Modification Highlight: Certain modifications require a dT base in the oligonucleotide sequence in order to be added. Learn which modifications these are, and how to add them to your oligo sequence.

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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.

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Alternative dyes for FISH, FRET, and qPCR

Use ATTO™ dye labeled oligonucleotides as alternatives in applications including fluorescence in situ hybridization (FISH), fluorescence resonance energy transfer (FRET), and dual-labeled probes used in qPCR experiments.

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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.

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Oligo modification—post-synthesis conjugation explained

Did you know IDT can add modifications to your oligos post-synthesis using NHS Ester chemistry? We can also add modifications through azide and alkyne groups post-synthesis, using click chemistry. Read about how these reactions are done, and get answers to common questions regarding post-synthesis conjugation.

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Which biotin modification to use?

Biotin is important in many kinds of molecular biology applications, in part due to its very high affinity for streptavidin and avidin. It is used in mobility shift assays, and for enrichment, purification, and attachment to solid surfaces. Biotin can also be used for tagging target molecules with dye- or enzyme-labeled streptavidin. But did you know there are numerous forms of biotin that can be used for such applications? Read about the differences between Standard Biotin, Biotin dT, Biotin-TEG. Dual Biotin, Photocleavable Biotin, DesthioBiotin-TEG, and Biotin Azide.

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DeoxyInosine: Don’t call me a universal base!

According to Nobel Laureate Michael Smith, deoxyinosine is not a universal base. Read why.

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A biotin:streptavidin alternative for non-radioactive hybridization assays—Digoxigenin

Modification Highlight: Learn about Digoxigenin—a modification suitable for use as an alternative to biotin/streptavidin for non-radioactive hybridization applications.

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Photo-cleavable spacer

Modification Highlight: This modification can be cleaved by a specific wavelength of UV light, fragmenting an oligo or releasing a terminal modification, such as a fluorophore.

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Towards real-time imaging in single, living cells

Learn how this research team is developing oligonucleotide technologies for detection and quantification of specific RNA transcripts in live cells using molecular beacons and gBlocks Gene Fragments..

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Oligonucleotide modifications: Choosing the right mod for your needs

Learn about our broad family of oligonucleotide modifications, and get suggestions for selecting modifications that can help you in your research.

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5-Hydroxymethyl-dC for epigenetic research

Naturally occurring 5-hydroxymethylcytosine (5-hmC) has been hypothesized to be an intermediate in a demethylation pathway or as an additional epigenetic factor. Learn more about this exciting new modification.

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Adenylated oligonucleotides provide direct substrates for T4 RNA ligase

Modification Highlight: Use the adenylation modification for ligation, miRNA library construction, next generation sequencing, 5’ end labeling, and ribosome assembly experiments.

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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.

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Increase oligo stability with phosphorothioate modifications

Modification Highlight: Need oligos that are nuclease resistant? Phosphorothioate bonds substitute a sulfur atom for one of the non-bridging oxygen atoms in the phosphate backbone of an oligonucleotide. Resistant to both endo- and exonucleases, this linkage provides increased oligo stability.

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Click chemistry-generated, internal dye-labeled oligonucleotides

Learn about "click chemistry" reactions, used to join small chemical subunits in a modular fashion, yielding singular reaction products that are typically physiologically stable and stereospecific.

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How biotin became a tool of molecular biologists

Have you noticed how biotechnology often coopts nature’s most useful tools? The naturally occurring, extraordinarily strong bond that forms between avidins and biotin has provided a useful tool that has enabled numerous techniques that would otherwise be impossible. Learn about biotin's history as a research tool.

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Attach oligos to ligands or surfaces—Dithiol modifier

Modification Highlight: Thiol-modified oligonucleotides are used in attachment chemistry reactions to bind an oligo to a target. Targets are commonly gold molecules, but can also include a variety of fluorescent and nonfluorescent moieties.

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Fluorescein—painting rivers green!

One of the most ubiquitous modifications attached to oligos is the bright green fluorophore known as Fluorescein, FITC, or FAM (Fluorescein amidite). Attaching the fluorophore to oligonucleotides is not its only use though. Read on.

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A modification that facilitates uptake into cells

Modification Highlight: Incorporate Cholesterol-TEG into your oligonucleotides to facilitate uptake into cells. This modification has been used as a transfection aid for antisense oligos and siRNAs, both in vitro and in vivo.

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IDT web tools for oligo properties

Free, online tools for oligo design, secondary structure, dilution, and resuspension.

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Related Articles

DNA Oligonucleotide Resuspension and Storage

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

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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 ≫

Understanding Melting Temperature

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

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Oligonucleotide Modifications: Choosing the Right Mod for Your Needs

Guidelines on selecting specific oligonucleotide modifications and how they can help you in your research.

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Which Biotin Modification to Use?

Applications of each of the different biotins available from IDT.

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