| Category | Description | Examples | Applications |
|---|---|---|---|
| Attachment chemistry and linkers | Link an oligo with another molecule or particular surface. | Amino modifiers, Biotin, Thiol, Alkynes | DNA arrays, solid-phase PCR, NGS |
| Fluorophores and dark quenchers | Fluorescent dyes re-emit light upon excitation while dark quenchers absorb the emitted light and release heat. | Fluorescein Dyes, Cy Dyes, Rhodamine Dyes, ATTO Dyes, Alexa Dyes, LI-COR Dyes, Iowa Black Quenchers | qPCR, dPCR, for gene expression or genotyping |
| Freedom dyes | Have no patent licensing restrictions. | FAM, SUN, Cy 5 | qPCR, dPCR, for gene expression or genotyping |
| Modified bases | A variety of modifications that can serve a range of functions, including cross-linking, duplex stabilization, and nuclease resistance. | Affinity Plus: +A, +G, +C, +T, O-Methyl: mA, mG, mC, mU, RNA: rA, rG, rC, rU | qPCR, dPCR, antisense Pending the modification can be used to adjust Tm, increase resistance to nuclease degradation, reduce toxicity/limit unwanted immune responses |
| Phosphorylation | Use if your oligo is being used as a substrate for DNA ligase. 3' phosphorylation will inhibit degradation by some 3' exonucleases and block extension by DNA polymerase. | 5' or 3' Phosphorylation | qPCR, dPCR for genotyping, Synthetic biology applications, NGS |
| Spacers | Create distance between a functional moiety and the hybridizing region of your oligo. | C3 Spacer, Spacer 18, Hexanediol | qPCR, dPCR for genotyping, Synthetic biology applications, molecular applications where bulky mods are attached to oligos (like Cholesterol) |
| Phosphorothioate bonds | Include these bonds in your oligo sequence for increased inter-nucleotide resistance to nuclease degradation. Especially useful in antisense oligos. | *A, *G, *C, *T | Antisense, FISH probes, and other cellular mapping |
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