Custom oligo synthesis, priced by base, scale and purification

Advertised prices, verified

The four things that set an oligo price

1. Length, charged per base. The base rate is per nucleotide, so a 40-mer costs roughly twice a 20-mer before anything else applies. Vendors publish this rate at their standard scale, and it is the only one of the four levers that scales linearly and predictably.
2. Synthesis scale. Scale is the amount of material made, quoted in nanomoles or micromoles. Ordering a larger scale than an assay needs is the most common way labs overspend on oligos; ordering too small means re-ordering, which costs the lead time as well as the money.
3. Purification grade. Desalted is the default and is fine for routine PCR primers. HPLC or PAGE purification is charged as an uplift and is genuinely needed for longer oligos, for anything going into a sequencing library, and for applications where a truncated failure sequence would confound the result.
4. Modifications. Fluorophores, quenchers, phosphorylation, biotin and locked nucleic acids are each priced per modification, and dual-labelled probes carry the largest uplifts in the whole category. A modified probe order is not comparable to a plain primer order on the per-base rate alone.

Where the money actually goes on a routine order

For a lab ordering plain desalted primers at the smallest useful scale, the per-base rate dominates and vendor choice is largely about turnaround and shipping. For a lab ordering probes, the modification lines dominate so completely that the per-base rate is close to irrelevant, and the right comparison is between vendors' modification catalogues and their published uplifts.

Both patterns exist in the same purchase order most weeks, which is why an oligo supplier is usually chosen once, for the whole range, rather than per order. Comparing on the routine line alone will pick the wrong supplier for the half of the spend that is not routine.

Turnaround and shipping are part of the price

Oligo synthesis is fast and largely automated, so vendors compete on despatch time and shipping cost rather than on synthesis time. For a lab that orders weekly, a shipping charge applied per order is a recurring cost that can exceed the per-base saving from switching suppliers.

Where a vendor publishes a despatch commitment and a shipping threshold, both are recorded here with the price, because they are part of what you actually pay for an oligo arriving on a bench.

Common questions

What does a custom oligo cost?

Per base, at the vendor's standard scale, with desalting. The table above shows what the vendors in this index advertise, quoted from their own pages. A modified or HPLC-purified oligo costs substantially more, and the uplift is priced separately by every supplier.

What synthesis scale should I order?

The smallest that covers your planned reactions with a margin. For routine PCR primers that is usually the smallest scale offered; ordering larger 'to be safe' is the most common oligo overspend, because primers are cheap to re-order and do not improve with age.

Do I need HPLC purification?

Not for routine PCR primers, where desalted is standard and adequate. Yes for long oligos, dual-labelled probes, and anything entering a sequencing library, where truncated failure sequences from the synthesis would otherwise carry into the result.

Why do modified oligos cost so much more?

Each modification is an extra coupling step with its own reagent, and dual-labelled probes need two, plus a purification the plain oligo would not require. Vendors price each modification as a separate line, so a probe order is best compared modification by modification rather than on the per-base rate.

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