Oligonucleotide synthesis is the chemistry behind every primer, probe and synthetic guide a lab orders, and understanding it explains the price list. Oligos are built one base at a time on a solid support by phosphoramidite chemistry, then cleaved, deprotected and optionally purified before they are quantified and shipped. Every step has a cost that scales differently with length and quantity, which is why a short desalted primer is cheap and a long modified probe is not. This page walks through the process and the price drivers, then points at the comparison.
How an oligo is built
Synthesis runs from the 3' end to the 5' end. Each cycle removes a protecting group from the growing chain, couples the next phosphoramidite, caps any chains that failed to couple so they do not carry on as deletion sequences, and oxidises the new linkage. The coupling efficiency per cycle is high but not perfect, so the fraction of full-length product falls as the oligo gets longer. That single fact is why long oligos cost more per base, why they need purification, and why a very long sequence is better ordered as a synthetic gene.
Scale and what it really means
Synthesis scale is the amount of starting support, quoted in nanomoles or micromoles. It sets the maximum yield, not the delivered amount, and the delivered yield of a long oligo at a small scale can be a fraction of the nominal figure. Choose the scale from the amount you will consume: a PCR primer used a few times needs the smallest scale, a probe used across a project needs a larger one, and a reagent going into a product needs the bulk tiers vendors price separately.
Purification grades
Desalting removes small molecules and is enough for routine primers, where the shorter failure sequences do not interfere. HPLC purification separates the full-length product from truncations and is the norm for probes, modified oligos and anything over a few dozen bases. PAGE purification gives the highest length purity for long unmodified oligos at the cost of yield. Each grade is a separate line on the price list, and a vendor's headline per-base price is almost always the desalted price.
Modifications, delivery and the quote
Fluorescent dyes, quenchers, biotin, phosphorylation, backbone and sugar modifications are each an additional reagent and often an additional purification, and they are the part of a quote that varies most between vendors. Delivery format matters too: dry in tubes, normalised in plates, or in solution at a stated concentration. The comparison on this site records what each vendor publishes for standard synthesis by scale and grade, verified and dated, so the like-for-like comparison is already done.
Questions people ask about oligonucleotide synthesis
What does oligonucleotide synthesis cost?
It is quoted per base, and the per-base figure depends on scale, purification and modifications. The comparison on this site lists what each vendor publishes for standard oligos, checked on the vendor's page.
What is the longest oligo I can order?
Vendors publish a maximum length per scale; beyond it the full-length yield is too low to sell, and the sequence should be ordered as a gene fragment or a synthetic gene instead.
Do I need HPLC purification for PCR primers?
Usually not. Desalted primers work for routine PCR. Probes, primers with modifications, and long oligos for cloning or sequencing library preparation benefit from HPLC.
How is an oligo quantified before shipping?
By ultraviolet absorbance, reported as optical density units or nanomoles, sometimes normalised to a stated concentration if you order it in solution.