From design to delivered oligo
Ordering a custom oligo hides a great deal of chemistry. Knowing what happens after you click order helps you choose the right scale, purification and quality control for your work.
Solid phase synthesis
Oligos are built one base at a time on a solid support using phosphoramidite chemistry. Each cycle couples the next nucleotide, caps any strands that failed to react, and oxidises the new linkage, repeating until the full sequence is assembled. The strand is then cleaved from the support and deprotected.
Because each cycle is slightly less than perfect, longer oligos accumulate more truncated by products, which is why length affects both yield and the purification you need.
Choosing a scale
Scale describes how much starting material is used and therefore how much product you can expect. A screening experiment might need only a small scale, while functional assays, animal work or clinical supply need progressively more. Ordering the right scale avoids paying for material you will not use, or running short mid project.
Purification options
- Desalting removes small molecule impurities and suits standard length, unmodified oligos for routine PCR and sequencing.
- Cartridge or reverse phase HPLC purification removes truncated strands and is recommended for probes, longer oligos and most modified oligos.
- PAGE purification gives the highest purity for demanding applications where every strand must be full length.
Quality control
A finished oligo should come with evidence that it is the right molecule at the stated purity. Mass spectrometry confirms identity by measuring the molecular weight, while HPLC or gel analysis reports purity. For onshore, traceable material, that documentation travels with every order through Syngenis One.
Related glossary terms
From theory to a synthesis ready oligo
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