Custom rna synthesis: where chemical synthesis stops and transcription begins, and the modification and purity specifications that set the price

Which route, and what it costs

1. Chemical synthesis for short RNA. Solid phase synthesis gives complete control over sequence and modification position and is the route for guide RNA, small interfering RNA, antisense oligonucleotides and probes. Yield falls with each coupling, so cost per base rises with length and long chemical RNA becomes impractical.
2. Transcription for long RNA. Enzymatic transcription from a template produces long RNA economically and restricts modifications to those the polymerase accepts, applied throughout rather than at chosen positions. Messenger RNA and long non-coding RNA come this way.
3. Modifications are priced individually. Backbone changes, sugar modifications, terminal caps, dyes, quenchers and conjugation handles each add a reagent and a step. List every one at quoting, since adding a modification afterwards can change the synthesis route entirely.
4. Purity grade follows the application. Desalted material suits many routine uses; chromatographic or gel purification is needed for long constructs, for anything going into cells and for quantitative work. Each purification step costs yield, so specify what the application needs rather than the highest grade offered.
5. Scale and the second order. Scale is quoted as a delivered quantity, and RNA degrades in storage, so ordering far more than will be used is a poor trade. Where the programme will re-order, agree the repeat price at the first order.

Handling RNA once it arrives

Ribonuclease contamination is ubiquitous and survives autoclaving, so dedicated consumables, gloves changed often and a separated working area matter more for RNA than for almost any other reagent. Aliquot on arrival rather than repeatedly thawing a stock.

Resuspend in the buffer the provider recommends and check integrity before committing the material to an experiment, particularly for long transcripts where shipping stress shows.

The analytics to ask for

Mass confirmation for short RNA, integrity and size distribution for long RNA, a purity determination with its method and trace, and concentration by a method that suits the molecule. For transcribed material, also residual template DNA.

Where the RNA goes into cells or animals, specify an endotoxin limit and require a lot result, because it is a common and avoidable confound.

Common questions

Chemical synthesis or in vitro transcription for custom RNA?

Chemical synthesis for short RNA where modification position matters, and transcription for long RNA where economy matters. The length of the molecule effectively decides it, and the route determines which modifications are available.

What purity grade should I order?

Desalted for routine short RNA, chromatographic or gel purification for long constructs, cell work and quantitative applications. Each step costs yield, so buy the grade the application needs.

How should custom RNA be stored?

Aliquoted on arrival and frozen, in nuclease-free conditions, with repeated freeze and thaw cycles avoided. Ribonuclease is ubiquitous and survives autoclaving, so dedicated consumables matter.

What analytics should accompany the order?

Mass confirmation for short RNA, integrity and size distribution for long RNA, purity with its method and trace, concentration, and for transcribed material residual template DNA.

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