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What's the typical route taken to obtain synthetic DNA/RNA samples in practice? Are they pretty much always custom ordered from a place that prints them using sold-phase synthesis, or can you cobble them together from random "common" samples?

Theoretically I could see an arbitrary 120bp oligonucleotide being made of 2-3 strands from random parts of across a genome or two, where you could separate out those parts with restriction enzymes and then anneal the snippets, but A) I don't know how you'd find those snippets reliably or whether my assumption that they'd exist in a random sequenced genome, or B) whether it's even efficient to try to digest, isolate, assemble and purify oligos that way when compared to buying a printed synthetic oligo

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    $\begingroup$ Depends on your application. For smaller to medium sized DNA oligos (<~120 bp) or medium sized dsDNA fragments (<3kb), I will always order them. What you're describing sounds a bit like Gibson assembly cloning (en.wikipedia.org/wiki/Gibson_assembly), and I would only go that route for fragments upwards of ~3kb, unless I needed to make several of them at once (also assuming I know the full sequence needed). Larger fragments can be purchased, but the price per bp can get high for very long fragments (still might be worth it for a one-off). $\endgroup$
    – MikeyC
    Commented Oct 2, 2023 at 17:01
  • $\begingroup$ I see, is the same true for RNAs or would you just order a template DNA and run in vitro transcription? $\endgroup$
    – Gumpf
    Commented Oct 2, 2023 at 17:22
  • $\begingroup$ @MikeyC i think that your comment is a different (and possibly more useful) answer from mine if you want to post it there $\endgroup$
    – Maximilian Press
    Commented Oct 2, 2023 at 17:44

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Depends.

For short defined sequences, IDT or a similar oligo synthesis provider is your best bet. It's very fast and straightforward, compared to trying to do something complicated with a genome. Recall that the number of possible e.g. 120mers is $4^{120}$, or $1.7668471*10^{72}$. That's an astronomically large number, and the probability of finding it in some random convenient genome is small.

For e.g. single well-studied genes, you might order a plasmid vector from AddGene or similar, which you can put into E. coli and grow up to make many copies.

If you are trying to isolate something a little less standard, you will usually clone it out of the genome though.

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