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RNA structure prediction is hard. How much does that matter?
4.8k words, 22 minute reading time
Note: I am not an expert in RNA structure, and am extremely grateful to Connor Stephens, Rishabh Anand, Ramya Rangan, and Chaitanya K. Joshi —all of whom are actual, bonafide experts—for their incredibly detailed comments on earlier drafts of this essay.All mistakes are, of course mine, and this essay should not be trusted to function as anything more than entertainment. Two, just logically thinking about it, the job of mRNA is to be fed into the ribosome and translated into protein, so as long as the coding region is readable and initiation isn’t blocked (hence probably why hairpins are undesirable), why would it matter for the RNA to maintain any particular higher-order fold? For instance, Arrakis Therapeutics, a RNA-targeting-with-small molecules biotech startup with a very fun name, has this really interesting presentation showing that multiple of their ligands are able to bind to conserved, accessible 3D pockets of mRNA of the MYC protein.
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