rose.blog

This one is from KaoriBlue, thanks!

Endogenous/viral pseudoknots have been proven to ‘encode’ frameshifts for eukaryotic ribosomes (see A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting for some beautiful cryoelectron images and a description of how this works). HIV, for example, uses a pseudoknot to redundantly encode proteins in multiple reading frames.

Pseudoknots also have a critical role in facilitating many protein binding/signaling events, and allowing the proper folding of ribozymes (like HDV, the extended hammerhead , not the microphone pimp), ribonucleoproteins (like telomerase and the ribosome), etc. .

I have no doubt that there are many many more endogenous and viral pseudoknots yet to be discovered. And beyond the (very) few that have been found, there are probably many more undiscovered regulatory ribozymes lurking in the LTRs of mRNAs.

Here is a paper related to the np-hardness of the problem.