How does RNA move and groove.

Is an RNA strand (in body temp.) like a wet noodle or more like a spring that is shaking? Are some areas more flexible than others? Would the presence of amino acids effect the probability for RNA to form is final shape? Also I am interested in how fast a formation takes place. milliseconds?

Interesting questions :slight_smile:

alan.robot wrote a tutorial that’s posted on his EteRNA profile here called “Kinetics and sub-optimal fold” that kind of answers the last one – anywhere between milliseconds and years :slight_smile:

This is a great question because the only correct way to answer it is to say RNA is like a bunch of magnets held together by springs that start off like a big noodle, but then the magnets let it snap into a nice compact shape and then it’s more like a tightly wound ball of yarn.

I’m not kidding. The appropriate model for a long, unfolded RNA is some sort of noodle (only physicists call it a “worm-like chain”, same thing). Each chemical bond is like really stiff springs (in fact, we model them that way and it’s accurate to a fraction of a percent). And I’m describing the base-pair hydrogen bonds as magnets, as they are very strong but very local through-space attractions.

RNA is super flexible, until you pin it into shape by forming lots of base-pairs, and also by binding positively charged metal ions to it like magnesium and potassium.

Tetraloops fold in fractions of a millisecond, and large RNAs can take seconds to fold.

Though in theory you could design something that took years to fold, in practice a real cell won’t tolerate that - it will either use some sort of folding machine to help it fold faster, or it will evolve the sequence to make it fold faster.