Its just a little thing thats been niggling at me.
If we go to the trouble of synthesizing the top 8 voted designs each week, when we are looking at the results, why do we have an estimate mode? (where the game approximates how it folded)
Shouldn’t we be able to exactly see how it folded?
My understanding is that they don’t look directly at the RNA in a super-microscope; instead they have a sneaky way to tell whether each base is bonded-with-something or not-bonded-with-something in most of the molecules. With that data in mind, the program can then say what is the most probable configuration that takes into account that some of the bases are bonded and others not.
You should pay attention to a future answer to Ding’s lovely question in this thread, which also gives a good explanation of how they are actually determining shape.
Chris already made a good answer so I’ll just add a bit.
Examining exactly how RNA folds is very expensive and time consuming job - the way we examine RNAs is to look at signals indicating whether each base is paired (with some other base) or not. The estimate mode uses these signals to guess what RNA probably folded into.
Thanks 5c and Jeehyung.
Ok, next question, for bonus points. How would you examine how the RNA folded? What is the process called? Does it ever get to the microscope level or what do molecular scientists use to get this answer?
Interested to do some further reading
I found this really useful link,