Influence of parity/ordering on loop/energy

  • 1
  • Question
  • Updated 8 years ago
  • Answered
A little long question: Why does the direction of the sequence matter?
I just found this and verified it as simple as possible in Hairpin Series:
You can build 2 solutions: (the order is from top to bottom if it's inline like at the start)
"cuuacaaaaagguggg" Total Energy: -1.8 Loopenergy:4
"ggguggaaaaacauuc" Total Energy: -2.5 Loopenergy:3
You can get from one to the other by a parity transformation (mirroring along the axis). Or if you just look at the sequence you have to reverse the order.
Now if RNA would be just a sequence of letters floating in space it shouldn't matter if i call one end of it first element and the other end last element or vice versa. So parity should be conserved/ the ordering shouldn't matter.
The only reason for this i can think of is if the real-world binding would be somehow directed. Is this the case ? And if not why does the ordering matter?
Also is there general rule how to use this effect ingame?
Photo of Liquid'Etzekiel

Liquid'Etzekiel

  • 2 Posts
  • 0 Reply Likes

Posted 8 years ago

  • 1
Photo of rhiju

rhiju, Researcher

  • 403 Posts
  • 123 Reply Likes
Good question -- in reality the RNA, when you draw out its chemical structure, looks different going in one direction than the other:



The representation in EteRNA is a bit simplified so it is hard to tell (look carefully at the arrows between letters). This has an impact on the RNA energy. for example, the energy measured for forming the following base pairs:

5'-GC-3'
3'-CG-5'

is different than that formed in

5'-CG-3'
3'-GC-5'

Here 5' to 3' means beginning to end. Its not actually understood from first principles why exactly these energies are different, but the asymmetry is certainly OK given the asymmetry in chemical structure.