How do I read this shape data?

  • 1
  • Question
  • Updated 4 years ago
  • Answered
This is a picture from Starry's asymmetric shape II. (100%)

As far as I understand shape data, the loops are supposed to be all yellow and the strings are supposed to be all blue. Blue means paired, yellow unpaired.

I marked nucleotide 22 with a black ring. My question is following. Do I read the blue nucleotide in the tetraloop as an error in how the structure folded and something to be corrected or avoided? I'm aware that this design is a 100% and a very good one. I'm just trying to make sense of what I see.

Or does it simply means this nucleotide in the tetraloop has bound up legally with something else, like eg. the string or in other cases, even in the loop itself, and thereby strengthening the loop and overall structure?



This is what it looks like in colors.



If this blue nucleotide at base 22 is a legal bind, then how do I distinguish an unwanted binding in a loop, from a wanted one?
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes

Posted 8 years ago

  • 1
Photo of Jeehyung Lee

Jeehyung Lee, Alum

  • 708 Posts
  • 94 Reply Likes
Hi Eli,

For various reasons such as tertiary interactions, looped bases can sometimes show low reactivity to SHAPE - that is become blue even though they are not paired.

To compensate this we overlook looped bases that are "slightly blue" and do not penalize them. If you look into the data in "continuous color mode" accessible from the view option, you'll see the bases you marked are very faintly blue.

EteRNA team
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes
Thanks for a great answer. Now I understand better. :)
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes
To enhance the understanding of the picture example above, here is a picture of the same design in the "continuous color mode" mentioned by Jee. Notice the blue nucleotide in the loop (base 22) goes more faint.



To turn this option on, open gear in the tools menu.



So to sum up how to read shape data:

Basicly you want basepairs to be blue and loops to be yellow

Yellow = unbinding
Blue = binding

Faint blue bases in loops = not binding.
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes
Check out here why sometimes bases in the opening of the loop is actually binding blue and why it is not bad.

Why do G stabilizes loops?

Also see Nando's cool advanced explanation:

SHAPE blog
Photo of stlnegril9

stlnegril9

  • 32 Posts
  • 0 Reply Likes
recently KWS/Justin posted a script with the basic algorithm used to score raw SHAPE data for lab solution scores.

http://eterna.cmu.edu/web/script/3258...
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes
Thx, Stlne. Could you show an example of how to use it?
Photo of stlnegril9

stlnegril9

  • 32 Posts
  • 0 Reply Likes
example script to call similar t KWS function:
http://eterna.cmu.edu/web/script/3264...
Photo of Eli Fisker

Eli Fisker

  • 2223 Posts
  • 485 Reply Likes
As shapedata is a bit different with the switch lab, I thought it was time for making an update on how to read it.

Shape data update for switch lab
Photo of Astromon

Astromon

  • 184 Posts
  • 23 Reply Likes
Great explanation!