FMN Switch 2.0 Thoughts Pt 3 - UCCA and UCCG tetraloops

  • 1
  • Article
  • Updated 7 years ago
For this post, we will focus on the UCCA, UCCG, and the other tetraloop sequences in bases 31-34 in the 2nd state of the FMN Switch 2.0 lab. It is interesting to note, that with these tetraloops and the locked position of a G-C, A-U, or G-U closing base pair, there appears to be a slight tendency for the base pair at 30-35 to be unstable, and to open up into a hexloop. Here are a few screenshots.

G-U closing base pair, UUCA


A-U closing base pair, UCCA


G-U closing base pair, UUCA


G-U closing base pair, UCCG


G-C closing base pair, UCCA


G-C closing base pair, UCCA


A-U closing base pair, UCCA


A-U closing base pair, UCCG


A-U closing base pair, UCCA


Now, just these 9 designs alone amount to a little over 25% of the 32 designs synthesized so far. This also does not include designs where only one base is considered accessible to SHAPE, or designs where the entire stack that tetraloop is on are all exposed. In the end, few designs were a perfect "Blue-Blue" base pair.

Luckily, this lab is not single-state, so these bases are scored on how they switch, not on how they form. Base 30 just needs to stay blue in the SHAPE data shift, and base 35 just has to go from light to dark. However, because there is the potential for that pair to be unstable, it can be difficult to determine what is necessary there, in order to get the 2 full points.
Photo of Brourd

Brourd

  • 454 Posts
  • 84 Reply Likes

Posted 7 years ago

  • 1
Photo of rhiju

rhiju, Researcher

  • 403 Posts
  • 123 Reply Likes
This is interesting -- we see this in natural RNA enzymes and switches too -- the closing base pairs for 'apical' loops are not entirely frozen to SHAPE or other chemical modifiers.

We should probably update our scoring system to take that fact into account. For now, as you pointed out, the switch score is not sensitive to it. We're actually working on a more general predictor of chemical modification from structure -- if you or others notice any other common patterns like this, please do post and let us know.