(5/27/13) I had a fun Veterans Day seeing if I could explain the cause of an anomalous SHAPE score on one interior base nt in a long stem of a recent lab project. I decided to see whether I could use one of the 3D structure prediction tools available on the Web could give me any insight, and I hit pay dirt! (Or perhaps it was just random luck that won't be repeated. But I'm an optimist.)
You can read a summary of what I found at Tracking down tertiary effects in lab puzzles.
Eli urged me to write another article on how I used RNA Composer and Chimera to predict and investigate the 3D structure of this design. The hope was that more Eterna players could start exploring the 3D aspects of RNA. After some discussion, we decided to team up to produce two documents, one for each tool. You can find them at
- Transforming a lab design in to Protein Database File, explaining how to use RNA Composer to predict the 3D structure of a design.
- Introduction to Chimera for EteRNA Players to view interactively the 3D structure predicted by RNA Composer.
Here's the page on the Reproducibility Test Lab.
Recently, I've been thinking more about the RNA backbone. The SHAPE procedure used in Eterna interacts directly with the backbone, not the A, C, G and U nucleic acids themselves. Although there is a high correlation between SHAPE values at a particular base position and whether or not the the ribonucleic acid at that position is paired with another base (C with G, A with U, or G with U), the correlation is not perfact. I think the SHAPE score is telling us more than just the secondary structure; we just need to figure out how to make use of that information. To hear more, see my Backbone SHAPE page.