A few chip riboswitch related queries

I believe the Das Lab mentioned in the April presentation by Johan that they were taking it into consideration to try and upload error rates for the individual Eterna scores. You guys should get Nando on adding that column into the Flash UI of the lab browser, as well as a column for the number of clusters, and the various subscores!


Currently, the “results” version of the flash game applet is unused for the chip riboswitches. If this data along with the Kd distribution graphs were posted there, that would be fantastic.

In addition, there is an experiment request I would like to see.

The mutate/map protocol was used by the Das lab previously to use chemical mapping to extract the ensemble of secondary structures that an RNA sequence can fold into. Would it be possible to use a similar series of mutations on a select number of on-chip riboswitch sequences in Johan’s protocol as well?

This would be useful for several reasons, including the fact that these experiments can be included as a part of the current protocol, that the data would provide some form of information on the ensemble of structures forming in solution, and it could indicate the level of robustness that these riboswitch sequences have to sequence permutations. In addition, if tied to SHAPE chemical mapping experiments, it should be possible to derive an accurate prediction of the free energy ensemble and affinities to the various ligands used.


Yes we need the number of clusters, and the various subscores displayed, adding the extra columns for the those would be a good start.