RNA SECONDARY STRUCTURE
Confirmation of RNA secondary structure by cryo-EM (2015):
Our proposed secondary structure of STMV RNA was very extended (see below). Gopal et al. (2012) had presented cryo-EM images of RNAs with sufficient resolution that we believed it might be possible to visualize the STMV RNA directly, to support or disprove our secondary structure model. This idea was tested by Rees Garman, who was then a graduate student working under the supervision of Bill Gelbart and Chuck Knobler at UCLA. Rees
Our comparative cryo-EM studies on the STMV genomic RNA and a control RNA of about the same size showed that both molecules have an ensemble of secondary structures, and that the viral RNA is significantly more extended than the control (Garmann et al., 2015). This confirmed the model we had previously proposed (below).
The secondary structure of STMV RNA by chemical probing (2013):
We determined the secondary structure of the ssRNA genome of satellite tobacco mosaic virus (STMV), using data from SHAPE probing as restraints. It has an exceptionally extended secondary structure, which we argued protects the RNA from degradation by host cell nucleases (Athavale, Gossett et al., 2013). This work was done in collaboration with Loren Williams and Nick Hud at Georgia Tech.
This model was subsequently supported by the cryo-EM results described above.