Computational and Systems Biology Summer Institute
Iowa State University

These are novel RNA structures that recruit translation initiation factors to mRNA in the absence of the standard 5' cap structure that is normally required.  This work will shed light on how mRNAs are recuited to ribosomes, a fundamental process that is well conserved in all eukaryotic cells.  We have performed substantial mutagenesis and translation assays to identify essential bases and stem-loops needed for the cap-independent translation function.  We have a lot of chemical and enzymatic structural probing data so we know the secondary structures of these RNAs.  Also, there is interesting phylogenetic conservation (and lack thereof) of related elements that can be used to identify key structures in the elements.  Importantly for a bioinformatics student, we are doing 3D modeling of RNA structure using a variety of different programs.