Class of 2004
desirae@jhu.edu

Research
I am interested in how ions affect RNA folding.  RNA is a long string of negatively charged phosphate groups (among other things).  In order to fold into more complex and compact structures capable of biological function--think tRNAs or the ribosome--these negative charges must find a way to stably pack together.  RNAs accomplish this by accumulating cations.  Mg+2 ion is a particularly effective stabilizer of RNA tertiary structure.  This ion acts through different modes of interaction, a spectrum that includes remaining fully hydrated and interacting diffusely, as well as being dehydrated and chelating specific RNA ligands.  Previous work in our lab has shown that, in contrast with how most people think about ion-RNA interactions, diffuse ions actually do most of the work in stabilizing RNA structure.  Indeed, the high energetic cost of dehydrating Mg+2 ion (~400kcal/mol) renders ion chelation prohibitive for most RNAs.  One of the goals of my research is to experimentally determine the free energy benefit of site-specifically chelating a Mg+2 ion, using an unusually compact RNA with regions of large phosphate burial and thus the potential (electrostatic and otherwise…) to chelate an ion.  Another of my research goals is to rigorously thermodynamically charactize the folding of an adenine-binding riboswitch, considering the effects of changing salt conditions on the nature of the folded and unfolded ensembles.

Publications