This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.RNA molecules are unique in life processes because they not only store heredity information (like DNA), but they also perform enzymatic functions (like proteins). RNA hairpins are particularly useful drug targets because they are the most common structure of RNA molecules, and their overall shape and geometry differ significantly from regular double-standed DNA. To understand the energetics and mechanisms by which RNA molecules, we will begin by performing molecular dynamic simulations of P5GA, a 22 nt group I intron that is capable of excising itself from the mRNA. Of particular interest is that the folding rate as calculated by simple polymer theory is predicted to be on th order of tens of nanoseconds. However, experimental measurements have demonstrated the folding rate to be on th order of tends of microseconds. An explanation for this separation of timescales (over 3 orders of magnitude) is currently absent from the literature. The source of the obstacle in the folding of the RNA hairpin is likely to be from frictional influences. Among the possible origins are the solvent, the neighbors in the crowded environment of a cell, and non-native interactions. We will explore these possibilities by analyzing the effect of these barriers on the folding rate of th RNA hairpin, P5GA.
Showing the most recent 10 out of 292 publications
