Neuronal BC1 RNA structure: Evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure

By chemical and enzymatic probing, we have analyzed the secondary structure of rodent BC1 RNA, a small brain-specific non-messenger RNA. BC1 RNA is sp ecifically transported into dendrites of neuronal cells, where it is propos ed to play a role in regulation of translation near synapses. In this study we demonstrate that the 5' domain of BC1 RNA, derived from tRNA(Ala), does not fold into the predicted canonical tRNA cloverleaf structure. We presen t evidence that by changing bases within the tRNA(Ala) domain during the co urse of evolution, an extended stem-loop structure has been created in BC1 RNA. The new structural domain might function, in part, as a putative bindi ng site for protein(s) involved in dendritic transport of BC1 RNA within ne urons. Furthermore, BC1 RNA contains, in addition to the extended stem-loop structure, an internal poly(A)-rich region that is supposedly single stran ded, followed by a second smaller stem-loop structure at the 3' end of the RNA. The three distinct structural domains reflect evolutionary legacies of BC1 RNA.