Probing the secondary structure of salmon SmaI SINE RNA

SmaI is a short interspersed element (SINE) of the salmon genome, and is derived from tRNALys. We probed the secondary structure of SmaI SINE RNA by enzymatic cleavage and found that the RNA structure comprises three separate domains. The 5′-terminal region (the 5′ domain) forms a tRNA-like cloverleaf structure, whereas the 3′-terminal region (the 3′ domain) forms an extended stem-loop. The loop region is thought to be recognized by the reverse transcriptase (RT) encoded by the long interspersed element (LINE). The two structural domains are linked by a single-stranded region (the linker domain). Our melting profile analyses indicated the presence of two structural domains having different thermal stabilities, thus supporting the domain composition described above. Based on these results, we discuss the structural generality and evolutionary advantage of the domain composition of SINE RNA.