Site specific target binding controls RNA cleavage efficiency by the Kaposi’s sarcoma-associated herpesvirus endonuclease SOX

Aaron S. Mendez; Carolin Vogt; Jens Bohne; Britt A. Glaunsinger

In silico RNA folding predictions of SOX targeting motifs, coupled with RNA mutagenesis experiments, have indicated that an RNA stem loop structure is an important determinant in SOX targeting both in vitro and in vivo (20, 21). Given the importance of this predicted motif, and in particular the proposed requirement for unpaired sequence at the cut site, we sought to experimentally determine the structure of LIMD1 54 using chemical based in-line probing (Fig. 3A ). This showed that the LIMD1 54 structure contains a largely base paired stem region, followed by a loop at positions 15-27 that encompasses the predicted SOX cleavage site between nt 26 and 27, and a short hairpin structure at positions 29-40 (Fig. 3B) . Notably, some differences exist between the predicted and observed structures of LIMD1 54, including a larger loop region and the subsequent short stem-loop (compare Fig. 3B to Fig. 2A ) However, in both cases the predicted cleavage site of SOX resides in a loop region.