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

. CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/320929 doi: bioRxiv preprint While the K2-31 RNA does contain adenosines upstream of the cleavage site, structural predictions indicate these residues are within a stem region (21), rather than in an exposed loop as is the case for LIMD1 and GFP. Together, these observations indicate that while upstream adenosines are important for binding, they must be present in an unpaired state to promote SOX binding. It is notable that prior studies reported much weaker interactions between SOX and RNA (K d = 75 µM) compared to its DNA substrates (K d = 1 µm) (9, 10, 21). However, in these cases binding assays were conducted with scrambled RNA sequences. We found that SOX binding affinities to RNA substrates vary over several orders of magnitude, in a manner that correlates with cleavage efficiency.