A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA

The VS ribozyme is a 154 nucleotide sequence found in certain natural strai ns of Neurospora. The RNA can be divided into a substrate and a catalytic d omain. Here we present the solution structure of the substrate RNA that is cleaved in a trans reaction by the catalytic domain in the presence of Mg2. The 30 nucleotide substrate RNA forms a compact helix capped by a flexibl e loop. The cleavage site bulge contains three noncanonical base-pairs, inc luding an A(+) C pair with a protonated adenine. This adenine (A622) is a p H controlled conformational switch that opens up the internal loop at highe r pH. The possible significance of this switch for substrate recognition an d cleavage is discussed. (C) 2001 Academic Press.