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

作者：Flinders J; Dieckmann T^*

来源：Journal of Molecular Biology, 2001, 308(4): 665-679.

DOI：10.1006/jmbi.2001.4627

• VS ribozyme
• tandem G center dot A base-pairs
• RNA structure
• NMR
• protonated adenine

The VS ribozyme is a 154 nucleotide sequence found in certain natural strains of Neurospora. The RNA can be divided into a substrate and a catalytic domain. 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 flexible loop. The cleavage site bulge contains three noncanonical base-pairs, including an A(+) C pair with a protonated adenine. This adenine (A622) is a pH controlled conformational switch that opens up the internal loop at higher pH. The possible significance of this switch for substrate recognition and cleavage is discussed.

• 出版日期2001-5-11