Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme

Mapping of UV cross-link between 4-thiouridine product and residue U167 of the a.6.10 ribozyme. A partial hydrolysis ladder of 5′-radiolabeled cross-linked RNA (Xlink, Alk) was compared to that of 5′-radiolabeled linear ribozyme partially digested with RNase T1 (Ref, T1) or partially hydrolyzed (Ref, Alk.) The gap in the ladder indicates the location of the lariat branchpoint in the cross-linked RNA.