Nucleic Acids Research, 2008, Vol. 36, No. 11 3605 surface of the RNA structure, became solvent-inaccessible upon dimerization (Figure 6, see Figure S2, Supplementary Data). This observation supports the physical interaction between the loop and #05 receptor under dimeric condi- tions. In contrast, several residues in the #05 receptor were cleaved eﬃciently under dimeric conditions but not under monomeric conditions (Figure 6, see Figure S2, Supplementary Data). The opposite eﬀects of lead(II)- induced cleavage on the C-loop and its #05 receptor may suggest that the interaction between the C-loop and #05 receptor is likely to be an induced-ﬁt type of recognition accompanying conformational rearrangement of the #05 receptor rather than a lock-and-key type recognition. Because there is no obvious sequence complementarity Figure 5. Electophoretic mobility shift assays (EMSA). (A and B) Secondary structures of TectoRNA-derived, homodimer-forming constructs. The UUCG tetraloop capping the end of the stem in the construct shown in (A) is eliminated in the construct shown in (B). The target C-loop and the obtained #05 receptor motifs are highlighted with gray boxes. (C and D) Respective autoradiograms of the EMSA experiments for constructs shown in (A) and (B). From left to right, 0, 50, 100, 200, 400, 800 and 1600 nM of unlabeled RNA were added. Figure 6. Lead(II)-induced RNA cleavage analysis. (A and B) Autoradiograms of the cleavage analysis of the construct shown in Figure 4B. Monomeric (without the unlabeled RNA) and dimeric (with 1 mM of the unlabeled RNA) conditions are indicated by M and D, respectively. OH and T1 correspond to alkaline treatment and digestion with RNase T1, respectively. Protected or cleaved residues under dimeric condition are indicated with blue and red arrowheads, respectively. (C) Mapping of the cleavage positions on the secondary structure of the construct. Positions more eﬃciently cleaved in the monomer than in the dimer are indicated with blue arrowheads, and the positions more eﬃciently cleaved in the dimer than in the monomer are indicated with red arrowheads.