FIGURE 2.

Structural probing of the neomycin-aptamer M1. (A) Secondary structure model of the neomycin–aptamer M1 in the context of the mRNA with the consensus sequence highlighted in gray. Positions with prominent cleavage and neomycin-dependent changes are indicated. (B) Enzymatic cleavage pattern in the absence (−) or presence (+) of 50 μM neomycin with the guanine-specific nuclease T1 and single-strand-specific nuclease S1. C and H represent no and partial digestion with alkali, respectively. Selected fragment bands corresponding to digestion by T1 are identified by nucleotide positions. The closing stem of the aptamer is shown as a black line, and the gray box corresponds to the consensus sequence. Neomycin-dependent changes are indicated.