FIGURE 5.

Partitioning of asDIM oligonucleotide with monomer and dimer species of 1–561 RNA upon dimer induction by as202 or as548 oligonucleotides. 1–561 RNA and oligonucleotides were mixed, heated to 90°C, quench cooled, then incubated at 55°C. Reactions shown in lanes 2,4,7,9 included a small amount of radioactively labeled asDIM oligonucleotide. Reactions shown in lanes 4 and 9 additionally contained a 20-fold excess of as202 or as548 oligonucleotides, respectively. The monomer and dimer species were separated on TBE/28°C gel as described in the previous figures. (A) The gel was stained with ethidium bromide and visualized by fluorescence scanning. (B) The same gel was then fixed and dried and the radioactivity associated with the free and bound oligonucleotide was visualized by phosphorimager analysis. Lanes 2,7 suggest that a different interacting region than SL1or Ψ mediated the low level of residual dimers. The exclusion of asDIM* from the dimer bands in lanes 4,9 suggests that nt 397–426 are required for dimerization. Lane 5 corresponds to free radioactively labeled asDIM oligonucleotide loaded without RNA.