FIGURE 1.

Protection pattern of tmRNA in ribosomal complexes. The secondary structure of tmRNA was adapted from data from rnp.uthct.edu/rnp/tmRDB/tmRDB.html. pk3 (nucleotides U212–A239) was substituted with an aptamer to streptavidin (inset). The effects that are similar for all complexes are shown at the secondary structure as a green circle for the protection, red for the exposure, blue for the nucleotides which are equally exposed for the modification both in the solution and in the complexes. Black circle indicates nucleotides that are inclined for degradation. The nucleotides 324GG325 which displayed different accessibility to the modifying reagents in different complexes are shown at the left side. The region A79–C137 is shown in details at the bottom. Protected nucleotides are colored in green, exposed in red, nucleotides which are equally exposed for the modification both in the solution and in the complexes are in blue, and nucleotides inclined for degradation are in gray.