Base-Pairing between 23S rRNA and tRNA in the Ribosomal A Site Daniel F Kim, Rachel Green  Molecular Cell  Volume 4, Issue 5, Pages 859-864 (November 1999) DOI: 10.1016/S1097-2765(00)80395-0

Figure 1 Secondary Structures Showing the Specific Nucleotides and the Location of the 2555 Loop of 23S rRNA (A) The 2555 loop (A loop) found in domain V of E. coli 23S rRNA. Universally conserved nucleotides are indicated with a gray square, the nucleotides protected from chemical modification by A site tRNA are circled (Moazed and Noller 1989), and the site of cross-linking (2553) by 4-thio-dT-p-C-p-puromycin (s4TCPm) (Green et al. 1998) is indicated with an arrow. Nucleotide positions Um2552 and G2553 are indicated. (B) Schematic of domain V of E. coli 23S rRNA showing the locations of the 2250 and 2555 loop regions implicated in direct pairing interactions with the P site (Samaha et al. 1995) and A site tRNA, respectively (the P and A loops). Molecular Cell 1999 4, 859-864DOI: (10.1016/S1097-2765(00)80395-0)

Figure 2 Effect of Mutations at U2552 and G2553 of 23S rRNA on Growth and Peptidyl Transferase Activity (A) Expression of rRNA genes carrying mutations at positions Um2552 and G2553 of 23S rRNA. DH1 E. coli cells transformed with the wild-type plasmid, pLK45, or the indicated mutant versions were plated on solid medium containing Amp40-Kan50 at 42°C. (B) Fragment peptidyl transferase assay. Phosphorimager exposure of paper electrophoresis analysis of PT “fragment” reaction catalyzed by wild-type and U2552 and G2553 mutant versions of 23S rRNA incorporated into B. stearothermophilus 50S subunits. Spots represent the product N-Ac-[35S]-Met-puromycin. (C) A-site limiting peptidyl transferase assay. Phosphorimager exposure of polyacrylamide denaturing gel resolving the input 5′-[32P]-labeled CPm derivative from the product of the PT reaction ([32P]-CPm-N-Ac-Phe) catalyzed by U2552 and G2553 mutant B. stearothermophilus 50S subunits reconstituted from in vitro–transcribed 23S rRNA. Molecular Cell 1999 4, 859-864DOI: (10.1016/S1097-2765(00)80395-0)

Figure 3 Suppression Analysis of G2553 Mutant Ribosomes with C74 and C75 tRNA Mutant A Site Substrates (A) Wild-type and mutant reconstituted B. stearothermophilus 50S subunits were incubated with 5′-[32P]-labeled C74 mutant puromycin derivatives of the form NCPm (where N = C, A, G, or U, respectively) in the A site limiting assay. Quantitated data were expressed on the y axis as percentage of input substrate converted to product. The Watson–Crick pairing partner is shaded dark gray in each set of four to highlight predicted patterns. (B) As in (A) except with 5′-[32P]-labeled C75 mutant puromycin derivatives of the form NPm (where N = C, A, G, or U, respectively). In both (A) and (B), standard deviations are included from a compilation of four experiments. Molecular Cell 1999 4, 859-864DOI: (10.1016/S1097-2765(00)80395-0)

Figure 4 Nucleotide Analog 2,6-diaminopurine Tests Watson–Crick Face Pairing Interaction (A) Chemical structures of Watson–Crick-type base pairs between uridine and adenosine (U:A) and between uridine and 2,6-diaminopurine (U:D) with two and three hydrogen bonds, respectively. (B) Deoxyadenosine-puromycin (dA-Pm) and deoxy-2,6-diaminopurine-puromycin (d26DAP-Pm) substrates were compared in the A site limiting assay for their level of activity on G2553 and G2553U mutant ribosomes. Quantitated data were expressed on the y axis as the percentage of input substrate converted to product. Standard deviations are included from a compilation of four experiments. Molecular Cell 1999 4, 859-864DOI: (10.1016/S1097-2765(00)80395-0)