Table 1.

Protection of bases in 23S rRNA by tRNA or tRNA fragments bound to the ribosomal P site

tRNA substrate	Ribosomes or subunits*	Protected bases†	Ref.
N-Ac-Phe-tRNAPhe	70S	A1916, A1918, U1926, G2252, G2253, A2439, A2451, G2505, U2506, U2584, U2585, A2602↑‡	2
CACCA-(Ac-Phe)§	70S¶	G2251‖, G2252,	3
UACCA-(Ac-Leu)		G2253, A2439,
CAACCA-(Ac-Met)		A2451, U2506, U2584, U2585, A2602↑
N-Ac-Tyr-tRNABiotTyr	50S**	G2251, G2252, G2253, A2439, A2451, U2506, U2584, U2585	This paper

^*E. coli 70S ribosomes or 50S large ribosomal subunits. 

^†Refers to relative reactivity of individual 23S rRNA bases to chemical modification. 

^‡Binding of the P site substrates to 70S ribosomes increases accessibility of A2602 to modification with dimethyl sulfate. 

^§Refers to 3′-terminal fragments generated by RNase T1 hydrolysis of corresponding N-acyl-aminoacyl-tRNAs. 

^¶Binding of tRNA fragments to 70S ribosomes was performed in the fragment reaction conditions. 

^‖Protection of G2251 was reported in ref. 22. 

^**Binding of biotinylated N-Ac-Tyr-tRNA_Biot^Tyr to 50S ribosomal subunits was performed in the fragment reaction conditions.