Sites of 18S rRNA contacting mRNA 3' and 5' of the P site codon in human ribosome: a cross-linking study with mRNAs carrying 4-thiouridines at specific positions.

Abstract Long synthetic mRNAs were used to study the positioning of the E site codon, the 2nd and 3rd nucleotides of the A site bound codon and a nucleotide 3′ of this codon with respect to the 18S rRNA in the human 80S ribosome. The mRNAs contained a GAC triplet coding for Asp and a single 4-thiouridine residue (s 4 U) upstream or downstream of the GAC codon. In the presence of tRNA Asp , the GAC codon of the mRNAs was targeted to the ribosomal P site thus placing s 4 U in one of the following positions − 3, − 2, − 1, + 5, + 6 or + 7 with respect to the first nucleotide of the P site bound codon. It was found that mRNAs that bore s 4 U in positions + 5 to + 7 cross-linked to the 18S rRNA nucleotides C1696, C1698 and 1820–1825, the distribution of cross-links among these targets depending on the position of s 4 U. Cross-links of mRNAs containing s 4 U in positions − 3 to − 1 were found in the region 1699–1704 of the 18S rRNA. In the absence of tRNA, all mRNAs cross-linked only to C1696 and C1698. Absence of the cross-linked nucleotides C1696 and C1698 in the case of mRNAs containing s 4 U in positions − 3 to − 1 confirmed that tRNA Asp actually phased the mRNA on the ribosome.