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Research Paper
Arrangement of mRNA 3’ of the A Site Codon on the Human 80S Ribosome
Maxim Molotkov, Dmitri Graifer, Natalia Demeshkna, Marina Repkova, Aliya Ven’yaminova and Galina Karpova
volume 2 | issue 2
april/may/june 2005Pages: 063-069
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Positioning of mRNA 3’ of the A site codon was studied with the use of short mRNA analogues carrying a UUU triplet at the 5’-termini and a perfluorophenylazide group at either the N7 atom of the guanosine or the C5 atom of the uridine 3’ of the triplet. Modified nucleotides were directed to positions +7, +9 or +12 with respect to the first nucleotide of the P site codon by tRNAPhe cognate to the UUU triplet targeted to the P site. Mild UV-irradiation resulted in cross-linking of the mRNA analogues to the 18S rRNA and to 40S proteins, the yield of cross-linking depending on the nature of the mRNA nucleotide bearing the modified group and its position on the ribosome. In addition, the yield of cross-linking to the 18S rRNA decreased strongly when the modified nucleotide was moved from position +7 to position +12. All the mRNA analogues cross-linked to the 18S rRNA nucleotides that had been found earlier at the decoding site, namely, to the invariant dinucleotide A1824/A1825 and the variable A1823 in the 3’-minidomain of the 18S rRNA, and also to the invariant nucleotide C1698 in the 3’-minidomain and the conserved region 605-620 in the apical region of helix 18 in the 5’-domain. The results indicate that (i) the mRNA makes a sharp turn between positions +6 and +7, (ii) the triplet immediately 3’ of the A site codon neighbors the 18S rRNA and proteins, and (iii) the codon 3’ of the triplet mentioned is surrounded mainly by proteins.
We now provide open access to journal articles published online for one year or more. This article may be downloaded at the following link:
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