A codon sugar structure strongly influences tRNA binding to programmed ribosomes

Continuous cell-free protein synthesis directed by messenger DNA and catalyzed by extract of Thermus thermophilus HB27

Polypeptide synthesis directed by DNA as the messenger in a cell-free system of Thermus thermophilus was investigated. Polypeptides were synthesized with the addition of neomycin in the presence of DNA catalyzed by the cell extract. The stability of messenger DNA was greater than that of messenger RNA. Continuous cell-free translation with messenger DNA produced polypeptides at the rate of more than 8 microg/h in the presence of spermine.

Ribosomal decoding processes at codons in the A or P sites depend differently on 2'-OH groups

The importance of 2'-OH groups of codons for binding of cognate tRNAs to ribosomal P and A sites was analyzed applying the following strategy. An mRNA of 41 nucleotides was synthesized with the structure C16-GAA-UUC-GUC-C16 coding for glutamic acid (E), phenylalanine (F) and valine (V), respectively, in the middle (EFV-mRNA). A second template, the E(dF)V-mRNA, was identical except that it carried a deoxyribo-codon-dUdUdC- for phenylalanine. tRNA binding to the P site is totally insensitive to the presence or absence of the 2'-OH group of the P-site codon, and tRNA binding to the P site is also not affected if the A-site codon lacks the 2'-OH groups. However, binding is impaired if the deoxy-codon is present at the E site. In sharp contrast, the A-site binding of Ac-aminoacyl-tRNA was severely reduced in the presence of the deoxy-codon at the A site as well as at the P site. The results demonstrate that the correctness of base pairing is also "sensed" via a correct sugar structure of the codon, e.g. positioning of the sugar pucker (2'-OH), during the decoding process at the A site (elongation) but not during the decoding at the P site (initiation).