Nucleic Acids Research, 1985, Vol. 13, No. 10 3667-3683
© 1985
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Mechanism of codon recognition by transfer RNA studied with oligonudeolides larger than triplets
Max-Planck-Institut für biophysikalischc chermie 3400 Göttingen, FRG
Received March 11, 1985. Accepted April 24, 1985.
The binding of yeast tRNAPha to UUCA, UUCC, UUCCC, UUCUUCU, U4 U5 U6 and U7 was analysed by fluorescence temperature jump and equilibrium sedimentation measurements. In all cases the two observed relaxation processes can be assigned to 
) an intramolecular conformation change of the anticodon loop and ß) preferential binding of the oligonucleotides to one of the anticodon conformations. The anticodon loop transition is associated with inner sphere complesation of Mg2+ and proceeds with rate constants of about 103 s–1. The rate constants of oligonucleotide binding are between 4 and 10*106 M–1s–1 and reflect an increase of the association rate with the number of binding sites compensated to some degree by electrostatic repulsion in the preequillbrlum complex. Neither temperature jump nor equilibrium sedimentation esperieents provided evidence for UUCA or UUCC induced tRNA diserisatlon, although UUC binding leads to strong tRNA diserisation underequivalent conditions. The results obtained for the longer oligonucieotides are similar. In thecase of UUCUUCU with its two potential binding sites for tRNAPha there was no evidence for the formation of ‘ternary’ complexes. Apparently tRNAPha binds preferentially to the second UUC of this ‘messenger’ and forms additional contacts with residues on either side of the codon. Some evidence for the formation of ternary complexes is obtained for U4, and U7 although the extent of this reaction remains very small. Our results demonstrate that the mode of tRNA binding to a codon is strongly influenced by residues next to the codon. The formation of cooperative contacts between tRNA molecules at adjacent codons apparently requires support by a catalyst adjusting an appropriate conformation of messenger and tRNA molecules.
*on leave from: Zakkad Biocheaii Biopolimeròw, Universytet im.Adama Mickiewicza, Poznan, Poland. Present address: Génétique Médical, Hôpital Sainte Justine, 3175 Côte Sainte Catherine, Montréal H3T 1C5 Canada.
+Present address: Laboratoire de Chimie biologique, Université de Bruxelles, 67 rue des Chevaux, 8-1640 Rhode-Saint Genise, Belgique
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