Anticodon Loop of tRNAphe: Structure, Dynamics, and Mg2+ Binding

W. Bujalowski, E. Graeser, L. W. McLaughlin, D. Porschke

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


The structure, dynamics, and Mg2+ binding reactions of the isolated anticodon hairpin loop from tRNAPhe (yeast) have been analyzed by fluorescence-detected temperature-jump relaxation, melting experiments, and equilibrium sedimentation. Most of the measurements were performed at an ionic strength of 0.15 M and at temperatures below 25 °C, where the hairpin loop proved to be stable. A relaxation effect with a time constant of ~100 μs, indicated by the Wye base fluorescence, is attributed to a conformational change of the anticodon loop and is very similar to a corresponding transition observed previously for the whole tRNAphe molecule. A Mg2+ binding site reflected by an inner-sphere relaxation process and associated with a strong increase of the Wye base fluorescence closely resembles a corresponding site observed in the complete tRNAphe and is attributed to a site in the anticodon loop identified by X-ray analysis. In addition to the Mg2+ site in the loop, which is associated with a binding constant of 2 X 103M-1 the existence of sites with a higher affinity is demonstrated by an unusual relaxation effect, showing a minimum in the reciprocal time constant with increasing Mg2+ concentration. The experimental data can be described by a transition between two states and Mg2+ binding to both states resulting in a reaction cycle, which is extended by an additional Mg2+ binding reaction to one of the states. The unusual effect has not been observed for the complete tRNAphe and is also not observed when Ca2+ is added instead of Mg2+. This result indicates the existence of a conformational change involving Mg2+ inner-sphere complexation. None of the relaxation effects is observed for a hexamer, which is excised from the anticodon loop and contains the Wye base but does not form the loop structure. Thus, the presence of the hairpin loop is necessary for the anticodon loop transition, the Mg2+ inner-sphere complexation in the anticodon loop, and the special transition coupled to the Mg2+ sites with high affinity; apparently, the hairpin loop structure is required for a specific arrangement of molecular contacts.

Original languageEnglish (US)
Pages (from-to)6365-6371
Number of pages7
Issue number21
StatePublished - Oct 1986

ASJC Scopus subject areas

  • Biochemistry


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