Dynamics of the RNA hairpin GNRA tetraloop.

Abstract

The dynamics of RNA hairpin tetraloops of the GNRA type [sequence G- any ribonucleotide (N)-purine (R)-A] was analyzed by fluorescence spectroscopy and by fluorescence-detected temperature-jump relaxation, using RNA oligomers with 2-aminopurine (2AP) substituted in two different positions of the loop sequence, Gp2APpApA (HP1) and GpAp2APpA (HP2), as indicator. The fluorescence of HP1 is much higher than that of HP2, indicating a lower degree of 2AP-stacking in HP1. Addition of Mg(2+) or Ca(2+) ions leads to an increase of fluorescence in HP1, whereas a decrease of fluorescence is observed in HP2. In both cases at least two ion-binding equilibria are required to fit titration data. T-jump experiments using fluorescence detection show a relaxation process with a time constant of 22 micros for HP1, whereas two relaxation processes with time constants 5 and 41 micros, are found for HP2. These results clearly demonstrate the existence of more than the single conformation state detected by NMR analysis. The T-jump amplitudes decrease with increasing bivalent ion concentration, indicating that one of the states is favored in the presence of bivalent ions. The loop relaxation processes are slower than standard stacking processes, probably because of activation barriers imposed by a restricted mobility of loop residues, and are assigned to a stacking rearrangement, probably between the 5' and the 3'-side. A similar process has been observed previously for the anticodon loop of tRNA(Phe). The rate constants of the transition are in the range of 10(4) s(-1) in the case of HP1. The data demonstrate the existence of structures that are not resolved by standard NMR because of fast exchange and are not found by X-ray analysis because of restrictions by crystal packing.