Wyebutine Fluorescence

The wyebutine base at position 37 in the anticodon loop of tRNAphehas also been used as a fluorescence probe/194-2001 The wyebutine base, like ethidium, exhibits a reduced fluorescence lifetime when exposed to aqueous 

The fluorescence decay is multiexponential.(199 200) This is unequivocal evidence that the wyebutine base can be bound in at least two different conformations with different solvent shielding. Wells and Lakowicz(200) resolved two exponential components. They measured the normalized amplitudes and lifetimes for the wyebutine fluorescence at two different concentrations of added Mg2+ S° = 0.50, t, = 1.7 ns, = 0.50, and t2 = 5.9 ns with no added Mg2+ present, and S°i = 0.16, t, =0.6 ns, S2 = 0.84, and r2 = 6.0ns with 10 nM Mg2+. Since the 6ns component is the longest lifetime present, it must represent the conformation that shields the wyebutine to the greatest extent and is generally believed to involve a 3 stack of bases 34-38.w 199-2011 The fraction of the tRNA in this conformation increases when Mg2 + is added to the solution. This structure is also observed in crystal structures which include Mg2+.(202 204) In the other conformation(s), the wyebutine is more exposed to the solvent. A 5 stack, which does not include bases 37 and 38, is one possibility. The wyebutine base would be more exposed to the solvent and have a shorter fluorescence lifetime as a result. However, both NMR data(205 206) and chemical modification studies(207) are inconsistent with a 5 stack. For the moment, this matter is unresolved. 

The results from fitting the anisotropy decay support the above conclusions. Wells and Lakowicz(200) resolved two exponential components in the anisotropy decay. They obtained ro = 0.11, t r = 0.3 ns, rj = 0.15, and t = 18.5 ns for the sample with no added Mg2+, and ro = 0.05, t R = 0.4 ns, r J = 0.17, and t R = 17.4 ns for a sample with 10 mM Mg2+. Here r 0 and r o are the amplitudes of the fast and slow components. The longer rotational relaxation time corresponds to overall tumbling of the tRNA, although its amplitude is reduced by much more rapid local motions. The shorter relaxation time corresponds directly to a rapid local motion. Upon addition of Mg2+, the relative amplitude of die rapid local motion decreases, while that of the overall tumbling increases. This implies that the wyebutine base is held in a more rigid or constrained state, such as a 3 stack, in the presence of Mg2+. In that state, the amplitude of local angular motion is substantially diminished in comparison with that in the alternate state that prevails in the absence of Mg2+. As noted before, the exact nature of these conformation(s) is unresolved. 

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