title: Effect of Mg2+ on solution conformation of two different transfer ribonucleic acids.
abstract: We have investigated the effect of Mg2+ on the solution conformation of two different tRNAs by studying the decay of the fluorescence polarization anisotropy of intercalated ethidium on a nanosecond time scale. In the presence of endogenous Mg2+, yeast tRNAPhe and Escherichia coli tRNAVal1 exhibit similar behavior; i.e., the fluorescence from the intercalated ethidium decays biexponentially with lifetimes of approximately 25 and approximately 5 ns, and the fluorescence polarization anisotropy decays with a lifetime of approximately 25 ns. However, once Mg2+ is removed from the two tRNAs, their behavior is no longer similar. In the case of yeast tRNAPhe, it appears that titrating with Mg2+ restores the tRNA to the condition that it was in prior to the Mg2+ removal. This is not so for E. coli tRNAVal1, in which case titrating with Mg2+ results in a two-component anisotropy decay with lifetimes of approximately 25 and approximately 6 ns. Rudimentary calculations indicate that the 6-ns component does not result simply from a change in conformation of the tRNA. However, torsional motions in the tRNA facilitated by a torsion "joint" with a rigidity approximately 1/40 that of intact linear phi 29 DNA would yield a decay component on this time scale with about the right amplitude. We are thus left with the possibility that (after initially removing magnesium) titrating tRNAVal1 with Mg2+ leads to increased internal flexibility and a significant amplitude of a deformational relaxation mode. At any rate, there is no question that after removal of Mg2+ tRNAPhe and tRNAVal1 display quite different solution conformation behavior. These findings are in qualitative agreement with recent 500-MHz 1H NMR results from solutions of these two tRNAs.
mesh_terms: D002413:Cations, Divalent; D004926:Escherichia coli / Q000032:analysis; D008274:Magnesium / Q000494:pharmacology*; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012346:RNA, Transfer, Amino Acyl; D012441:Saccharomyces cerevisiae / Q000032:analysis; D012996:Solutions
chemical_list: D002413:Cations, Divalent; D012329:RNA, Bacterial; D012331:RNA, Fungal; D012346:RNA, Transfer, Amino Acyl; D012996:Solutions; D008274:Magnesium