Mg2+ binding to tRNA revisited: The nonlinear Poisson-Boltzmann model

Our current understanding of Mg2+ binding to RNA, in both thermodynamic and structural terms, is largely based on classical studies of transfer RNAs. Based on these studies, it is clear that magnesium ions are crucial for sta bilizing the folded structure of tRNA. We present here a rigorous theoretic al model based on the nonlinear Poisson-Boltzmann (NLPB) equation for under standing Mg2+ binding to yeast tRNA(Phe). We use this model to interpret a variety of experimental Mg2+ binding data. In particular, we find that the NLPB equation provides a remarkably accurate description of both the overal l stoichiometry and the free energy of Mg2+ binding to yeast tRNA(Phe) with out any fitted parameters. In addition, the model accurately describes the interaction of Mg2+ with localized regions of the RNA as determined by the pK(a) shift of differently bound fluorophores. In each case, we find that t he model also reproduces the univalent salt-dependence and the anticooperat ivity of Mg2+ binding. Our results lead us to a thermodynamic description o f Mg2+ binding to yeast tRNA(Phe) based on the NLPB equation. In this model , Mg2+ binding is simply explained by an ensemble of ions distributed accor ding to a Boltzmann weighted average of the mean electrostatic potential ar ound the RNA. It arrears that the entire ensemble of electrostatically boun d ions superficially mimics a few strongly coordinated ions. Ln this regard , we find that Mg2+ stabilizes the tertiary structure of yeast tRNA(Phe) in part by accumulating in regions of high negative electrostatic potential. These regions of Mg2+ localization correspond to bound ions that are observ ed in the X-ray crystallographic structures of yeast tRNA(Phe). Based on ou r results and the available thermodynamic data, there is no evidence that s pecifically coordinated Mg ions have a significant role in stabilizing the native tertiary structure of yeast tRNA(Phe) in solution. (C) 2000 Academic Press.