3 Importance of Diffuse Metal Ion Binding to RNA

Abstract

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

Heavy metal contamination in processed seafood and the associated health risk for Malaysian women

“…Contamination of Pb, especially in canned food is possible owe to poor quality soldering work (Russo et al , 2013). However, in Malaysia, can for processed food used tinplate as its internal lacquer and has the ability to withstand corrosion to acids, available in processed food as preservatives (Tan, 2015). In addition, the pH of the canned product, the quality of the lacquer coatings of canned products, oxygen concentration in the headspace, quality of coating and storage place may also control metal levels in canned fishes (Boadi et al , 2011).…”

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

“…The number of binding ions is important to DNA/RNA structure and stability, and can be measured via several experimental methods such as the small angle X-ray scattering (SAXS) [128][129][130][131][132][133][134][135][136][137][138][139], the ion-counting method [132], and the thermodynamic method [133][134][135][136][137][138]. The experimental methods have been applied to various RNAs/DNAs, including yeast 58-nt ribosomal RNA fragment [136], tRNA [137,138], poly(A.U) [133], beet western yellow virus pseudoknot fragment [135], polymeric calf thymus DNA [134], oligomeric DNA/RNA duplexes [132], and DNA triplex [132]; see Ref [72] for a collection on the experimental data for ion binding to RNAs/DNAs. The extensive experimental data have yielded the following major conclusions:…”

“…Most of the experiments were performed in a Na + solution or a mixed Na + /Mg 2+ solution; see Ref. [72] for a brief summary on the experimental data [148][149][150][151][152][153][154][155][156][157][158][159]. These thermodynamic data lead to the following major features for ion effects in helix and hairpin stability: The thermodynamic parameters for the formation of helix and loop have been measured extensively at 1 M Na + (i.e., the standard ion condition).…”

“…; see Ref. [72] for a summary for the experimental data of ion effects in RNA tertiary folding [165][166][167][168][169][170][171][172][173][174][175][176][177][178][179]. These experiments have revealed the following important major features on the effects of metal ions, especially Mg 2+ :…”

“…In addition to the non-specific effects of metal ions shown above, some experiments also suggest that, depending on the sequence and geometry, specific interactions of binding ions with the RNA could make critical contribution to RNA tertiary structure [72,135,136]. The unclear understanding on roles of specific binding ions suggest the demand for the further more careful and extensive investigations, especially theoretical investigations, on the role of specific binding ions.…”