Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.
Osmolytes are small organic molecules accumulated by cells in response to osmotic stress. Although their effects on protein stability have been studied, there has been no systematic documentation of their influence on RNA. Here, the effects of nine osmolytes on the secondary and tertiary structure stabilities of six RNA structures of differing complexity and stability have been surveyed. Using thermal melting analysis, m-values (change in DeltaG degrees of RNA folding per molal concentration of osmolyte) have been measured. All the osmolytes destabilize RNA secondary structure, although to different extents, probably because they favor solubilization of base surfaces. Osmolyte effects on tertiary structure, however, can be either stabilizing or destabilizing. We hypothesize that the stabilizing osmolytes have unfavorable interactions with the RNA backbone, which becomes less accessible to solvent in most tertiary structures. Finally, it was found that as a larger fraction of the negative charge of an RNA tertiary structure is neutralized by hydrated Mg(2+), the RNA becomes less responsive to stabilizing osmolytes and may even be destabilized. The natural selection of osmolytes as protective agents must have been influenced by their effects on the stabilities of functional RNA structures, though in general, the effects of osmolytes on RNA and protein stabilities do not parallel each other. Our results also suggest that some osmolytes can be useful tools for studying intrinsically unstable RNA folds and assessing the mechanisms of Mg(2+)-induced RNA stabilization.
Lambert
Dominic
D
Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA.
Draper
David E
DE
D001483:Base Sequence; D001622:Betaine / Q000737:chemistry; D002413:Cations, Divalent; D019855:Ethylene Glycol / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry*; D000432:Methanol / Q000737:chemistry; D008744:Methylamines / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009997:Osmotic Pressure; D011392:Proline / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D013395:Sucrose / Q000737:chemistry; D013402:Sugar Alcohols / Q000737:chemistry; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry
D002413:Cations, Divalent; D008744:Methylamines; D013402:Sugar Alcohols; D001622:Betaine; D013395:Sucrose; D012313:RNA; D014508:Urea; D011392:Proline; D019855:Ethylene Glycol; C005855:trimethyloxamine; D008274:Magnesium; D000432:Methanol