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Ions interacting with hydrated RNA play a central role in defining itssecondary and tertiary structure. While spatial arrangements of ions, watermolecules, and phosphate groups have been inferred from X-ray studies, the roleof electrostatic and other noncovalent interactions in stabilizing compactfolded RNA structures is not fully understood at the molecular level. Here, wedemonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groupsembedded in local water shells stabilize the tertiary equilibrium structure oftransfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA fromEscherichia coli, we follow the population of Mg2+ sites close to phosphategroups of the ribose-phosphodiester backbone step by step, combining linear andnonlinear infrared spectroscopy of phosphate vibrations with molecular dynamicssimulations and ab initio vibrational frequency calculations. The formation ofup to six Mg2+/phosphate contact pairs per tRNA and local field-inducedreorientations of water molecules balance the phosphate-phosphate repulsion innonhelical parts of tRNA, thus stabilizing the folded structureelectrostatically. Such geometries display limited sub-picosecond fluctuationsin the arrangement of water molecules and ion residence times longer than 1{\mu}s. At higher Mg2+ excess, the number of contact ion pairs per tRNAsaturates around 6 and weakly interacting ions prevail. Our results suggest apredominance of contact ion pairs over long-range coupling of the ionatmosphere and the biomolecule in defining and stabilizing the tertiarystructure of tRNA.

the journal of physical chemistry. b

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA:  Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical  Simulations