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- ItemMagnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations(Washington, DC : Soc., 2021) Schauss, Jakob; Kundu, Achintya; Fingerhut, Benjamin P.; Elsaesser, ThomasIons interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA from Escherichia coli, we follow the population of Mg2+ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg2+/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate-phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 µs. At higher Mg2+ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA. © 2020 American Chemical Society.
- ItemTwo-color two-dimensional terahertz spectroscopy: A new approach for exploring even-order nonlinearities in the nonperturbative regime(Melville, NY : American Institute of Physics, 2021) Woerner, Michael; Ghalgaoui, Ahmed; Reimann, Klaus; Elsaesser, ThomasNonlinear two-dimensional terahertz (2D-THz) spectroscopy at frequencies of the emitted THz signal different from the driving frequencies allows for exploring the regime of (off-)resonant even-order nonlinearities in condensed matter. To demonstrate the potential of this method, we study two phenomena in the nonlinear THz response of bulk GaAs: (i) The nonlinear THz response to a pair of femtosecond near-infrared pulses unravels novel fourth- and sixth-order contributions involving interband shift currents, Raman-like excitations of transverse-optical phonon and intervalence-band coherences. (ii) Transient interband tunneling of electrons driven by ultrashort mid-infrared pulses can be effectively controlled by a low-frequency THz field with amplitudes below 50 kV/cm. The THz field controls the electron–hole separation modifying decoherence and the irreversibility of carrier generation.