The Phosphate Vibration as a Sensor for Ion-Pair Formation Studied by Nonlinear Time-Resolved Vibrational Spectroscopy

Die Struktur und Dynamik von Biomolekülen wird durch ein komplexes Wechselspiel mit Ionen und Wassermolekülen der Hydratationshülle beeinflusst. Die Wechselwirkungen sind kaum verstanden, zum Teil weil es an experimentellen molekularen Sonden mangelt. Lokale Schwingungen des RNA-Rückgrats bieten solch nicht-invasive Sonden, empfindlich gegenüber den ersten Schichten der RNA-Solvatationshülle. Die Empfindlichkeit rührt von elektrischen Feldern auf der biomolekularen Oberfläche. Diese Dissertation nutzt die Sensitivität aus, um mit Femtosekunden-2D-IR-Spektroskopie der asymmetrischen Phosphatstreckschwingung die Rolle positiv geladener Ionen, insbesondere Magnesium, Mg2+, zu untersuchen, die negativ geladene Phosphatgruppen des Rückgrats kompensieren. Erste Experimente an Dimethylphosphat, zusammen mit theoretischen Berechnungen, zeigen eine Blauverschiebung der Phosphatmode aufgrund der Bildung von Kontaktionenpaaren. Kurze Abstände zwischen Mg2+ und der Phosphatgruppe führen zu repulsiven Austauschwechselwirkungen, die die Potentialfläche der Schwingung stören. Bei Doppelstrang-RNA zeigt sich eine starke Abhängigkeit der Phosphatschwingung von lokalen Wasserstrukturen. Frequenzverschiebungen durch den Starkeffekt führen zu drei Schwingungsbanden, die unterschiedliche lokale Geometrien widerspiegeln. Elektrische Felder von solvatisierenden Wassermolekülen beeinflussen dabei das Bindungspotential. Abschließend erlaubt es die Blauverschiebung der Phosphatmode, die Bildung von Mg2+/Phosphat Kontaktionenpaaren in Transfer-RNA quantitativ zu verfolgen. Es wird gezeigt, dass diese die Tertiärstruktur der tRNA stabilisieren, indem sie die Coulombabstoßung zwischen negativ geladenen Phosphatgruppen kompensieren, besonders in kompakten Regionen. Die Dissertation demonstriert das Potential zeitaufgelöster Schwingungsspektroskopie, kombiniert mit theoretischen Beschreibungen auf molekularer Ebene, um die komplexen Interaktionen biomolekularer Solvatationsumgebungen zu erforschen.The structure and dynamics of biomolecules are influenced by a complex interplay with ions and water molecules in the local hydration shell. The underlying interactions are poorly understood, partly because of a lack of experimental probes that can access the molecular scale. Local vibrations of the RNA backbone provide non-invasive probes sensitive to the first hydration layers of the RNA solvation shell via the imposed electric field on the biomolecular surface. This thesis exploits this sensitivity in femtosecond 2D-IR spectroscopy experiments on the asymmetric phosphate stretch vibration to investigate the role of positively charged ions, particularly the magnesium cation Mg2+, in counteracting the negatively charged phosphate backbone. Initial experiments with the model system dimethyl phosphate in combination with theoretical calculations report a frequency blue-shift due to the formation of contact ion pairs. Short distances between Mg2+ and phosphate lead to exchange repulsion interactions that perturb the vibrational potential energy surface. In double helical RNA, a strong dependence of the phosphate mode on the local hydration structure of the phosphate group is found. Three distinct vibrational peaks reflect different hydration geometries as a result of vibrational Stark shifts. Responsible for the frequency shifts are electric fields from solvating water molecules. Ultimately, the blue-shift of the phosphate mode allows to quantitatively follow the formation of Mg2+-phosphate contact pairs in transfer RNA systems. It is shown that these configurations stabilize the tertiary structure of tRNA molecules by efficiently compensating the Coulomb repulsion from negatively charged phosphate groups, particularly in highly congested regions. The thesis demonstrates the potential of time-resolved vibrational spectroscopy combined with theoretical descriptions on the molecular level to probe the complex interactions of biomolecular solvation environments

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

Ions 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

Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions

Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)− stretching vibration νAS(PO2)−, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions

Interactions of RNA and Water probed by 2D-IR Spectroscopy

Combined experimental-theoretical investigation of ultrafast hydration dynamics of an A-form RNA double helix in water reveals an ordered arrangement of water molecules and provides boundary conditions for the ion atmosphere around the polyanionic RNA

Interactions of RNA and Water probed by 2D-IR Spectroscopy

Combined experimental-theoretical investigation of ultrafast hydration dynamics of an A-form RNA double helix in water reveals an ordered arrangement of water molecules and provides boundary conditions for the ion atmosphere around the polyanionic RNA

Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study

The equilibrium structure of the RNA sugar–phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm^–1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate–ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes. Interactions with the fluctuating water shell give rise to spectral diffusion on a 300 fs time scale, leading to a quasi-homogeneous line shape of the symmetric (PO₂)⁻ stretching mode of the strongly hydrated phosphate groups. The RNA results are benchmarked by 2D-IR spectra of DNA oligomers in water and analyzed by molecular dynamics and quantum mechanical molecular mechanics simulations