Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5′-GΨC/3′-CAG and 5′-CΨG/3′-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5′-GΨC/3′-CAG, 5′-CΨG/3′-GAC, 5′-AΨU/3′-UAA and 5′-UΨA/3′-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.

The use of natural pigments such as betalains in food and health-related products is often limited by said pigments’ relative oxidative stabilities in the products or physiological matrices. Determination of the mechanism of oxidation may inform future development and delivery of better stabilized molecules for improved outcomes. In order to best determine the oxidation mechanism of betanin, a natural food colorant, our efforts were directed toward structural elucidation (LCMS-IT-TOF and NMR) of previously tentatively identified key dehydrogenation products that had been generated as a result of betanin, decarboxylated betanin, and neobetanin oxidation by 2,2′-azino-bis­(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) cation radicals. The resultant oxidation products, the neo-derivatives, were the most stable and survived the preparative isolation and purification process. Structural analyses subsequently confirmed that these compounds, as well as neobetanin, were also the key products of alternative pathways of betanin and 2-decarboxy-betanin oxidation when catalyzed by Cu2+ cations in aqueous solutions at pH close to neutral. Therefore, the structures of the following five neo- or xanneo-derivatives (14,15- or 2,3,14,15-dehydrogenated derivatives, respectively) were confirmed: neobetanin, 2-decarboxy-neobetanin, 2-decarboxy-xanneobetanin, 2,17-bidecarboxy-xanneobetanin, and 2,15,17-tridecarboxy-xanneobetanin. This research confirmed that Cu2+-catalyzed oxidation of betanin and 2-decarboxy-betanin results in generation of neo-derivatives of betanin. In contrast, Cu2+-catalyzed oxidation of 17-decarboxy-betanin and 2,17-bidecarboxy-betanin resulted mostly in formation of betanin xan-derivatives. A relevant mechanism of Cu2+-catalyzed oxidation of the pigments is proposed herein that suggests that the oxidation of betanin can possibly occur in the region of the dihydropyridinic ring and can omit the stage of methide quinone formation in the dihydroindolic system.

The RNA single bulge motif is an unpaired residue within a strand of several complementary base pairs. To gain insight into structural changes induced by the presence of the adenosine bulge on RNA duplex, the solution structures of RNA duplex containing a single adenine bulge (5'-GCAGAAGAGCG-3'/5'-CGCUCUCUGC-3') and a reference duplex with all Watson-Crick base pairs (5'-GCAGAGAGCG-3'/5'-CGCUCUCUGC-3') have been determined by NMR spectroscopy. The reference duplex structure is a regular right-handed helix with all of the attributes of an A-type helix. In the bulged duplex, single adenine bulge stacks into the helix, and the bulge region forms a well-defined structure. Both structures were analyzed by the use of calculated helical parameters. Distortions induced by the accommodation of unpaired residue into the helical structure propagate over the entire structure and are manifested as the reduced base pairs inclination and x-displacement. Intrahelical position of bulged adenine A5 is stabilized by efficient stacking with 5'-neighboring residues G4.

The aim of this work is to analyze in detail the effect of small hydrogen bonding (HB) structures and enantiomeric composition on the dynamics of glass-forming liquid ketoprofen. For that purpose dielectric relaxation, rheological and NMR studies were performed. Investigated samples are racemic ketoprofen, a single enantiomer of ketoprofen and a racemic ketoprofen methyl ester with no tendency to form HB dimers. The combination of complementary experimental techniques enables us to show that macroscopic viscosity η and α-relaxation time τα have nearly the same temperature dependencies, whereas the relation between the viscosity (or molecular reorientation) and the translational self-diffusion coefficient violates Stokes-Einstein law already at high temperature. Additionally, based on dielectric relaxation studies performed on increased pressure we were able to identify similarities and key differences in the supercooled liquid dynamics of investigated materials affected by their tendency to form intermolecular hydrogen bonds. This includes the effect of pressure on the glass transition temperature Tg, changes in the fragility parameter m and activation volume ΔV, the role of thermal energy and density fluctuations in governing the viscous liquid dynamics (Ev/Ep ratio). Finally, we have also demonstrated that the dynamic behaviour of a single enantiomer and the racemic mixture of the same compound are very much alike. Nevertheless, some slight differences were observed, particularly in the τα(T) dependencies measured in the vicinity of glass transition both at ambient and elevated pressure.

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