Time-Dependent Hydrogen Bond Network Formation in Glycerol-Based Deep Eutectic Solvents.

The front cover artwork is provided by Patryk Palenque Marcinkowski. The image shows a glycerol-choline network accommodating water molecules over time. The glycerol molecules are represented as pandas adapting to the change. Read the full text of the Research Article at 10.1002/cphc.202100806.

Simulations of electric field gradient fluctuations and dynamics around sodium ions in ionic liquids.

The T1 relaxation time measured in nuclear magnetic resonance experiments contains information about electric field gradient (EFG) fluctuations around a nucleus, but computer simulations are typically required to interpret the underlying dynamics. This study uses classical molecular dynamics (MD) simulations and quantum chemical calculations, to investigate EFG fluctuations around a Na+ ion dissolved in the ionic liquid 1-ethyl 3-methylimidazolium tetrafluoroborate, [Im21][BF4], to provide a framework for future interpretation of NMR experiments. Our calculations demonstrate that the Sternheimer approximation holds for Na+ in [Im21][BF4], and the anti-shielding coefficient is comparable to its value in water. EFG correlation functions, CEFG(t), calculated using quantum mechanical methods or from force field charges are roughly equivalent after 200 fs, supporting the use of classical MD for estimating T1 times of monatomic ions in this ionic liquid. The EFG dynamics are strongly bi-modal, with 75%-90% of the de-correlation attributable to inertial solvent motion and the remainder to a highly distributed diffusional processes. Integral relaxation times, ⟨τEFG⟩, were found to deviate from hydrodynamic predictions and were non-linearly coupled to solvent viscosity. Further investigation showed that Na+ is solvated by four tetrahedrally arranged [BF4]- anions and directly coordinated by ∼6 fluorine atoms. Exchange of [BF4]- anions is rare on the 25-50 ns timescale and suggests that motion of solvent-shell [BF4]- is the primary mechanism for the EFG fluctuations. Different couplings of [BF4]- translational and rotational diffusion to viscosity are shown to be the source of the non-hydrodynamic scaling of ⟨τEFG⟩.

Manipulating DNA G-Quadruplex Structures by Using Guanosine Analogues.

The ability to control the folding topology of DNA G-quadruplexes allows for rational design of quadruplex-based scaffolds for potential use in various therapeutic and technological applications. By exploiting the distinct conformational properties of some base- and sugar-modified guanosine surrogates, conformational transitions can be induced through their judicious incorporation at specific sites in the quadruplex core. Changes may involve tetrad polarity inversions with conservation of the global fold or complete refolding to new topologies. Reliable predictions relating to low-energy conformers formed upon specific chemical perturbations of the system and the rational design of modified sequences suffer from our still limited understanding of the subtle interplay of various favorable and unfavorable interactions within a particular quadruplex scaffold. However, aided by an increasing number of systematic substitution experiments and high-resolution structures of modified quadruplex variants, critical interactions, in addition to glycosidic bond angle propensities, are starting to emerge as important contributors to modification-driven quadruplex refolding.

Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations.

The oligomer d(GCGTG3 TCAG3 TG3 TG3 ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti→syn transitions and tetrad stackings.

Ligand-Induced Dimerization of a Truncated Parallel MYC G-Quadruplex.

Binding of an indoloquinoline derivative with an aminoalkyl side chain to a truncated sequence from the MYC promoter region was studied through isothermal titration calorimetry (ITC). The targeted MYC3 sequence lacks 3'-flanking nucleotides and forms a monomeric parallel quadruplex (G4) with a blunt-ended 3'-outer tetrad under the solution conditions employed. Analysis of ITC isotherms reveals multiple binding equilibria with the initial formation of a 1:2 ligand/quadruplex complex. Evaluation of electrophoretic mobilities as well as NMR spectral data confirm ligand-induced dimerization of MYC3 quadruplexes with the ligand sandwiched between the two 3'-outer tetrads. Additional ligand molecules in excess bind to the 5'-outer tetrads of the sandwich complex. Such a ligand-promoted G4 dimerization may be exploited for the controlled assembly or disassembly of G4 aggregates to expand on present quadruplex-based technologies.

Loop Length Affects Syn-Anti Conformational Rearrangements in Parallel G-Quadruplexes.

A G-quadruplex forming sequence from the MYC promoter region was modified with syn-favoring 8-bromo-2'-deoxyguanosine residues. Depending on the number and position of modifications in the intramolecular parallel G-quadruplex, substitutions with the bromoguanosine analogue at the 5'-tetrad induce conformational rearrangements with concerted all-anti to all-syn transitions for all residues of the modified G-quartet. No unfavorable steric interactions of the C8-substituents in the medium grooves are apparent in the high-resolution structure as determined for a tetrasubstituted MYC quadruplex that exclusively forms the all-syn isomer. In contrast, considerable steric clashes with 5'-phosphate oxygen atoms for those analogues that follow a less flexible 1-nucleotide loop in the native all-anti conformation seem to constitute the major driving force for the tetrad inversion and allow for the rational design of appropriately substituted sequences. Correlations found between the population of species subjected to a tetrad flip and melting temperatures indicate that more effective conformational transitions are compromised by lower thermal stabilities of the modified parallel quadruplexes.

Preparation and characterization of pyrene modified uridine derivatives as potential electron donors in RNA.

Charge transfer across double stranded DNA was observed for the first time about 20 years ago, and ever since it has been the subject of a large number of studies. RNA has been hardly investigated in this regard, which not least is due to the lack of suitably functionalized ribonucleotide building blocks to serve as electron sources upon incorporation into oligoribonucleotides. We have synthesized two uridine derivatives carrying pyrene or dimethylaminopyrene linked to C5 of the nucleobase. The key to successful synthesis was the adaptation of Suzuki-Miyaura conditions to the coupling of the pyrene moiety with the ribonucleoside. Final decoration of the pyrenylated nucleosides with standard 5'-O- and 2'-O-protecting groups and subsequent 3'-O-phosphitylation delivered the building blocks for incorporation into RNA. Spectroscopic analysis of the two pyrenylated uridines and of the accordingly modified oligonucleotides showed that in particular the dimethyaminopyrene functionalized nucleoside is a promising candidate as an electron source for RNA charge transport studies.

Selective Targeting of G-Quadruplex Structures by a Benzothiazole-Based Binding Motif.

A benzothiazole derivative was identified as potent ligand for DNA G-quadruplex structures. Fluorescence titrations revealed selective binding to quadruplexes of different topologies including parallel, antiparallel, and (3+1) hybrid structures. The parallel c-MYC sequence was found to constitute the preferred target with dissociation constants in the micromolar range. Binding of the benzothiazole-based ligand to c-MYC was structurally and thermodynamically characterized in detail by employing a comprehensive set of spectroscopic and calorimetric techniques. Job plot analyses and mass spectral data indicate noncooperative ligand binding to form complexes with 1:1 and 2:1 stoichiometries. Whereas stacking interactions are suggested by optical methods, NMR chemical shift perturbations also indicate significant rearrangements of both 5'- and 3'-flanking sequences upon ligand binding. Additional isothermal calorimetry studies yield a thermodynamic profile of the ligand-quadruplex association and reveal enthalpic contributions to be the major driving force for binding. Structural and thermodynamic information obtained in the present work provides the basis for the rational development of benzothiazole derivatives as promising quadruplex binding agents.

Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes.

A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (BrG) analogues in one of its outer G-tetrads. The propensity of the BrG analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues with BrG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (kex) of 0.2 s-1 is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disruption of the corresponding outer G-tetrad but not of the whole quadruplex core during the tetrad flip. Conformational syn-anti isomers with homopolar and heteropolar stacking interactions are nearly isoenergetic with a transition enthalpy of 18.2 kJ/mol in favor of the all-syn isomer.

Molecular Recognition and Visual Detection of G-Quadruplexes by a Dicarbocyanine Dye.

The interactions of a dicarbocyanine dye 3,3'-diethylthiadicarbocyanine, DiSC2(5), with DNA G-quadruplexes were studied by means of a combination of various spectroscopic techniques. Aggregation of excess dye as a result of its positive charge is promoted by the presence of the polyanionic quadruplex structure. Specific high-affinity binding to the parallel quadruplex of the MYC promoter sequence involves stacking of DiSC2(5) on the external G-tetrads; the 5'-terminal tetrad is the favored binding site. Significant energy transfer between DNA and the dye in the UV spectral region is observed upon DiSC2(5) binding. The transfer efficiency strongly depends on the DNA secondary structure as well as on the G-quadruplex topology. These photophysical features enable the selective detection of DNA quadruplexes through sensitized DiSC2(5) fluorescence in the visible region.

Influence of alkali metals on water dynamics inside imidazolium-based ionic liquid nano-domains.

The global need to expand the design of energy-storage devices led to the investigation of alkali metal - Ionic Liquid (IL) mixtures as a possible class of electrolytes. In this study, 1D and 2D Nuclear Magnetic Resonance (NMR) and Electrochemical Impedance Spectroscopy (EIS) as well as Molecular Dynamics (MD) simulations were used to study the intermolecular interactions in imidazolium-based IL - water - alkali halide ternary mixtures. The 1H and 23Na 1D and 1H DOSY NMR spectra revealed that the presence of small quantities of NaCl does not influence the aggregation of water molecules in the IL nano-domains. The order of adding ionic compounds to water, as well as the certain water and NaCl molecular ratios, lead to the formation of isolated water clusters. Two ternary solutions representing different orders of compounds mixing (H2O+ IL + NaCl or H2O+ NaCl + IL) showed a strong dependence of the initial solvation shell of Na+ and the self-clustering of water. Furthermore, the behaviour of water was found to be independent from the conditions applied during the solution preparation, such as temperature and/or duration of stirring and aging. These findings could be confirmed by large differences in the amount of ionic species, observed in the ternary solutions and depending on the order of mixing/solute preparation.