Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study.

The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.

All-DNA System Close to the Percolation Threshold.

We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.

Water-like Behavior of Formamide: Jump Reorientation Probed by Extended Depolarized Light Scattering.

Water is a strong self-associated liquid with peculiar properties that crucially depend on H-bonding. As regards its molecular dynamics, only recently has water reorientation been successfully described based on a jump mechanism, which is responsible for the overall H-bonding exchange. Here, using high-resolution broad-band depolarized light scattering, we have investigated the reorientational dynamics of formamide (FA) as a function of concentration from the neat liquid to diluted aqueous solutions. Our main findings indicate that in the diluted regime the water rearrangement can trigger the motion of FA solute molecules, which are forced to reorient at the same rate as water. This highlights an exceptional behavior of FA, which perfectly substitutes water within its network. Besides other fundamental implications connected with the relevance of FA, its water-like behavior provides rare experimental evidence of a solute whose dynamics is completely slaved to the solvent.

Correlation between collective and molecular dynamics in pH-responsive cyclodextrin-based hydrogels.

UV Raman and Brillouin light scattering (BLS) experiments have been used in this study to explore the complex phase change behavior occurring in pH-responsive polysaccharide hydrogels as a function of temperature. Due to the different physical quantities measured by the two techniques, the joint analysis of Raman and BLS spectra has provided an unprecedented large-scale characterization of the molecular rearrangements and of the different kinds of hydrophilic and hydrophobic interactions that cooperate to determine the phase transformation observed in these hydrogels during the heating of the gel. As the main result, the analysis of the Raman and BLS spectra showed the existence of a correlation between the local (molecular) and collective properties of the gels during the phase transformation undergone by the system, which is markedly triggered by pH. The joint set of experimental results suggests a model according to which the mechanism of pH dependence in the hydrogels under investigation is dominated by the interactions involving the hydrophobic parts of the polymer skeleton, whereas the solvation process observed under heating of the gels is driven by the progressive distancing of the polymer domains among them, as monitored by the Brillouin sound velocity.

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars.

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water.

When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.

Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide.

Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules.

Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: a neutron scattering study.

The dynamics of the human oligonucleotide AG3(T2AG3)3 has been investigated by incoherent neutron scattering in the sub-nanosecond timescale. A hydration-dependent dynamical activation of thermal fluctuations in weakly hydrated samples was found, similar to that of protein powders. The amplitudes of such thermal fluctuations were evaluated in two different exchanged wave-vector ranges, so as to single out the different contributions from intra- and inter-nucleotide dynamics. The activation energy was calculated from the temperature-dependent characteristic times of the corresponding dynamical processes. The trends of both amplitudes and activation energies support a picture where oligonucleotides possess a larger conformational flexibility than long DNA sequences. This additional flexibility, which likely results from a significant relative chain-end contribution to the average chain dynamics, could be related to the strong structural polymorphism of the investigated oligonucleotides.

Painting biological low-frequency vibrational modes from small peptides to proteins.

Protein low-frequency vibrational modes are an important portion of a proteins' dynamical repertoire. Yet, it is notoriously difficult to isolate specific vibrational features in the spectra of proteins. Given an appropriately chosen model peptide, and using different experimental conditions, we can simplify the system and gain useful insights into the protein vibrational properties. Combining neutron scattering, depolarized light scattering, and molecular dynamics simulations, we analyse the low frequency vibrations of biological molecules, comparing the results from a small globular protein, lysozyme, and an amphiphilic peptide, NALMA, both in solution and in powder states. Lysozyme and NALMA present similar spectral features in the frequency range between 1 and 10 THz. With the aid of MD simulations, we assign the spectral features to methyl groups' librations (1-5 THz) and hindered torsions (5-10 THz) in NALMA. Our data also show that, while proteins display boson peak vibrations in both powder and solution forms, NALMA exhibits boson peak vibrations in powder form only. This provides insight into the nature of this feature, suggesting a connection of BP collective motions to a characteristic length scale of heterogeneities present in the system. These results provide context for the use of model peptide systems to study protein dynamics; demonstrating both their utility, and the great care that has to be used in extrapolating results observed in powder to solutions.

Hydrophobic Hydration in Water-tert-Butyl Alcohol Solutions by Extended Depolarized Light Scattering.

Molecular dynamics and structural properties of water-tert-butyl alcohol (TBA) mixtures are studied as a function of concentration by extended depolarized light scattering (EDLS) experiments. The wide frequency range, going from fraction to several thousand GHz, explored by EDLS allows distinguishing TBA rotational dynamics from structural relaxation of water and intermolecular vibrational and librational modes of the solution. Contributions to the water relaxation originating from two distinct populations, i.e. hydration and bulk water, are clearly identified. The dynamic retardation factor of hydration water with respect to the bulk, ξ ≈ 4, almost concentration independent, is one of the smallest found by EDLS among a variety of systems of different nature and complexity. This result, together with the small number of water molecules perturbed by the presence of TBA, supports the idea that hydrophobic simple molecules are less effective than hydrophilic and more complex molecules in perturbing the H-bond network of liquid water. At increasing TBA concentrations the average number of perturbed water molecules shows a pronounced decrease and the characteristic frequency of librational motions reduces significantly, both of which are results consistent with the occurrence of self-aggregation of TBA molecules.

Hydration and rotational diffusion of levoglucosan in aqueous solutions.

Extended frequency range depolarized light scattering measurements of water-levoglucosan solutions are reported at different concentrations and temperatures to assess the effect of the presence and distribution of hydroxyl groups on the dynamics of hydration water. The anhydro bridge, reducing from five to three the number of hydroxyl groups with respect to glucose, considerably affects the hydration properties of levoglucosan with respect to those of mono and disaccharides. In particular, we find that the average retardation of water dynamics is ≈3-4, that is lower than ≈5-6 previously found in glucose, fructose, trehalose, and sucrose. Conversely, the average number of retarded water molecules around levoglucosan is 24, almost double that found in water-glucose mixtures. These results suggest that the ability of sugar molecules to form H-bonds through hydroxyl groups with surrounding water, while producing a more effective retardation, it drastically reduces the spatial extent of the perturbation on the H-bond network. In addition, the analysis of the concentration dependence of the hydration number reveals the aptitude of levoglucosan to produce large aggregates in solution. The analysis of shear viscosity and rotational diffusion time suggests a very short lifetime for these aggregates, typically faster than ≈20 ps.

Hydration and aggregation in mono- and disaccharide aqueous solutions by gigahertz-to-terahertz light scattering and molecular dynamics simulations.

The relaxation properties of hydration water around fructose, glucose, sucrose, and trehalose molecules have been studied by means of extended frequency range depolarized light scattering and molecular dynamics simulations. Evidence is given of hydration dynamics retarded by a factor ξ = 5-6 for all the analyzed solutes. A dynamical hydration shell is defined based on the solute-induced slowing down of water mobility at picosecond time scales. The number of dynamically perturbed water molecules N(h) and its concentration dependence have been determined in glucose and trehalose aqueous solutions up to high solute weight fractions (ca. 45%). For highly dilute solutions, about 3.3 water molecules per sugar hydroxyl group are found to be part of the hydration shell of mono- and disaccharide. For increasing concentrations, a noticeable solute-dependent reduction of hydration number occurs, which has been attributed, in addition to simple statistical shells overlapping, to aggregation of solute molecules. A scaling law based on the number of hydroxyl groups collapses the N(h) concentration dependence of glucose and trehalose into a single master plot, suggesting hydration and aggregation properties independent of the size of the sugar. As a whole, the present results point to the concentration of hydroxyl groups as the parameter guiding both sugar-water and sugar-sugar interactions, without appreciable difference between mono- and disaccharides.

Hydration properties of small hydrophobic molecules by Brillouin light scattering.

We study the relaxation of water molecules next to hydrophobic solutes with different functional groups by Brillouin light scattering. Evidence is given for (i) water activation energy in trimethylamine-N-oxide, proline and t-butyl alcohol diluted solutions which is comparable to that of neat water, almost independent from solute mole fraction and (ii) moderate slowdown of relaxation time of proximal water compared to the bulk, which is consistent with excluded volume models. Assuming that the main contribution to viscosity comes from bulk and hydration water, a rationale is given of the phenomenological Arrhenius' laws for the viscosity of diluted aqueous solutions.

Equivalence of the boson peak in glasses to the transverse acoustic van Hove singularity in crystals.

We compare the atomic dynamics of the glass to that of the relevant crystal. In the spectra of inelastic scattering, the boson peak of the glass appears higher than the transverse acoustic (TA) singularity of the crystal. However, the density of states shows that they have the same number of states. Increasing pressure causes the transformation of the boson peak of the glass towards the TA singularity of the crystal. Once corrected for the difference in the elastic medium, the boson peak matches the TA singularity in energy and height. This suggests the identical nature of the two features.

Acoustic dissipation and density of states in liquid, supercooled, and glassy glycerol.

Combined Brillouin spectra collected at visible, ultraviolet, and x-ray frequencies are used to reconstruct the imaginary part of the acoustic compliance J'' over a wide frequency range between 0.5 GHz and 5 THz. For liquid, supercooled, and glassy glycerol, J'' is found to be linearly dependent on the tagged-particle susceptibility measured by incoherent neutron scattering up to ≃1 THz, giving evidence of a clear relation between acoustic power dissipation and density of states. A simple but general formalism is presented to quantitatively explain this relation, thus clarifying the connection between the quasielastic component observed in neutron scattering experiments and the fast relaxation dynamics probed by Brillouin scattering.

Hydrophobic hydration of tert-butyl alcohol studied by Brillouin light and inelastic ultraviolet scattering.

The longitudinal viscosity of diluted water-tert-butyl alcohol solutions in the 10 GHz frequency region has been measured by means of Brillouin light scattering and inelastic ultraviolet scattering. The main advantage of our hypersonic investigation compared to more traditional ultrasonic measurements is that in the gigahertz frequency range slow relaxation processes involving the alcohol dynamics are completely unrelaxed, so that the measured viscosity mainly originates from the hydrogen bond restructuring of water. In contrast with previous determinations, we estimate an activation energy which is independent from the alcohol mole fraction up to X = 0.1, and comparable to that of bulk water. A simple two-component model is used to describe the steep increase of viscosity with increasing alcohol mole fraction, and a retardation factor 1.7 ± 0.2 is found between the relaxation times of hydration and bulk water. These findings endorse a dynamic scenario where the slowing down of hydration water is mainly due to a reduction of configurational entropy and does not involve an arrested, icelike, dynamics.

Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering.

High resolution depolarized light scattering spectra, extended from 0.5 to 2x10(4) GHz by the combined used of a dispersive and an interferometric setup, give evidence of separated solute and solvent dynamics in diluted trehalose aqueous solutions. The slow relaxation process, located in the gigahertz frequency region, is analyzed as a function of temperature and concentration and assigned to the rotational diffusion of the sugar molecule. The results are discussed in comparison with the data obtained on glucose solutions and they are used to clarify the molecular origin of some among the several relaxation processes reported in literature for oligosaccharides solutions. The concentration dependence of relaxation time and of shear viscosity are also discussed, suggesting that the main effect of carbohydrate molecules on the structural relaxation of diluted aqueous solutions is the perturbation induced on the dynamics of the first hydration shell of each solute molecule.

Light scattering spectra of water in trehalose aqueous solutions: evidence for two different solvent relaxation processes.

Light scattering spectra on aqueous solutions of trehalose were recorded in a wide frequency range combining the use of a double monochromator and a multipass Fabry-Perot interferometer. Experimental results indicate the presence of a slow relaxation mode related to the solute dynamics, which is clearly separated from the solvent one. The spectral analysis reveals the existence of two separate solvent relaxation processes assigned to hydrating and bulk water molecules. The picosecond dynamics of water molecules directly interacting with the solute (proximal water) is consistently delayed with the corresponding relaxation time increase is about 5-6 times compared to the bulk. The slowing down induced by the sugar on the water dynamics mainly involves a restricted hydration layer constituted of 16-18 water molecules. These results improve our knowledge about the influence of carbohydrates on the fast rearrangement dynamics of water and may serve as a model to gain important insight on basic solvation properties of other biorelevant systems in aqueous media.

Onset of the alpha-relaxation in the glass-forming solution LiCl-6H2O revealed by Brillouin scattering techniques.

We measured the dynamic structure factor of the liquid and glassy phases of the LiCl-6H(2)O solution by means of inelastic scattering of radiation in the visible, UV, and x-ray range, between 1 GHz and 10 THz, and by means of photon-correlation spectroscopy, between 0.01 Hz and 20 kHz. The measurements were performed in the temperature range between 353 and 80 K. Our data show that a single-relaxation process exists at high temperature, which has features similar to those of the single relaxation of pure water. Upon cooling the system below approximately 220 K, this single mode starts to differentiate two processes, a structural (alpha-) and a secondary (beta-) relaxation. As the temperature is decreased, the beta-relaxation is the vanishing continuation of the single, high-temperature process, while the onset of the alpha-relaxation occurs at the expense of the beta-process.

Concentration-temperature dependencies of structural relaxation time in trehalose-water solutions by brillouin inelastic UV scattering.

A Brillouin scattering investigation has been carried out on trehalose-water solutions in a wide range of concentrations (0