Stacking Interactions and Flexibility of Human Telomeric Multimers.

G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions, G4s undergo multimerization. Here, we investigate the stacking interactions and structural features of telomeric G4 multimers by means of a novel low-resolution structural approach that combines small-angle X-ray scattering (SAXS) with extremely coarse-grained (ECG) simulations. The degree of multimerization and the strength of the stacking interaction are quantitatively determined in G4 self-assembled multimers. We show that self-assembly induces a significant polydispersity of the G4 multimers with an exponential distribution of contour lengths, consistent with a step-growth polymerization. On increasing DNA concentration, the strength of the stacking interaction between G4 monomers increases, as well as the average number of units in the aggregates. We utilized the same approach to explore the conformational flexibility of a model single-stranded long telomeric sequence. Our findings indicate that its G4 units frequently adopt a beads-on-a-string configuration. We also observe that the interaction between G4 units can be significantly affected by complexation with benchmark ligands. The proposed methodology, which identifies the determinants that govern the formation and structural flexibility of G4 multimers, may be an affordable tool aiding in the selection and design of drugs that target G4s under physiological conditions.

Trehalose-induced slowdown of lysozyme hydration dynamics probed by EDLS spectroscopy.

We use extended depolarized light scattering spectroscopy to study the dynamics of water in a lysozyme-trehalose aqueous solution over a broad time scale, from hundreds to fractions of picoseconds. We provide experimental evidence that the sugar, present in the ternary solution in quantity relevant for biopreservation, strongly modifies the solvation properties of the protein. By comparing aqueous solutions of lysozyme with and without trehalose, we show that the combined action of sugar and protein produces an exceptional dynamic slowdown of a fraction of water molecules around the protein, which become more than twice slower than in the absence of trehalose. We speculate that this ultraslow water may be caged between the sugar and protein surface, consistently with a water entrapment scenario. We also demonstrate that the dynamics of these water molecules gets slower and slower upon cooling. On the basis of these findings, we believe such ultraslow water close to the lysozyme is likely to be involved in the mechanism of bioprotection.

On the interplay between the slowdown of dynamics and the kinetics of aggregation: The case study of a reactive binary mixture.

Modeling the kinetics of aggregation requires a proper strategy to take into account not only the reactivity of reagents but also the ability they have to diffuse. The lack of direct information about diffusion represents the most serious experimental obstacle to the use of diffusion-corrected mean-field equations, which is usually overcome by using information on the structural relaxation dynamics. A very accurate description of the entire kinetics of aggregation can be made by introducing a single time scale of diffusion, set by the structural relaxation time τ of the system according to ∼τ(ξ), with ξ a fractional exponent. Here, we apply this modeling to the case of a reactive binary mixture made of diglycidyl ether of bisphenol-A and 1,3-phenylenediamine, where the reaction proceeds along an autocatalyic (hydroxyl catalyzed) and a non-catalytic (impurity catalyzed) pathway and find that a very small value of the exponent ξ = 0.27 ± 0.03 is needed to reproduce all the data. Our results help revise some preconceived ideas: contrary to widely held assumptions, we find that (i) the time scale of diffusion neither increases proportionally to the structural relaxation time nor is related to τ by a power law with the same fractional exponent as that relating τ to conductivity; (ii) no direct connection exists between the transition to diffusion-control and the development of a gel network or formation of a glassy phase; and (iii) there is no significant difference in the enthalpy barrier for bond formation in the presence of hydroxyl or other than hydroxyl catalyst groups.

Concentration dependence of hydration water in a model peptide.

The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells.

Hydration Dynamics of Model Peptides with Different Hydrophobic Character.

The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6-8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.

Protein Hydration in a Bioprotecting Mixture.

We combined broad-band depolarized light scattering and infrared spectroscopies to study the properties of hydration water in a lysozyme-trehalose aqueous solution, where trehalose is present above the concentration threshold (30% in weight) relevant for biopreservation. The joint use of the two different techniques, which were sensitive to inter-and intra-molecular degrees of freedom, shed new light on the molecular mechanism underlying the interaction between the three species in the mixture. Thanks to the comparison with the binary solution cases, we were able to show that, under the investigated conditions, the protein, through preferential hydration, remains strongly hydrated even in the ternary mixture. This supported the water entrapment scenario, for which a certain amount of water between protein and sugar protects the biomolecule from damage caused by external agents.

Thermoresponsivity of poly(N-isopropylacrylamide) microgels in water-trehalose solution and its relation to protein behavior.

HYPOTHESES: Additives are commonly used to tune macromolecular conformational transitions. Among additives, trehalose is an excellent bioprotectant and among responsive polymers, PNIPAM is the most studied material. Nevertheless, their interaction mechanism so far has only been hinted without direct investigation, and, crucially, never elucidated in comparison to proteins. Detailed insights would help understand to what extent PNIPAM microgels can effectively be used as synthetic biomimetic materials, to reproduce and study, at the colloidal scale, isolated protein behavior and its sensitivity to interactions with specific cosolvents or cosolutes. EXPERIMENTS: The effect of trehalose on the swelling behavior of PNIPAM microgels was monitored by dynamic light scattering; Raman spectroscopy and molecular dynamics simulations were used to explore changes of solvation and dynamics across the swelling-deswelling transition at the molecular scale. FINDINGS: Strongly hydrated trehalose molecules develop water-mediated interactions with PNIPAM microgels, thereby preserving polymer hydration below and above the transition while drastically inhibiting local motions of the polymer and of its hydration shell. Our study, for the first time, demonstrates that slowdown of dynamics and preferential exclusion are the principal mechanisms governing trehalose effect on PNIPAM microgels, at odds with preferential adsorption of alcohols, but in full analogy with the behavior observed in trehalose-protein systems.

Ketoprofen poly(lactide-co-glycolide) physical interaction studied by Brillouin spectroscopy and molecular dynamics simulations.

The performances of poly(lactic-co-glycolic acid) drug delivery systems are affected by the molecular interactions established between the drug and the polymer matrix as well as by the physical state of the drug embedded. Indeed, the drug may induce polymer plasticization with a drastic change in the release kinetics and medicinal product performances. The aim of this study was to better understand the interactions between poly(lactic-co-glycolic acid) and ketoprofen, the latter known to plasticize hydrophilic and hydrophobic polymers. Ketoprofen interacts with poly(lactic-co-glycolic acid) exerting a maximum plasticizing effect at weight fractions around 0.25. Higher ketoprofen amounts form heterogeneous mixtures with the non-soluble molecules dispersed in the matrix as crystals or amorphous domains, depending on the preparation method. Unexpectedly, the amorphous ketoprofen dispersed in the poly(lactic-co-glycolic acid) matrix is remarkably stable. H-bonding seems responsible for the glass transition temperature reduction and the limited solubility. Brillouin spectroscopy and molecular dynamics simulation data suggest that ketoprofen solubility increases with temperature and non-polar interactions are responsible for this phenomenon.

Synchrotron-based X-ray fluorescence imaging of human cells labeled with CdSe quantum dots.

Synchrotron-based X-ray fluorescence (S-XRF) is a powerful technique for imaging the distribution of many biologically relevant elements as well as of "artificial" elements deliberately introduced into tissues and cells, for example, through functionalized nanoparticles. In this study, we explored the potential of S-XRF for chemical nanoimaging (100 nm spatial resolution, nanoXRF) of human cells through the use of functionalized CdSe/ZnS quantum dots (QDs). We used a commercially available QD-secondary antibody conjugate to label the cancer marker HER2 (human epidermal growth factor receptor 2) on the surface of SKOV3 cancer cells and beta-tubulin, a protein associated with cytoskeleton microtubules. We set up samples with epoxy inclusion and intracellular labeling as well as samples without epoxy inclusion and with surface labeling. Epoxy inclusion, also used in electron microscopy, has the advantage of preserving cell morphology and guaranteeing long-term stability. QDs proved to be suitable probes for nanoXRF due to the Se emission band, which is not in close proximity to any other emission band, and the signal specificity, which is preserved in both types of labeling. Therefore, nanoXRF using QD-based markers can be very effective at colocalizing specific intracellular targets with elements naturally present in the cell and may complement confocal fluorescence microscopy in a synergistic fashion.

A molecular dynamics study of chemical gelation in a patchy particle model.

We report event-driven molecular dynamics simulations of the irreversible gelation of hard ellipsoids of revolution containing several associating groups, characterizing how the cluster size distribution evolves as a function of the extent of reaction, both below and above the gel point. We find that over a very large interval of values of the extent of reaction, parameter-free mean-field predictions are extremely accurate, providing evidence that in this model the Ginzburg zone near the gel point, where non-mean field effects are important, is very limited. We also find that the Flory's hypothesis for the post-gelation regime properly describes the connectivity of the clusters even if the long-time limit of the extent of reaction does not reach the fully reacted state. This study shows that irreversibly aggregating asymmetric hard-core patchy particles may provide a close realization of the mean-field model, for which available theoretical predictions may help control the structure and the connectivity of the gel state. Besides chemical gels, the model is relevant to network-forming soft materials like systems with bioselective interactions, functionalized molecules and patchy colloids.

Cauchy relation in relaxing liquids.

The Cauchy-like relation M(infinity) = A + BG(infinity) has recently been found to hold for the high frequency limit values of the longitudinal modulus M(infinity) and transverse modulus G(infinity) of viscoelastic liquids, with B approximately 3 in all the investigated systems. The Brillouin scattering results here reported for curing epoxy systems and thermal glass formers give evidence for the validity of a Cauchy-like relation M(') = A + BG(') for the real part of the elastic moduli measured at finite frequencies. Our results suggest as well the validity of a pure Cauchy relation DeltaM = 3 DeltaG for the relaxation strengths of longitudinal and shear moduli in relaxing liquids.

Exploiting limited valence patchy particles to understand autocatalytic kinetics.

Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description.

Stress-induced modification of the boson peak scaling behavior.

The scaling behavior of the so-called boson peak in glass-formers and its relation to the elastic properties of the system remains a source of controversy. Here the boson peak in a binary reactive mixture is measured by Raman scattering (i) on cooling the unreacted mixture well below its glass-transition temperature and (ii) after quenching to very low temperature the mixture at different times during isothermal polymerization. We find that the scaling behavior of the boson peak with the properties of the elastic medium - as measured by the Debye frequency - holds for states in which the elastic moduli follow a generalized Cauchy-like relationship, and breaks down in coincidence with the departure from this relation. A possible explanation is given in terms of the development of long-range stresses in glasses. The present study provides new insight into the boson peak behavior and is able to reconcile the apparently conflicting results presented in literature.

Networking properties of cyclodextrin-based cross-linked polymers probed by inelastic light-scattering experiments.

An integrated experimental approach, based on inelastic light-scattering techniques, has been here employed for a multilength scale characterization of networking properties of cyclodextrin nanosponges, a new class of cross-linked polymeric materials built up from natural oligosaccharides cyclodextrins. By using Raman and Brillouin scattering experiments, we performed a detailed inspection of the vibrational dynamics of these polymers over a wide frequency window ranging from gigahertz to terahertz, with the aim of providing physical descriptors correlated to the cross-linking degree and elastic properties of the material. The results seem to suggest that the stiffness of cross-linked polymers can be successfully tuned by acting on the type and the relative amount of the cross-linker during the synthesis of a polymer matrix, predicting and controlling their swelling and entrapment properties. The proposed experimental approach is a useful tool for investigating the structural and physicochemical properties of polymeric network systems.

Bond-controlled configurational entropy reduction in chemical vitrification.

Glass formation is usually viewed in terms of physical vitrification: a liquid in a metastable state is cooled or compressed so as to avoid crystallization. However, glasses may also be formed by chemical vitrification, a process involving progressive polymerization of the constituent molecules via the formation of irreversible chemical bonds. The formation of most of the materials used in engineering plastics and the hardening of natural and synthetic resins are based on chemical vitrification. Despite the differences in the molecular processes involved in chemical and physical vitrification, surprising similarities are observed in the slowing down of the dynamics and in the thermodynamical properties of the resulting glasses. Explaining such similarities would improve general understanding of the glass transition and may disclose its universal nature. Here we report dielectric and photon-correlation measurements that reveal the origin of the similarity in the dynamical behaviour of physical and chemical glass formers. We find that the evolution of their configurational restrictions proceeds in a similar manner. In particular, we make a connection between the reduction in configurational entropy and the number of chemical bonds, a quantity that can be controlled in experiments.