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.

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.

Study of network composition in interpenetrating polymer networks of poly(N isopropylacrylamide) microgels: The role of poly(acrylic acid).

HYPOTHESIS: The peculiar swelling behaviour of poly(N-isopropylacrylamide) (PNIPAM)4-based responsive microgels provides the possibility to tune both softness and volume fraction with temperature, making these systems of great interest for technological applications and theoretical implications. Their intriguing phase diagram can be even more complex if poly(acrylic acid) (PAAc)5 is interpenetrated within PNIPAM network to form Interpenetrating Polymer Network (IPN)6 microgels that exhibit an additional pH-sensitivity. The effect of the PAAc/PNIPAM polymeric ratio on both swelling capability and dynamics is still matter of investigation. EXPERIMENTS: Here we investigate the role of PAAc in the behaviour of IPN microgels across the volume phase transition through dynamic light scattering (DLS),7 transmission electron microscopy (TEM)8 and electrophoretic measurements as a function of microgel concentration and pH. FINDINGS: Our results highlight that aggregation is favored at increasing weight concentration, PAAc content and pH and that a crossover PAAc content CPAAc∗9 exists above which the ionic charges on the microgel become relevant. Moreover we show that the softness of IPN microgels can be tuned ad hoc by changing the PAAc/PNIPAM ratio. These findings provide new insights into the possibility to control experimentally aggregation properties, charge and softness of IPN microgels by varying PAAc content.