arXiv subjects

Andrea Orecchini

Publications and source records attributed to Andrea Orecchini.

3 recordsLinked to original sources

arXiv2022

Connecting Structure, Conformation and Energetics of Human Telomere G-quadruplex 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 address the structural, conformational and energetic features of G4 multimers formed in solutions by the human telomere sequence. A novel multi-technique approach is used combining Small Angle X-ray Scattering (SAXS) and circular dichroism experiments with coarse-grained simulations, to provide quantitative information about large-scale structural features and the stability of G4 multimers. The latter show a significant polydispersity with an exponential distribution of contour lengths, suggesting a step-growth polymerization. On increasing DNA concentration, the strength of G4 stacking interaction increases, as well as the number of the units in the aggregates, with dimers and trimers as the most probable forms. At the same time, a variation of G4 conformation is observed. Our findings provide a quantitative picture of human telomere G4 multimers, which must be accounted for to achieve a rational design of anticancer drugs targeting DNA structures.

physics.bio-ph↗

arXiv2019

Water-polymer coupling induces a dynamical transition in microgels

The long debated protein dynamical transition was recently found also in non-biological macromolecules, such as poly-N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature Td are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as the main responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.

cond-mat.soft↗

arXiv2019

Evidence of a low-temperature dynamical transition in concentrated microgels

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature $T_d\sim250$~K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.

cond-mat.soft↗