Biology subjects

Petrolli, L.

Publications and source records attributed to Petrolli, L..

4 recordsLinked to original sources

bioRxiv2025

Dynamical insights on the role of supercoiling on DNA radiosensitivity

Ionizing radiation (IR) is a major source of biological hazard, associated with a broad range of detrimental lesions of the structural and molecular integrity of the DNA molecule--often leading to genomic instabilities and severe cellular outcomes. The radiosensitivity of DNA is deeply affected by a variety of chemical and biophysical factors, which control the dynamical behavior of the molecule as well as diverse cellular processes and response pathways. Among these factors, the role of supercoiling in modulating DNA radiosensitivity remains controversial, with the existing literature being inconclusive on its effective contribution. Here, we characterize the linearization of a supercoiled DNA minicircle by double-strand breaks (i.e., the rupture of the covalent DNA backbone on both complementary strands of the double helix) via classical coarse-grained molecular dynamics simulations, and verify how the initial supercoiling regime of the molecule influences the kinetics of the rupturing process. We observe that the excess torsional stress overall enhances the rupturing likelihood but in one specific scenario--associated with a biologically-significant level of (negative) superhelical density: This effect highlights a strong asymmetry between positive and negative supercoiling regimes and provides critical insights on the role of topology on the radiosensitivity of DNA molecules.

biophysics↗

bioRxiv2025

Sequence- and supercoiling-dependent effects on the structural dynamics of DNA minicircles

The degree of over-/under-winding of the DNA double helix quantified by the superhelical density, is a key feature modulating critical biological processes such as gene expression and regulation: In fact, DNA molecules are able to channel the excess levels of mechanical stress into local defective and denatured states that are promptly detected by, e.g., transcription factors and nuclease enzymes. The occurrence and stability of these motifs is dictated by a complex interplay between topological and sequence-dependent effects, ultimately affecting the global conformational dynamics of the DNA molecule itself. Here, we characterize the impact of the sequence and of the super-helical density on the structural evolution of a 672-bp DNA minicircle via classical molecular dynamics simulations employing the coarse-grained oxDNA force field. We observe that moderately-to-highly undercoiled regimes are associated with the occurrence of stable, some- what broad denaturation bubbles, typically co-localizing with flexible nucleotide sequences on the DNA minicircle: These defects are hardly re-adsorbed by the system, thereby pinning the subsequent dynamics of the molecule. In fact, a similar behavior was recapitulated by enforcing "synthetic", adjoining DNA mismatches, regardless of the underlying nucleotide sequence, suggesting an effective manner of DNA manipulation.

biophysics↗

bioRxiv2024

Chromatin condensates tune nuclear mechano-sensing in Kabuki Syndrome by constraining cGAS activation

Cells and tissue integrity is constantly challenged by the necessity to adapt and respond to mechanical loads. Among the cellular components, the nucleus possesses mechano-sensing and mechanotransduction capabilities, yet the molecular mechanisms involved remain poorly defined. We postulated that the mechanical properties of the chromatin and its compartmentalization into condensates contribute to the nuclear adaptation to external forces, while preserving its integrity. By interrogating the effects of MLL4 loss-of-function in Kabuki Syndrome, we found that the balancing of transcriptional and Polycomb condensates tunes the nuclear responsiveness to external mechanical forces. We showed that MLL4 acts as a chromatin mechano-sensor by clustering into condensates through its Prion-like domain, and its response was regulated by the chromatin context. Furthermore, the mechano-sensing activity of MLL4 condensates is instrumental to withstand the physical challenges that nuclei experience during cell confinement and migration by preserving their integrity. In Kabuki Syndrome persistent rupture of nuclear envelope triggers cGAS-STING activation, which leads to programmed cell death. Ultimately, these results demonstrate the critical role chromatin compartments play in mechano-responses and how they impact pathological conditions by stimulating cGAS-STING signaling.

molecular biology↗

bioRxiv2022

Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations

Double-strand breaks (DSBs), i.e. the covalent cut of the DNA backbone over both strands, are a detrimental outcome of cell irradiation, bearing chromosomal aberrations and leading to cell apoptosis. In the early stages of the evolution of a DSB, the disruption of the residual interactions between the DNA moieties drives the fracture of the helical layout; in spite of its biological significance, the details of this process are still largely uncertain. Here, we address the mechanical rupture of DNA by DSBs via coarse-grained molecular dynamics simulations: the setup involves a 3855-bp DNA filament and diverse DSB motifs, i.e. within a range of distances between strand breaks (or DSB distance). By employing a coarse-grained model of DNA, we access the molecular details and characteristic timescales of the rupturing process. A sequence-nonspecific, linear correlation is observed between the DSB distance and the internal energy contribution to the disruption of the residual (Watson-Crick and stacking) contacts between DNA moieties, which is seemingly driven by an abrupt, cooperative process. Moreover, we infer an exponential dependence of the characteristic rupture times on the DSB distances, which we associate to an Arrhenius law of thermally-activated processes. This work lays the foundations of a detailed, mechanistic assessment of DSBs in silico, as a benchmark to both numerical simulations and data from single molecule experiments.

biophysics↗