Berlin 2024 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 21: Poster IIIb

BP 21.11: Poster

Mittwoch, 20. März 2024, 11:00–14:30, Poster C

Dynamical and kinetic assessment of nucleic acid systems by CG simulations — •Lorenzo Petrolli, Manuel Micheloni, and Giovanni Mattiotti — Physics Department, University of Trento - via Sommarive, 14 I-38123 Trento, Italy

The in silico characterisation of nucleic acids at the molecular scale by Molecular Dynamics (MD) techniques has been extremely insightful in depicting the essential dynamics underlying a variety of biological activities. To relieve the numerical overhead associated with MD simulations of nucleic acids at the atomistic scale, coarse-grained (CG) force fields have been developed, such as oxDNA [1], that capture the global behaviour of nucleic acids, while keeping an appropriate level of resolution accounting for sequence-specific thermodynamic properties.

Here, we leverage the oxDNA force field and address two significant biological scenarios. On one hand, we characterise the equilibrium dynamics of a viral RNA fragment - and the evolution of the secondary and tertiary motifs thereof. On the other hand, we assess the kinetics of the DNA disruption by double strand breaks on circular DNA molecules, expanding on an earlier work [2], and describe the implications on the experimental characterization of the effects from cell irradiation.

[1] Snodin et al., J. Chem. Phys. 2015; [2] Micheloni et al., Biophys. J. 2023

Keywords: Nucleic acids; Molecular Dynamics; Coarse-Grained force fields; Viral RNA; DNA lesions