Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.

ABSTRACT: Biomolecular condensates are dynamic, membraneless compartments that emerge through phase separation of specific proteins and nucleic acids, regulating key biochemical processes within cells. Inspired by these natural systems, we recently developed a modular platform for engineering synthetic ribonucleic acid (RNA) condensates using a multistranded branched RNA motif, termed a nanostar. Here, we employ coarse-grained modeling and molecular dynamics (MD) simulations using the oxRNA2 platform to quantify conformational dynamics of 3-, 4-, and 5-arm nanostars. We define flexibility as the standard deviation of interarm angle distributions and geometry as the mean interarm angle. Across valencies at 37 °C and 0.15 M monovalent salts (NaCl), increasing the arm number reduces the mean angle as e

SUBMITTER: Kadam PR 

PROVIDER: S-EPMC12833626 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature