Poster V6 - Coarse-grained modeling and simulation of multi-stranded RNA nanostars

Introduction: Biomolecular condensates are membraneless organelles which are phase-separated compartments of RNA and protein. These biological compartments are responsible for the spatial and temporal organization of molecules and biochemical reactions. Our recent work has demonstrated the ability to design and synthesize artificial RNA condensates using multi-stranded RNA motifs consisting of three- and four-way junctions, called RNA nanostars. Nanostars bind to each other through programmed single-stranded overhangs, called sticky-ends. These artificial condensates have the potential to be utilized to study biological processes as well as design novel biosensors and drug delivery mechanisms. Studying the behavior of these structures will help us gain insight into developing useful artificial RNA condensate systems.

Materials and

Methods: Here, we use oxRNA, a coarse-grained model to perform molecular dynamics simulations on three- and four-arm nanostars with varying sticky-end length in different temperature and salt concentration conditions. Nanostars were simulated against incrementally changing temperature ranging from 10°C to 35°C and salt concentrations ranging from 0.1 M to 1.0 M Na+. We analyzed our simulation results using Python to study various nanostar features, such as bond angles and arm length.

Results, Conclusions, and Discussions: Overall, the implications of this study reveal that the simulation of both three- and four-arm nanostars at standard simulation conditions yields results similar to the values expected in ideal trigonal planar and tetrahedral geometries. Further, we found that altering the simulations salt concentration resulted in more noticeable differences in bond angles between nanostar arms than altering the temperature.

Acknowledgements (Optional): We acknowledge The Alfred P. Sloan Foundation Matter-to-Life Seed Grant.