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CPP: Fachverband Chemische Physik und Polymerphysik
CPP 21: Poster II
CPP 21.31: Poster
Tuesday, March 19, 2024, 18:00–20:00, Poster E
oxDNA Molecular Dynamics ecosystem applied to the analysis of "Hairygami". — •Michael Matthies1, Matthew Sample2, Hao Liu2, and Petr Šulc1,2 — 1Technische Universität München, Garching bei München, Germany — 2Arizona State University, Tempe, USA
In the rapidly evolving field of nucleic acid and nucleic acid-protein hybrid nanostructure design, computational methods play a crucial role. oxDNA is a popular coarse-grained Molecular dynamics model which recently got extended by an extensive ecosystem. We showcase these improvements on the practical case of analyzing the conformational space of several archetypical rectangular DNA origami structures influenced by oligonucleotide extensions (nicknamed "Hairygami")[1]. These extensions, usually used to attach functional elements to the origami structures induce a curvature of the structures in the bulk. We characterize the phenomenon using the oxDNA ecosystem and provide experimental verification.
[1] M. Sample, H. Liu, M. Matthies, P. Šulc, arXiv:2302.09109 , (2023)
Keywords: Nucleic acid nanotechnology; Molecular Dynamics; Polymer Physics