Regensburg 2025 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 3: Computational Biophysics I

BP 3.5: Vortrag

Montag, 17. März 2025, 10:30–10:45, H44

Computational bridging between sequence design and network-level behaviour of programmable DNA-nanomotifs — •Aaron Gadzekpo¹ and Lennart Hilbert^1,2 — ¹Karlsruhe Institute of Technology, Institute of Biological and Chemical Systems — ²Karlsruhe Institute of Technology, Zoological Institute

DNA can serve as a programmable material, by using the DNA sequence to control the 3D-structure of building blocks at the nanometre-scale. In our work, we construct X-shaped particles, or "nanomotifs", from four single-stranded DNA-oligomers, each 46 nucleotides in length. The X-motifs' four arms selectively and transiently hybridize, linking into large, dynamic networks guided by DNA sequence complementarity. We present our scale-bridging computational methods to predict how DNA-oligomer sequences translate into physical properties of X-motifs and the emergent behaviour of networks. In particular, we leverage machine learning to transition from base-pair resolution simulations of single X-motifs and linked pairs to coarse-grained molecular dynamics simulations of networks at increased time and length scales. These simulations are used to explore how nanomotif design at nucleotide level influences emergent behaviour, including liquid-liquid phase separation and condensation on target DNA strands with complementary binding motifs. We connect our observation to corresponding experiments, showcasing model-aided design of DNA-based materials.

Keywords: DNA nanomotifs; phase separation; molecular dynamics simulations; machine learning