SKM 2023 – wissenschaftliches Programm
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CPP: Fachverband Chemische Physik und Polymerphysik
CPP 30: Biopolymers and Biomaterials I (joint session BP/CPP)
CPP 30.11: Vortrag
Mittwoch, 29. März 2023, 12:30–12:45, TOE 317
Reimplementing the formation and dispersal of transcriptional clusters with synthetic DNA-nanomotifs and Langevin-dynamics simulations — •Aaron Gadzekpo1, Xenia Tschurikow1, Mai Tran2, Rakesh Chatterjee3,4, Vasily Zaburdaev3,4, Kerstin Göpfrich2, and Lennart Hilbert1 — 1Karlsruhe Institute of Technology — 2Max Planck Institute for Medical Research — 3Max Planck Zentrum für Physik und Medizin — 4Friedrich-Alexander Universität Erlangen-Nürnberg
Spatial organisation of the genome is emerging as a crucial aspect of gene transcription. In pluripotent cells, self-interacting molecular factors, such as RNA polymerase II, form microphase-separated domains, which become increasingly dispersed due to amphiphilic effects of newly transcribed genes. To understand the principles that lead to this behaviour, we designed synthetic DNA-nanomotifs that form droplets due to self-interaction and allow for the addition of an amphiphilic tail of thymines. Time-lapse microscopy, titration experiments and analysis of the resulting distributions of droplet properties demonstrate that the synthetic system reproduces the dispersal of phase-separated domains found for increasing transcription levels. Simulations based on Langevin-dynamics equally reproduce this behaviour after tuning interaction strengths and number ratios. Our findings illustrate how model-guided design of DNA-based systems can elucidate the mechanisms that control spatio-temporal compartmentalisation in cells.