[セミナー］第32回IPB セミナー

[セミナー］第32回IPB セミナーを下記の通り開催します。
日時：2022年10月11日(火) 10:30-12:00
場所：hybrid (対面参加は関係者のみ)
講演者：Dr. Enrico Carlon (KU Leuven)
タイトル：The signal in the noise: size and dynamics of topological domains from DNA
Fluctuations
参加登録フォーム https://u-tokyo-ac-jp.zoom.us/meeting/register/tZwpc-CqrD0rHNTU6Ibo1ES0YKIM6D8I-3SA

In the cell, long DNA molecules carry the genetic information and must be stored yet remain accessible to interact with various biomolecules which control for read out and processing. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains using the analysis of fluctuations: a protein-binding event causes a drop in the variance in the end-end distance of a stretched over-wound DNA molecule. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise not detectable.

References

1. E. Skoruppa, E. Carlon, “Equilibrium Fluctuations of DNA Plectonemes” Phys. Rev. E 106, 024412 (2022)
https://arxiv.org/pdf/2205.07735.pdf
2. W. Vanderlinden, E. Skoruppa, P. Kolbeck, E. Carlon, J. Lipfert, “DNA fluctuations reveal the size and dynamics of topological domains” biorXiv:2021.12.21.473646
https://www.biorxiv.org/content/10.1101/2021.12.21.473646v1