NUMEV Seminar #8 : « The signal in the noise: size and dynamics of topological domains from DNA fluctuations », Enrico Carlon, KU Leuven

The next NUMEV seminar will take place on Friday, March 10 at 11am at Amphi Moreau, Campus Saint Priest.

What : « The signal in the noise: size and dynamics of topological domains from DNA fluctuations » – Enrico Carlon, Soft Matter and Biophysics, KU Leuven, Belgium

When : 11am on Friday, March 10 + Lunch

Where : Amphi Moreau, Bât. 2 (LMGC), Campus Saint Priest, 860 rue de Saint Priest, Montpellier

Open to all researchers from all disciplines. Registration is free but mandatory.

Abstract

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

E. Skoruppa, E. Carlon
« Equilibrium Fluctuations of DNA Plectonemes »
Phys. Rev. E 106, 024412 (2022)

W. Vanderlinden, E. Skoruppa, P. Kolbeck, E. Carlon, J. Lipfert
« DNA fluctuations reveal the size and dynamics of topological domains »
PNAS Nexus 1, pgac268 (2022)