Publications by Andrzej Stasiak

Periodic Motion of Sedimenting Flexible Knots

Giovanni Dietler, Andrzej Stasiak, Krishnan Thyagarajan

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwi ...

APS2018

Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S-pombe

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

The question of how self-interacting chromatin domains in interphase chromosomes are structured and generated dominates current discussions on eukaryotic chromosomes. Numerical simulations using standard polymer models have been helpful in testing the vali ...

Oxford University Press (OUP)2017

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Yannis Burnier, Giovanni Dietler, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti, Aleksandre Japaridze, Robert Sebastian Kwapich

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from ...

Oxford University Press2015

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

Yannis Burnier, Andrzej Stasiak, Julien Dorier, Fabrizio Benedetti

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide in ...

Oxford University Press2014

Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots

Cédric Weber, Giovanni Dietler, Andrzej Stasiak, Mathias Carlen

We address the general question of the extent to which the hydrodynamic behaviour of microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In particular, we compare the sedimentation speeds of knotted DNA molecules undergoin ...

Nature Publishing Group2013

Cooperative kinking at distant sites in mechanically stressed DNA

Andrzej Stasiak, Guillaume Witz, Julien Dorier, Davide Demurtas

In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are c ...

Oxford University Press2011

Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases

Giovanni Dietler, Andrzej Stasiak, Guillaume Witz

Using numerical simulations, we compare properties of knotted DNA molecules that are either torsionally relaxed or supercoiled. We observe that DNA supercoiling tightens knotted portions of DNA molecules and accentuates the difference in curvature between ...

2011

DNA knots and DNA supercoiling

Giovanni Dietler, Andrzej Stasiak, Guillaume Witz

2011

Interplay of DNA supercoiling and catenation during the segregation of sister duplexes

Andrzej Stasiak, Guillaume Witz, Pablo Hernandez

The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as a ...

Oxford University Press2009

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

John Maddocks, Jacques Dubochet, Andrzej Stasiak, Arnaud Amzallag, Davide Demurtas

We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary ...

Oxford University Press2009

Simulations of electrophoretic collisions of DNA knots with gel obstacles

Cédric Weber, Giovanni Dietler, Andrzej Stasiak, Paolo De Los Rios

Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and ...

Institute of Physics2006

3D Reconstruction and Comparison of Shapes of DNA Minicircles Observed by Cryo-Electron Microscopy

Michaël Unser, Andrzej Stasiak, Mathews Jacob, Arnaud Amzallag

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that corr ...

The Author(s)2006

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields

Cédric Weber, Giovanni Dietler, Andrzej Stasiak, Paolo De Los Rios

2006