Cover Page
The handle http://hdl.handle.net/1887/21856 holds various files of this Leiden University dissertation.
Author: Lanzani, Giovanni
Title: DNA mechanics inside plectonemes, nucleosomes and chromatin fibers Issue Date: 2013-10-02
DNA mechanics inside
plectonemes, nucleosomes and chromatin bers
PROEFSCHRIFT
D U L ,
R M
. . C.J.J.M. S ,
C P
2 2013
16:15
Giovanni Lanzani
P , I 1984
Promotiecommissie
Promotor:
Overige leden:
Prof. dr. H. Schiessel Prof. dr. J.-M. Victor
Université Pierre et Marie Curie, Paris Prof. dr. G. Wuite
Vrije Universiteit Amsterdam Dr. V. Vitelli
Prof. dr. E.R. Eliel
Prof. dr. C.W.J. Beenakker
Casimir PhD series, Del -Leiden 2013-7
is work is part of the research program ’DNA in action: Physics of the genome’ of the ’Stichting voor Fundamenteel Onderzoek der Materie (FOM)’, which is nancially supported by the ’Nederlandse Organisa- tie voor Wetenschappelijk Onderzoek (NWO)’.
Typeset in LATEX, written in VIM, version controlled with git and printed by Proefschri maken.nl || Uitgeverij BOXPress.
e word cloud on the cover was partially realized thanks to an amazing tool by Jonathan Feinberg, wordle (http://www.wordle.net).
Contents
Introduction 1
1 Foundations 5
1.1 A semi exible polymer? . . . 6
1.2 e Euler angles . . . 15
1.3 Twist and shout . . . 21
1.4 DNA binding proteins. . . 24
1.5 Buckling . . . 25
1.6 Nucleosomes . . . 27
2 e chromatin ber 35 2.1 Introduction . . . 35
2.2 Results . . . 37
2.3 Discussion . . . 46
3 Unwrapping 49 3.1 General model . . . 49
3.2 Writhe . . . 52
3.3 Energy . . . 53
3.4 Plectoneme . . . 55
3.5 Twist defects . . . 56
3.6 Results . . . 56
4 Plectonemes? 61
4.1 e DNA shape . . . 63
4.2 e writhe . . . 64
4.3 Mechanical and electrostatic energy . . . 66
4.4 Fluctuations . . . 68
4.5 Multi-plectoneme phase . . . 71
4.6 Comparison to experiments . . . 73
Bibliography 75
Samenvatting 83
Publications 87
Curriculum 89
Acknowledgments 91
Index 93
