Magnetic tweezers based force spectroscopy studies of the structure and dynamics of nucleosomes and chromatin
Kruithof, M.C.
Citation
Kruithof, M. C. (2009, October 1). Magnetic tweezers based force spectroscopy studies of the structure and dynamics of nucleosomes and chromatin. Retrieved from https://hdl.handle.net/1887/14030
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Magnetic Tweezers Based Force Spectroscopy Studies of the Structure and Dynamics of Nucleosomes and
Chromatin
Proefschrift
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden, op gezag van Rector Magnificus prof.mr. P.F. van der Heijden,
volgens besluit van het College voor Promoties te verdedigen op donderdag oktober
klokke : uur
door
Maarten Christiaan Kruithof
geboren te Andernach (Duitsland),
in
Promotiecommissie
Promotor: Prof. Dr. T. Schmidt Co-promotor: Dr. Ir. J. van Noort Overige Leden: Prof. Dr. N. Dekker
Prof. Dr. M. Noteborn Prof. Dr. J. van Ruitenbeek Prof. Dr. H. Schiessel Dr. R. Seidel
Dr. G. Wuite
Casimir PhD Series, Delft-Leiden, -
ISBN ----
An electronic version of this thesis can be found at https://openaccess.leidenuniv.nl
Dit werk wordt financieel gesteund door de Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO).
This thesis is dedicated to my son Chris.
CONTENTS
Introduction
. DNA Compaction by Nucleosomes . . .
. Single Molecule Force Spectroscopy . . .
. Magnetic Tweezers . . .
. Nucleosome and Chromatin Properties . . .
. Overview of the Thesis . . . Bibliography . . .
Sub-Piconewton Dynamic Force Spectroscopy Using Magnetic Tweezers
. Introduction . . .
. Materials and Methods . . .
. Validation of the method . . .
. Energy analysis . . .
. Dynamic force spectroscopy on nucleosome-nucleosome interactions . . .
. Conclusion . . .
Bibliography . . .
v
Hidden Markov Analysis of Nucleosome Unwrapping Under Force
. Introduction . . .
. The Probability Distribution of the End-To-End distance of a DNA-Bead System
. Brownian Dynamics Simulations . . .
. Analysis of Mono-nucleosome Unwrapping Under Force . . .
. Structural Implications . . .
. Conclusion . . .
. Appendix: The Effect of Camera Filtering on the Measured Height Fluctua- tions of a Bead in a Trap . . .
Bibliography . . .
Single Molecule Force Spectroscopy Reveals a Highly Compliant Helical Folding
for the nm Chromatin Fiber
. Introduction . . .
. Results . . .
. Discussion . . .
Bibliography . . .
Thermal Fluctuations of Neighbouring Nucleosomes increase Nucleosome Stabil-
ity
. Introduction . . .
. A Model for a Single Nucleosome Under Force . . .
. The Effect of Thermal Motion on Wrapping Dynamics . . .
. Comparison With Experiments on Mononucleosomes . . .
. Contributions of Neighbouring Nucleosomes . . .
. Second Turn Unwrapping . . .
. Rupture Forces Depend on Force Fluctuations . . .
. Conclusion . . .
Bibliography . . .
vi
Summary
Samenvatting
Curriculum Vitae
List of Publications
vii
viii
