Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length...

Solid-state nanopores for probing DNA and protein

Solid-state nanopores are small nanometer-scale holes in thin membranes. When used to separate two chambers containing salt solution, any biomolecule passing from one chamber to the other is forced to pass through the pore constriction. An electric field applied across the membrane is used to create an ionic current and electrophoretically drive...

Assembling a single-molecule view on nucleosome dynamics

The main focus of this thesis is a better understanding of the basic compaction mechanism of our DNA using multiple single-molecule techniques. The stretched-out length of our DNA is enormous compared with the dimensions of a cell. To make DNA fit within a cell it is systematically wrapped around proteins (histone octamers), forming nucleosomes....

Single-molecule studies of the twisted, knotted, and broken genome

This thesis describes a series of single-molecule experiments aimed at understanding the physical properties of DNA itself and the proteins that interact with it. We developed and applied sensitive techniques that allowed us to directly probe the conformation and interactions of individual DNA molecules and proteins. Magnetic and optical...

Repairing DNA

Thousands of DNA molecules break inside our bodies every day. Professor Cees Dekker’s Bionanoscience research group has shown how the loose ends get back together.

A method to track rotational motion for use in single-molecule biophysics

The double helical nature of DNA links many cellular processes such as DNA replication, transcription, and repair to rotational motion and the accumulation of torsional strain. Magnetic tweezers (MTs) are a single-molecule technique that enables the application of precisely calibrated stretching forces to nucleic acid tethers and to control...

Solid-state nanopores for scanning single molecules and mimicking biology

Solid-state nanopores, nanometer-size holes in a thin synthetic membrane, are a versatile tool for the detection and manipulation of charged biomolecules. This thesis describes mostly experimental work on DNA translocation through solid-state nanopores, which we study at the single-molecule level. In particular, we demonstrate length-wise ...

All that glitters is gold: Nucleic acid detection using tethered gold

Charge Carriers and Excited States in Supramolecular Materials

The field of organic electronics has been thriving for the last decades due to growing commercial interest. One of the advantages of using organic materials as semiconductors is the possibility to tune their optoelectronic properties by modifying the chemical structure and organization of the building blocks. In this thesis, the properties of...

Forcing DNA and RNA through Artifical Nanopores

Biological molecules can be forced to pass through an aperture in a thin membrane of only several nanometres in diameter (a nanopore). Under the right experimental conditions, the molecules will induce a change in an ionic current flowing through the nanopore. Here, we exploit this principle to detect individual molecules of DNA and RNA and...

The persistence length of double stranded DNA determined using dark field tethered particle motion

The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are...

Scaling theory of DNA confined in nanochannels and nanoslits

A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on itself giving rise to a global persistence length that may be very large owing to entropic deflection....

DNA confined in nanochannels: Hairpin tightening by entropic depletion

A theory is presented of the elongation of double-stranded DNA confined in a nanochannel based on a study of the formation of hairpins. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The DNA in the hairpin remains double-stranded. The free energy of the...