Nynke H. Dekker

Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.

Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB.

Torque-limited RecA polymerization on dsDNA.

Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA.

Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion.

Nanopore tomography of a laser focus.

Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I.

Salt dependence of ion transport and DNA translocation through solid-state nanopores.

Multiple events on single molecules: unbiased estimation in single-molecule biophysics.

When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.

Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.

Antitumour drugs impede DNA uncoiling by topoisomerase I.

Fast dynamics of supercoiled DNA revealed by single-molecule experiments.

An RNA toolbox for single-molecule force spectroscopy studies.

Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence.

Dynamics of phosphodiester synthesis by DNA ligase.

Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate.

Control of shape and material composition of solid-state nanopores.

Quantitative modeling and optimization of magnetic tweezers.

Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores.

Single-molecule magnetic tweezers studies of type IB topoisomerases.

Direct force measurements on double-stranded RNA in solid-state nanopores.

Controlling nanopore size, shape and stability.

Torsional sensing of small-molecule binding using magnetic tweezers.

Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data.

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.

Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores.

Electron beam fabrication of birefringent microcylinders.

The passage of homopolymeric RNA through small solid-state nanopores.

Single-molecule investigations of the stringent response machinery in living bacterial cells.

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids.

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

Calibration of the optical torque wrench.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography.

Studying genomic processes at the single-molecule level: introducing the tools and applications.

Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria.

Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament.

Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments.

Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells.

A force calibration standard for magnetic tweezers.

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes.

Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase.

Biological magnetometry: torque on superparamagnetic beads in magnetic fields.

Essential validation methods for E. coli strains created by chromosome engineering.

Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier.

Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria.

Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments.

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site.

Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes.

High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers.

Hysteresis in DNA compaction by Dps is described by an Ising model.

Tunable top-down fabrication and functional surface coating of single-crystal titanium dioxide nanostructures and nanoparticles.

The progression of replication forks at natural replication barriers in live bacteria.

Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics.

Applying torque to the Escherichia coli flagellar motor using magnetic tweezers.

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.

Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics.

Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding.

Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers.

What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments.

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics.

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species.

Probing Chromatin Structure with Magnetic Tweezers.

Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription.

Predicting Intraserotypic Recombination in Enterovirus 71.

Single-Crystal Rutile TiO Nanocylinders are Highly Effective Transducers of Optical Force and Torque.

DNA Sequence Is a Major Determinant of Tetrasome Dynamics.

Chromatin fibers stabilize nucleosomes under torsional stress.

Versatile Multilayer Metamaterial Nanoparticles with Tailored Optical Constants for Force and Torque Transduction.

DNA replication origins retain mobile licensing proteins.

High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription.

Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers.

Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation.

A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint.

De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features.

Automated cell counting for Trypan blue-stained cell cultures using machine learning.

A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy.