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List of works by Nynke Dekker

A force calibration standard for magnetic tweezers

scientific article published in December 2014

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

scientific article published in October 2011

Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage

An RNA toolbox for single-molecule force spectroscopy studies

scientific article published on 28 September 2007

An optimized software framework for real-time, high-throughput tracking of spherical beads

scientific article published in October 2014

Antitumour drugs impede DNA uncoiling by topoisomerase I

scientific article published in Nature

Applying torque to the Escherichia coli flagellar motor using magnetic tweezers

scientific article

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

scientific article

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

scientific article published on 22 October 2015

Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields

scientific article published in Physical Review Letters

CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands

Calibration of the optical torque wrench

scientific article

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

scientific article published on August 2010

Characterization of Supercoiled Double-Stranded RNA, and Comparison to Double-Stranded DNA

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

Chromatin fibers stabilize nucleosomes under torsional stress

scientific article published on 08 January 2020

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

scientific article

Control of Shape and Material Composition of Solid-State Nanopores

article

Controlling nanopore size, shape and stability

scientific article

Controlling the surface properties of nanostructures for studies of polymerases

scientific article published on 21 October 2008

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

scientific article

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

scientific article published on 27 May 2015

DNA Sequence Is a Major Determinant of Tetrasome Dynamics

scientific article published on 21 August 2019

DNA replication origins retain mobile licensing proteins

scientific article published on 26 March 2021

Direct force measurements on DNA in a solid-state nanopore

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

scientific article published in February 2010

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

scientific article

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

scientific article

Distinguishing Single- and Double-Stranded Nucleic Acid Molecules Using Solid-State Nanopores

article by Gary M. Skinner et al published 12 August 2009 in Nano Letters

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

scientific article

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

scientific article

Dynamics of phosphodiester synthesis by DNA ligase

scholarly article

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

scientific article published on 8 June 2012

Electron Beam Fabrication of Birefringent Microcylinders

scientific article published on 31 January 2011

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

scientific article published on 10 April 2013

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

scientific article published on 11 February 2015

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

scientific article

Excitable particles in an optical torque wrench

article published in 2010

Fast dynamics of supercoiled DNA revealed by single-molecule experiments

scientific article

Freely Orbiting Magnetic Tweezers: A New Twist on Single Molecule Force Spectroscopy

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

scientific article

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

scientific article

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

scientific article published on 26 July 2018

Global correction of optical distortions in multicolor single-molecule microscopy using Zernike polynomial gradients

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

scientific article

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

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

scientific article published on 30 March 2016

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

scientific article

In Vivo Investigation of DNA Replication in Escherichia Coli using Single-Molecule Fluorescence Microscopy

scientific article published in 2012

Induced copy-back RNA synthesis as a novel therapeutic mechanism against RNA viruses

Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses

Introducing the Electromagnetic Torque Tweezers

Investigating DNA Replication in Escherichia Coli on the Single Cell Level Utilizing Microfluidics and Single-Molecule Fluorescence Microscopy

scientific article published in 2013

Investigating Stator Dynamics of the Escherichia Coli Flagellar Motor

scientific article published in 2013

Investigating the Dynamics of the β2 Sliding Clamp in Escherichia Coli at the Single-Cell Level Utilizing Single-Molecule Fluorescence Microscopy

scientific article published in 2014

Investigation of the Tus-ter Blocking Efficacy during the Chromosome Replication of Live Escherichia Coli Cells

scientific article published in 2015

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

scientific article

Les enzymes qui contrôlent la torsion de l’ADN

scientific article published on 01 April 2003

Localization of Metastable Atom Beams with Optical Standing Waves: Nanolithography at the Heisenberg Limit

scientific article published in Science

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

scientific article

Magnetic tweezers for the measurement of twist and torque

scientific article published on 19 May 2014

Magnetization Properties of Superparamagnetic Beads

Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics

scientific article published on January 2017

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

scientific article

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

scientific article published in March 2018

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

scientific article

Nanobubbles in solid-state nanopores

scientific article published on 24 August 2006

Nanopore tomography of a laser focus

scientific article

Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes

Nucleosome Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes

scientific article published on 8 January 2015

Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation

Observation of Landau-Zener dynamics in classical optical systems

scientific article published on 01 January 1995

Optimizing single-molecule experimental approaches for the study of complex protein assemblies on DNA

Origin of the electrophoretic force on DNA in solid-state nanopores

article published in 2009

Physics meets biology: The joining of two forces to further our understanding of cellular function

Predicting Intra- and Intertypic Recombination in Enterovirus 71

Predicting Intraserotypic Recombination in Enterovirus 71

scientific article published on 05 February 2019

Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system

Probing Chromatin Structure with Magnetic Tweezers

scientific article published on 01 January 2018

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

scientific article

Publisher's Note: Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields [Phys. Rev. Lett. 114, 218301 (2015)]

scientific article published on 01 June 2018

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

Quantifying the Resolution of Single-Molecule Torque Measurements by Allan Variance

Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria

scientific article published on September 2015

Quantitative Guidelines for Force Calibration Through Spectral Analysis of Magnetic Tweezers Data

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

scientific article

Quantitative modeling and optimization of magnetic tweezers

scientific article

RNA Structure, Function, and (Thermo-) Dynamics: A SAXS and Single-Molecule Perspective

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

scientific article published on 26 October 2012

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

scientific article published on 8 August 2004

Real-time observation of replicative helicase assembly onto single-stranded DNA

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

scientific article published on 18 October 2016

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

scientific article published on 5 November 2008

Role of Tension and Twist in Single-Molecule DNA Condensation

scientific article published in Physical Review Letters

Salt Dependence of Ion Transport and DNA Translocation through Solid-State Nanopores

scientific article published on 01 January 2006

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

scientific article published in October 2017

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

scientific article published on 22 April 2019

Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases

scientific article published on 01 January 2009

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

scientific article published on 30 August 2017

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

scientific article

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

scientific article published on 21 February 2008

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

scientific article published on 18 December 2014

Small-Molecule Binding to DNA under Tension and Twist Studied by Magnetic Tweezers

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

scientific article

Structural analysis of hyperperiodic DNA from Caenorhabditis elegans

scientific article published on 31 May 2006

Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament

scientific article published on 22 May 2013

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

scientific article published on 30 October 2012

Supercoiling Double-Stranded RNA

The passage of homopolymeric RNA through small solid-state nanopores

scientific article

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

scientific article

Thermophilic topoisomerase I on a single DNA molecule

scientific article published in May 2003

Topoisomerase IB Activity Investigated By Single Molecule Magnetic Tweezers: Mechanisms of Cytotoxicity

Torque spectroscopy for the study of rotary motion in biological systems

scientific article published on 26 December 2014

Torque-limited RecA polymerization on dsDNA.

scientific article

Torsional sensing of small-molecule binding using magnetic tweezers

scientific article published on 12 July 2010

Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation

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

scientific article published on 10 May 2016

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

scientific article published on 30 September 2015

Using neutral metastable argon atoms and contamination lithography to form nanostructures in silicon, silicon dioxide, and gold

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

scientific article published on 10 November 2020

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

scientific article published on 6 November 2017

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

scientific article

de Broglie wave-front engineering

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