Nynke H. Dekker

Department of Bionanoscience, Delft University of Technology

Affiliated withDelft University of Technology University of Oxford

Research Area

BioengineeringUnit 1Biochemistry

Biography

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title	2014
Publication title	2024

Other Publications

Article	Year
Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nature structural & molecular biology\| PubMed ID: 15300241	2004
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature\| PubMed ID: 15800630	2005
Torque-limited RecA polymerization on dsDNA. Nucleic acids research\| PubMed ID: 15824062	2005
Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA. Nature\| PubMed ID: 16163361	2005
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion. Nucleic acids research\| PubMed ID: 16237128	2005
Nanopore tomography of a laser focus. Nano letters\| PubMed ID: 16277463	2005
Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I. The EMBO journal\| PubMed ID: 16292342	2005
Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano letters\| PubMed ID: 16402793	2006
Multiple events on single molecules: unbiased estimation in single-molecule biophysics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16439482	2006
When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I. The EMBO journal\| PubMed ID: 16642041	2006
Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic acids research\| PubMed ID: 16738142	2006
Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature\| PubMed ID: 17589503	2007
Fast dynamics of supercoiled DNA revealed by single-molecule experiments. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17623785	2007
An RNA toolbox for single-molecule force spectroscopy studies. Nucleic acids research\| PubMed ID: 17905817	2007
Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence. Nucleic acids research\| PubMed ID: 18292117	2008
Dynamics of phosphodiester synthesis by DNA ligase. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18458338	2008
Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate. Nucleic acids research\| PubMed ID: 18986997	2008
Control of shape and material composition of solid-state nanopores. Nano letters\| PubMed ID: 19143508	2009
Quantitative modeling and optimization of magnetic tweezers. Biophysical journal\| PubMed ID: 19527664	2009
Distinguishing single- and double-stranded nucleic acid molecules using solid-state nanopores. Nano letters\| PubMed ID: 19537802	2009
Single-molecule magnetic tweezers studies of type IB topoisomerases. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 19763943	2009
Direct force measurements on double-stranded RNA in solid-state nanopores. Nano letters\| PubMed ID: 20050676	2010
Controlling nanopore size, shape and stability. Nanotechnology\| PubMed ID: 20173233	2010
Torsional sensing of small-molecule binding using magnetic tweezers. Nucleic acids research\| PubMed ID: 20624816	2010
Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data. Biophysical journal\| PubMed ID: 20713015	2010
Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell\| PubMed ID: 20723754	2010
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments. Nature methods\| PubMed ID: 20953173	2010
Distinguishable populations report on the interactions of single DNA molecules with solid-state nanopores. Biophysical journal\| PubMed ID: 21112309	2010
Electron beam fabrication of birefringent microcylinders. ACS nano\| PubMed ID: 21280614	2011
The passage of homopolymeric RNA through small solid-state nanopores. Small (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 21638785	2011
Single-molecule investigations of the stringent response machinery in living bacterial cells. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21730169	2011
Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids. Nature communications\| PubMed ID: 21863006	2011
A method to track rotational motion for use in single-molecule biophysics. The Review of scientific instruments\| PubMed ID: 22047303	2011
Calibration of the optical torque wrench. Optics express\| PubMed ID: 22418136	2012
Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque. Nano letters\| PubMed ID: 22642488	2012
Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography. Nanotechnology\| PubMed ID: 23103750	2012
Studying genomic processes at the single-molecule level: introducing the tools and applications. Nature reviews. Genetics\| PubMed ID: 23150038	2013
Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria. Journal of nanobiotechnology\| PubMed ID: 23575419	2013
Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament. Nucleic acids research\| PubMed ID: 23703213	2013
Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments. Nucleic acids research\| PubMed ID: 25140010	2014
Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25313077	2014
Slow unloading leads to DNA-bound β2-sliding clamp accumulation in live Escherichia coli cells. Nature communications\| PubMed ID: 25520215	2014
A force calibration standard for magnetic tweezers. The Review of scientific instruments\| PubMed ID: 25554279	2014
Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell reports\| PubMed ID: 25578730	2015
Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase. Cell reports\| PubMed ID: 25683720	2015
Biological magnetometry: torque on superparamagnetic beads in magnetic fields. Physical review letters\| PubMed ID: 26066460	2015
Essential validation methods for E. coli strains created by chromosome engineering. Journal of biological engineering\| PubMed ID: 26140052	2015
Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. Nature chemical biology\| PubMed ID: 26147356	2015
Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria. Biophysical journal\| PubMed ID: 26331246	2015
Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments. Current opinion in structural biology\| PubMed ID: 26434413	2015
Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site. Nucleic acids research\| PubMed ID: 26496948	2015
Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes. PloS one\| PubMed ID: 26506534	2015
High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics. Biophysical journal\| PubMed ID: 26588570	2015
High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers. Methods (San Diego, Calif.)\| PubMed ID: 27038745	2016
Hysteresis in DNA compaction by Dps is described by an Ising model. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 27091987	2016
Tunable top-down fabrication and functional surface coating of single-crystal titanium dioxide nanostructures and nanoparticles. Nanoscale\| PubMed ID: 27160731	2016
The progression of replication forks at natural replication barriers in live bacteria. Nucleic acids research\| PubMed ID: 27166373	2016
Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophysical reviews\| PubMed ID: 28058066	2016
Applying torque to the Escherichia coli flagellar motor using magnetic tweezers. Scientific reports\| PubMed ID: 28266562	2017
Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic acids research\| PubMed ID: 28460037	2017
Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 28842888	2017
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding. The Journal of biological chemistry\| PubMed ID: 28855255	2017
Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers. Cell reports\| PubMed ID: 29069588	2017
What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments. Critical reviews in biochemistry and molecular biology\| PubMed ID: 29108427	2018
Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics. The Journal of chemical physics\| PubMed ID: 29604863	2018
Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance. Biophysical journal\| PubMed ID: 29694873	2018
Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species. Emerging microbes & infections\| PubMed ID: 29930332	2018
Probing Chromatin Structure with Magnetic Tweezers. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29956240	2018
Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. Cell\| PubMed ID: 30057118	2018
Predicting Intraserotypic Recombination in Enterovirus 71. Journal of virology\| PubMed ID: 30487277	2019
Single-Crystal Rutile TiO Nanocylinders are Highly Effective Transducers of Optical Force and Torque. ACS photonics\| PubMed ID: 31119185	2019
DNA Sequence Is a Major Determinant of Tetrasome Dynamics. Biophysical journal\| PubMed ID: 31521330	2019
Chromatin fibers stabilize nucleosomes under torsional stress. Nature communications\| PubMed ID: 31913285	2020
Versatile Multilayer Metamaterial Nanoparticles with Tailored Optical Constants for Force and Torque Transduction. ACS nano\| PubMed ID: 33170655	2020
DNA replication origins retain mobile licensing proteins. Nature communications\| PubMed ID: 33772005	2021
High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription. Cell reports\| PubMed ID: 35476989	2022
Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers. STAR protocols\| PubMed ID: 35959497	2022
Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation. Nature communications\| PubMed ID: 37059705	2023
A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint. Nature communications\| PubMed ID: 37872142	2023
De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features. Biophysical journal\| PubMed ID: 37968907	2024
Automated cell counting for Trypan blue-stained cell cultures using machine learning. PloS one\| PubMed ID: 38015925	2023
A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy. ACS photonics\| PubMed ID: 38645993	2024