Publications

Louis Kuijpers, Wouter van den Braak, Abbas Freydoonian, Nynke H. Dekker, and Leo van der Pol
Optimization of enterovirus-like particle production and purification using Design of Experiments
submitted (2025)

Louis Kuijpers, Natasha Giannopoulou, Yuzhen Feng, Wouter van den Braak, Abbas Freydoonian, Ramon Ramlal, Hugo Meiring, Belén Solano, Wouter Roos, Arjen Jakobi, Leo A. van der Pol, and Nynke H. Dekker
Enterovirus-like particles encapsidate viral RNA and exhibit decreased stability due to lack of maturation
under review (2025)

Chew Theng Lim, Thomas C.R. Miller, Kang Wei Tan, Saurabh Talele, Anne Early, Philip East, Humberto Sánchez, Nynke H. Dekker, Alessandro Costa, and John F.X. Diffley
Cell Cycle Regulation has Shaped Budding Yeast Replication Origin Structure and Function
under review (2025)

Daniel Ramírez Montero, Humberto Sánchez, Edo van Veen, Theo van Laar, Belén Solano, John F.X. Diffley, and Nynke H. Dekker
Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG
Journal of Visualized Experiments (209), e67076 (2024)

Zhaowei Liu*, Edo van Veen*, Humberto Sánchez, Belén Solano, Francisco J. Palmero Moya, Kaley A. McCluskey, Daniel Ramírez Montero, Theo van Laar, and Nynke H. Dekker
(* = equal contribution)
A biophysics toolbox for reliable data acquisition and processing in integrated force-confocal fluorescence microscopy
ACS Photonics, published online March 18 (2024)

Daniel Ramírez Montero, Zhaowei Liu, and Nynke H. Dekker
De novo fabrication of custom-sequence plasmids for the efficient synthesis of long DNA constructs including extrahelical features for single-molecule experiments
Biophysical Journal, 123, 31-41 (2024)

Louis Kuijpers, Edo van Veen, Leo A. van der Pol, and Nynke H. Dekker
Automated cell counting for Trypan blue-stained cell cultures using machine learning
PloSONE 18(11):e0291625 (2023);

Humberto Sánchez, Zhaowei Liu, Edo van Veen, Theo van Laar, John F.X. Diffley, and Nynke H. Dekker
A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint
Nature Communications 14, 6735 (2023);

Daniel Fan, Jelmer Cnossen, Shih-Te Hung, Dimitri Kromm, Sung Hyun Kim, Chirlmin Joo, Nynke H. Dekker, Gerard J. Verbiest, and Carlas Smith
Improved axial super-resolution of single emitters via rapid TIRF angle scanning
Optics Communications 542:129548 (2023);

Daniel Ramírez Montero, Humberto Sánchez, Edo van Veen, Theo van Laar, Belén Solano, John F.X. Diffley, and Nynke H. Dekker
Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation
Nature Communications 14:2082 (2023);

Kaley McCluskey and Nynke H. Dekker
Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system
Optics Communications 538: 129474 (2023);

Clément Rouillon, Bruna Eckhardt, Leonie Kollenstart, Fabian Gruss, Alexander Verkennis, Inge Rondeel, Peter Krijger, Giulia Ricci, Alva Biran, Theo van Laar, Charlotte Delvaux de Fenffe, Georgiana Luppens, Pascal Albanese, Richard Scheltema, Wouter de Laat, Nynke H. Dekker, Anja Groth, and Francesca Mattiroli
CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands
Nucleic Acids Research (2023);

Louis Kuijpers, Theo van Laar, Richard Janissen, and Nynke H. Dekker
Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers
Star Protocols 3, 101606 (2022);

Richard Janissen*, Behrouz Eslami Mossallam*, Irina Artsimovitch#, Martin Depken#, and Nynke H. Dekker#
High-throughput single-molecule experiments reveal heterogeneity, state-switching, and three interconnected pause states in bacterial transcription
(* = equal contribution, # = corresponding author)
Cell Reports 39, 110749 (2022);

Kaley McCluskey*, Edo N.W. van Veen*, Jelmer P. Cnossen, Wouter J. Wesselink, Filip M. Asscher, Carlas S. Smith#, and Nynke H. Dekker#
Global correction of optical distortions in multicolor single-molecule microscopy using Zernike polynomial gradients
(* = equal contribution, # = corresponding author)
Optics Express 29 (25), 42251-42264 (2021);

Richard Janissen*, Andrew Woodman*, Djoshkun Shengjuler, Thomas Vallet, Kuo-Ming Lee, Ibrahim Moustafa, Fiona Fitzgerald, Peng-Nien Huang, Louis Kuijpers, Angela L. Perkins, Daniel A. Harki, Jamie J Arnold, Belén Solano, Shin-Ru Shih, Marco Vignuzzi, Craig E. Cameron#, Nynke H. Dekker#
Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses
(* = equal contribution, # = corresponding author)
Molecular Cell 81, 1–14 (2021);

Michelle D. Wang, Mario Nicodemi, Nynke H. Dekker, Thomas Gregor, David Holcman, Antoine M. van Oijen, and Suliana Manley
Physics meets biology: The joining of two forces to further our understanding of cellular function
Molecular Cell 81 (15), 3033-3037 (2021);

Humberto Sánchez, Kaley McCluskey, Theo van Laar, Edo van Veen, Filip M. Asscher, Belén Solano, John F.X. Diffley# and Nynke H. Dekker#
DNA replication origins retain mobile licensing proteins
(# = corresponding author)
Nature Communications 12, 1908 (2021);

Ying Tang*, Seungkyu Ha*, Thomas Begou, Julien Lumeau, H. Paul Urbach, Nynke H. Dekker#, and Aurèle J. L. Adam#
Versatile multilayer metamaterial nanoparticles with tailored optical constants for force and torque transduction
(* = equal contribution, # = corresponding author)
ACS Nano 14, 14895−14906 (2020)

A. Kaczmarczyk, M. He, O. Ordu, J. van Noort#, and N.H. Dekker#
Chromatin fibers stabilize nucleosomes under torsional stress
(# = corresponding author)
Nature Communications 11, 126 (2020)

Orkide Ordu, Alexandra Lusser, and Nynke H. Dekker
DNA sequence is a major determinant of tetrasome dynamics
Biophysical Journal (2019)

Seungkyu Ha, Ying Tang, Maarten van Oene, Richard Janissen, Roland Dries, Belén Solano, Aurele Adam, and Nynke H. Dekker
Single-crystal rutile TiO2 nanocylinders are highly effective transducers of optical force and torque
ACS Photonics, online publication April 22 (2019)

Andrew Woodman, Kuo-Ming Lee, Richard Janissen, Yu-Nong Gong, Nynke H. Dekker, Shin-Ru Shih, and Craig Cameron
Predicting Intra- and Intertypic Recombination in Enterovirus 71
Journal of Virology 5, 93 (2019), doi: 10.1128/JVI.02057-18

R. Janissen*, M. Arens*, N. Vtyurina*, Z. Rivai, N.D. Sunday, B. Eslami-Mossallam, A. Gritsenko, L. Laan, D. de Ridder, I. Artsimovitch, N.H. Dekker#, E. A. Abbondanzieri#, and A. S. Meyer#
Global DNA compaction in stationary-phase bacteria does not affect transcription
(* = equal contribution, # = corresponding author)
Cell 174, 1188-1199 (2018) (online publication July 26)

Kuo-Ming Lee, Yu-Nong Gong, Tzu-Hsuan Hsieh, Andrew Woodman, Nynke H. Dekker, Craig Cameron, and Shin-Ru Shih
Discovery of Enterovirus A71-like non-structural genome in recent circulating viruses of the Enterovirus A species
Emerging Microbes & Infections 7, 111 (2018) (online publication June 21)

Artur Kaczmarczyk, Thomas B. Brouwer, Chi Pham, Nynke H. Dekker, and John van Noort
Methods for probing chromatin structure with magnetic tweezers
Nanoscale Imaging: Methods and Protocols, Methods in Molecular Biology 1814, 297-323 (2018)

M. M. van Oene*, S. Ha*, T. Jager, M. Lee, F. Pedaci, J. Lipfert, and N. H. Dekker
Quantifying the Resolution of Single-Molecule Torque and Twist Measurements Using Allan Variance
(* = equal contribution)
Biophysical Journal 114, 1970–1979 (2018) (online publication April 24)

O. Ordu, L. Kremser, A. Lusser, and N.H. Dekker
Modification of the Histone Tetramer at the H3-H3 Interface Impacts Tetrasome Conformations and Dynamics
Journal of Chemical Physics 148, 123323 (2018)

Bojk A. Berghuis, Vlad-Stefan Raducanu, Mohamed M. Elshenawy, Slobodan Jergic, Martin Depken, Nicholas E. Dixon, Samir M. Hamdan, and Nynke H. Dekker
What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments
Critical Reviews in Biochemistry and Molecular Biology 53(1):49-63 (2017) (published online November 7)

David Dulin, Jamie J. Arnold, Theo van Laar, Hyung-Suk Oh, Cheri Lee, Daniel A. Harki, Martin Depken, Craig E. Cameron, and Nynke H. Dekker
Signatures of nucleotide analogue incorporation by an RNA-dependent RNA polymerase revealed by using high-throughput magnetic tweezers
Cell Reports 21, 1063–1076 (2017)

Artur Kaczmarczyk, Abdollah Allahverdi, Thomas Brouwer, Lars Nordenskiöld, Nynke H. Dekker, and John van Noort
Single-molecule force spectroscopy on H4 tail cross-linked chromatin reveals fiber folding
Journal of Biological Chemistry 292(42), 17506–17513 (2017)

Roy de Leeuw, Peter Brazda, M. Charl Moolman, Belén Solano, and Nynke H. Dekker
Measuring in vivo protein dynamics throughout the cell cycle using microfluidics
Methods in Molecular Biology, online publication August 28 (2017)

Franziska Kriegel, Niklas Ermann, Ruaridh Forbes, David Dulin, Nynke H. Dekker, and Jan Lipfert
Probing the Salt Dependence of the Torsional Stiffness of DNA by Multiplexed Magnetic Torque Tweezers
Nucleic Acids Research 45, 5920-5929 (2017) (online publication April 29)

Maarten M. van Oene, Laura E. Dickinson, Bronwen Cross, Francesco Pedaci, Jan Lipfert, and Nynke H. Dekker
Applying torque to the Escherichia coli flagellar motor using magnetic tweezers
Scientific Reports 7, 43285 (2017)

O. Ordu, A. Lusser, and N.H. Dekker
Recent insights from single-molecule studies into nucleosome structure and dynamics
Biophysical Reviews 8, 33-49 (2016) (online publication October 16)

D. Dulin, Z. Yu, T. Cui, B.A. Berghuis, S.M. Depken, and N.H. Dekker,
Real-time observation of replicative helicase assembly onto single-stranded DNA
BioRxiv, doi: https://doi.org/10.1101/077800 (2016)

M.C. Moolman*, S. Tiruvadi Krishnan*, J.W.J. Kerssemakers, R. de Leeuw, V. Lorent, D.J. Sherratt, and N.H. Dekker
The progression of replication forks at natural replication barriers in live bacteria
Nucleic Acids Research 44 (13), 6262-6273 (2016) (online publication May 10)

(* = equal contribution)

Natalia N. Vtyurina, David Dulin, Margreet W. Docter, Anne S. Meyer, Nynke H. Dekker, and Elio A. Abbondanzieri
An Ising model describes hysteresis in the process of DNA compaction by Dps
Proceedings of the National Academy of Sciences (USA) 113 (18), 4982–4987 (2016)

S. Ha, R. Janissen, Ye.Ye. Ussembayev, M.M. van Oene, B. Solano, and N.H. Dekker
Tunable Top-Down Fabrication and Functional Surface Coating of Single-Crystal Titanium Dioxide Nanostructures and Nanoparticles
Nanoscale 8, 10739-10748 (2016) (online publication April 18)

B.A. Berghuis, M. Koeber, T. van Laar, and N.H. Dekker
High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers
Methods 105, 90-98 (2016) (online publication March 30)

David Dulin, Thijs Cui, Jelmer Cnossen, Margreet W. Docter, Jan Lipfert, and Nynke H. Dekker
High Spatiotemporal Resolution Magnetic Tweezers for Single-Molecule Force Spectroscopy: Calibration and Applications to DNA Dynamics
Biophysical Journal 109, 2113–2125 (2015)

D. Dulin, I.D. Vilfan, B. Berghuis, M. Poranen, M. Depken, and N.H. Dekker
Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site
Nucleic Acids Research 43, 10421-9 (2015) (online publication October 22)

R. Vlijm, M. Lee, O. Ordu, A. Boltengagen, A. Lusser, N.H. Dekker, and C. Dekker
Comparing the assembly and handedness dynamics of (H3.3-H4)2 tetrasomes to canonical tetrasomes
Plos One 10, e0141267 (2015) (online publication October 28)

D. Dulin, B.A. Berghuis, M. Depken, and N.H. Dekker
Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments
Current Opinion in Structural Biology 34, 116–122 (2015) (online publication October 1)

M. Charl Moolman*, Jacob W.J. Kerssemakers*, and Nynke H. Dekker
Quantitative analysis of intracellular fluorescent foci in live bacteria
Biophysical Journal 109, 883-891 (2015) (online publication September 4)
(* = equal contribution)

B.A. Berghuis, D. Dulin, Z.-Q. Xu, T. van Laar, B. Cross, R. Janissen, S. Jergic, N.E. Dixon, S.M. Depken, and N.H. Dekker
Strand separation establishes a sustained lock at the Tus–Ter replication fork barrier
Nature Chemical Biology 11, 579–585 (2015) (online publication July 6)

S. Tiruvadi Krishnan, M. C. Moolman, T. van Laar, A. S. Meyer, and N.H. Dekker
Essential validation methods for E. coli strains created by chromosomal engineering
Journal of Biological Engineering 9 (2015), DOI: 10.1186/s13036-015-0008-x (online publication July 1)

Jan Lipfert and Nynke H. Dekker
De RNA helix lijkt niet altijd op die van DNA
Nederlands Tijdschrift voor Natuurkunde 81(6), 224-227 (2015) (online publication May 28)(Dutch)

M.M. van Oene, L. Dickinson, F. Pedaci, M. Koeber, D. Dulin, J. Lipfert, and N.H. Dekker
Biological magnetometry: the torque on superparamagnetic beads in magnetic fields
Phys. Rev. Lett. 114, 218301 (2015) (online publication May 27)

D. Dulin, I.D. Vilfan, B.A. Berghuis, S. Hage, D. Bamford, M. Poranen, S.M. Depken, and N.H. Dekker
Elongation-competent pauses govern the fidelity of a viral RNA-dependent RNA polymerase
Cell Reports 10(6), 983-992 (2015) (online publication Feb. 12)

R. Vlijm*, M. Lee*, J. Lipfert, A. Lusser, C. Dekker, and N.H. Dekker
Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes
Cell Reports 10, 216–225 (2015) (online publication Jan. 8)

Jan Lipfert, M.M. van Oene, M. Lee, F. Pedaci, and Nynke H. Dekker
Torque Spectroscopy for the Study of Rotary Motion in Biological Processes
Chemical Reviews 115 (3), 1449–1474 (2015) (online publication Dec. 26, 2014)

Zhongbo Yu, David Dulin, Jelmer P. Cnossen, Mariana Köber, Maarten M. van Oene, Orkide Ordu, Bojk A. Berghuis, Toivo Hensgens, Jan Lipfert, and Nynke H. Dekker
A force calibration standard for magnetic tweezers
Review of Scientific Instruments 85(12):123114 (2014) (online publication Dec. 23)

M. Charl Moolman, Sriram Tiruvadi Krishnan, Jacob W.J. Kerssemakers, Aafke van den Berg, Pawel Tulinski, S. Martin Depken, Rodrigo Reyes-Lamothe, David J. Sherratt, and Nynke H. Dekker
Slow unloading leads to DNA-bound beta-2 sliding clamp accumulation in live Escherichia coli cells
Nature Communications 5, article number 5820 (2014) (online publication Dec. 18)

David Dulin, Stephane Barland, Xavier Hachair, and Francesco Pedaci
Efficient Illumination for Microsecond Tracking Microscopy
PLoS One 9(9) e107335 (2014)

J.P. Cnossen, D. Dulin, and N.H. Dekker
An optimized software framework for real-time, high-throughput tracking of spherical beads
Review of Scientific Instruments 85, 103712 (2014)

Fang-Chieh Chou, Jan Lipfert, and Rhiju Das
Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
PLOS Computational Biology 10(8), e1003756 (2014)

Jan Lipfert, Gary M. Skinner, Johannes M. Keegstra, Toivo Hensgens, Tessa Jager, David Dulin, Mariana Koeber, Zhongbo Yu, Serge P. Donkers, Fang-Chieh Chou, Rhiju Das, and Nynke H. Dekker
Double-Stranded RNA under Force and Torque: Similarities and Striking Differences to Double-Stranded DNA
Proceedings of the National Academy of Sciences (USA) 111 (43), 15408–15413 (2014)

R. Janissen, B.A. Berghuis, D. Dulin, M. Wink, T. van Laar, and N.H. Dekker
Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments
Nucleic Acids Research, doi: 10.1093/nar/gku677 (2014

Jan Lipfert, Mina Lee, Orkide Ordu, Jacob Kerssemakers, and Nynke H. Dekker
Magnetic Tweezers for the Measurement of Twist and Torque
Journal of Visual Experiments 87, e51503, doi: 10.3791/51503 (2014)

Nynke H. Dekker
Impact van fysica op ontdekkingen in de biomoleculaire wereld
Nederlands Tijdschrift voor Natuurkunde, March (2014)

M. Lee, J. Lipfert, H. Sánchez, C. Wyman, and N.H. Dekker
Structural and Torsional Properties of the RAD51-dsDNA Nucleoprotein Filament
Nucleic Acids Research 41, 7023–7030 (2013)

M.C. Moolman, Z. Huang, S. Tiruvadi Krishnan, J.W.J. Kerssemakers and N.H. Dekker
Electron-beam Fabrication of a Microfluidics Device for Submicron-scale Bacteria
J. Nanobiotechnology, published online April (2013)

D. Dulin, J. Lipfert, M.C. Moolman, and N.H. Dekker
Genomic Processes Studied at the Single-Molecule Level: Introducing the Tools and Applications
Nature Reviews Genetics, published online November (2012)

X.J.A. Janssen*, M.P. Jonsson*, C. Plesa, G.V. Soni, C. Dekker, and N.H. Dekker
Rapid Manufacturing of Low-Noise Membranes for Nanopore Sensors by Trans-chip Illumination Lithography
Nanotechnology (2012)

(*=equal contribution)

X.J.A. Janssen*, J. Lipfert*, T. Jager, R. Daudey, J. Beekman, and N.H. Dekker
Electromagnetic Torque Tweezers: A Versatile Approach for the Measurement of Single-Molecule Twist and Torque
Nano Letters, in press (2012)

(*=equal contribution)

F. Pedaci*, Z. Huang*, M. van Oene, and N.H. Dekker
Calibration of the optical torque wrench
Optics Express 20, 3787-3802 (2012)

(*=equal contribution)

Jan Lipfert, Jacob J. W. Kerssemakers, Maylon Rojer, and Nynke H. Dekker
A method to track rotational motion for use in single-molecule biophysics
Review of Scientific Instruments 82, 103707 (2011)

J. Lipfert*, M. Wiggin*, J.W.J. Kerssemakers, F. Pedaci, and N.H. Dekker
Freely Orbiting Magnetic Tweezers To Directly Monitor Changes in the Twist of Nucleic Acids
Nature Communications (2011)

(*=equal contribution)

Brian P. English, Vasili Hauryliuk, Arash Sanamrad, Stoyan Tankov, Nynke H. Dekker, and Johan Elf
Single Molecule Investigations of the Stringent Response Machinery in Individual Living Bacterial Cells
Proceedings of the National Academy of Sciences USA (2011)

M. van den Hout, G.M. Skinner, S. Klijnhout, V. Krudde, and N.H. Dekker
The Passage of Homopolymeric RNA through Small Solid-State Nanopores
Small 7, 2217–2224 (2011)

Z. Huang*, F. Pedaci*, M. van Oene, M. Wiggin, and N.H. Dekker
Electron Beam Fabrication of Micron-Scale Birefringent Quartz Cylinders for Use in Optical Trapping
ACS Nano 5, 1418–1427 (2011) (online January 31, 2011)

(*=equal contribution)

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