Daniel Ramírez Montero, Humberto Sánchez, Edo van Veen, Theo van Laar, Belén Solano, John F.X. Diffley, and Nynke H. Dekker
A hybrid ensemble and single-molecule assay to image the motion of fully reconstituted CMG
submitted (2024)

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 (2024)

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
submitted (2024)

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
submitted (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); PDF SI

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); PDF SI


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); PDF SI

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); PDF SI

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); PDF (see journal article page for SI)

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); PDF SI

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

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); PDF SI


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); PDF

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); PDF SI


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); PDF SI

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); PDF PDF with SI

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); PDF

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


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) PDF SI

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) PDF SI


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

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) PDF SI

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 PDF


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) PDF

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) PDF

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) PDF

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) PDF Extended PDF

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) PDF


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) PDF SI

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) PDF Extended PDF

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) PDF

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) PDF

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) PDF SI

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) PDF


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) PDF

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: (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) PDF SI
(* = 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) PDF

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) PDF SI

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) PDF