{"id":55,"date":"2020-06-10T09:27:33","date_gmt":"2020-06-10T09:27:33","guid":{"rendered":"http:\/\/nynkedekkerlab.tudelft.nl\/new\/?page_id=55"},"modified":"2024-04-13T10:16:37","modified_gmt":"2024-04-13T10:16:37","slug":"publications","status":"publish","type":"page","link":"https:\/\/nynkedekkerlab.tudelft.nl\/?page_id=55","title":{"rendered":"Publications"},"content":{"rendered":"\n

2024<\/h3>\n\n\n\n

Daniel Ram\u00edrez Montero, Humberto S\u00e1nchez, Edo van Veen, Theo van Laar, Bel\u00e9n Solano, John F.X. Diffley, and Nynke H. Dekker
A hybrid ensemble and single-molecule assay to image the motion of fully reconstituted CMG<\/strong>
submitted <\/em>(2024)<\/p>\n\n\n\n

Louis Kuijpers, Wouter van den Braak, Abbas Freydoonian, <\/sup>Nynke H. Dekker, and Leo van der Pol
Optimization of enterovirus-like particle production and purification<\/strong> using Design of Experiments<\/strong>
submitted <\/em>(2024)<\/p>\n\n\n\n

Chew Theng Lim, Thomas C.R. Miller, Kang Wei Tan, Saurabh Talele, Anne Early, Philip East, Humberto S\u00e1nchez, Nynke H. Dekker, Alessandro Costa, and John F.X. Diffley
Cell Cycle Regulation has Shaped Budding Yeast Replication Origin Structure and Function<\/strong>
submitted <\/em>(2024)<\/p>\n\n\n\n

Louis Kuijpers, Natasha Giannopoulou, Yuzhen Feng, Wouter van den Braak, Abbas Freydoonian, Ramon Ramlal, Hugo Meiring, Bel\u00e9n 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<\/strong>
submitted <\/em>(2024)<\/p>\n\n\n\n

Zhaowei Liu*, Edo van Veen*, Humberto S\u00e1nchez, Bel\u00e9n Solano, Francisco J. Palmero Moya, Kaley A. McCluskey, Daniel Ram\u00edrez 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<\/strong>
ACS Photonics<\/em>, published online March 18 (2024); PDF<\/strong><\/a> SI<\/a><\/strong><\/p>\n\n\n\n

Daniel Ram\u00edrez 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 <\/strong>
Biophysical Journal<\/em>, 123<\/strong>, 31-41 (2024); PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

2023<\/h3>\n\n\n\n

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 <\/strong>
PloSONE <\/em>18(11):e0291625 (2023); PDF<\/strong><\/a> SI<\/a><\/strong><\/p>\n\n\n\n

Humberto S\u00e1nchez, 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 <\/strong>
Nature Communications<\/em> 14<\/strong>, 6735 (2023); PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

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<\/strong><\/strong>
Optics Communications<\/em> 542<\/strong>:129548 (2023); PDF<\/strong><\/a> (see journal article page for SI)<\/p>\n\n\n\n

Daniel Ram\u00edrez Montero, Humberto S\u00e1nchez, Edo van Veen, Theo van Laar, Bel\u00e9n Solano, John F.X. Diffley, and Nynke H. Dekker
Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation<\/strong>
Nature Communications<\/em> 14<\/strong>:2082 (2023); PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

Kaley McCluskey and Nynke H. Dekker
Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system<\/strong><\/strong>
Optics Communications <\/em>538<\/strong>: 129474 (2023); PDF<\/strong><\/a><\/p>\n\n\n\n

Cl\u00e9ment 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<\/strong><\/strong>
Nucleic Acids Research<\/em> (2023); PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

2022<\/h3>\n\n\n\n

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<\/strong>
Star Protocols<\/em> 3<\/strong>, 101606 (2022); PDF<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
(* = equal contribution, # = corresponding author)
Cell Report<\/em>s 39<\/strong>, 110749 (2022); PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

2021<\/h3>\n\n\n\n

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<\/strong><\/strong>
(* = equal contribution, # = corresponding author)
Optics Express<\/em> 29<\/strong> (25), 42251-42264 (2021); PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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, Bel\u00e9n 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<\/strong><\/strong>
(* = equal contribution, # = corresponding author)
Molecular Cell<\/em> 81<\/strong>, 1\u201314 (2021); PDF<\/a><\/strong> PDF with SI<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
Molecular Cell<\/em> 81<\/strong> (15), 3033-3037 (2021); PDF<\/strong><\/a><\/p>\n\n\n\n

Humberto S\u00e1nchez, Kaley McCluskey, Theo van Laar, Edo van Veen, Filip M. Asscher, Bel\u00e9n Solano, John F.X. Diffley# and Nynke H. Dekker#
DNA origins retain mobile licensing proteins<\/strong>
(# = corresponding author)
Nature Communications<\/em> 12<\/strong>, 1908 (2021); PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

2020<\/h3>\n\n\n\n

Ying Tang*, Seungkyu Ha*, Thomas Begou, Julien Lumeau, H. Paul Urbach, Nynke H. Dekker#, and Aur\u00e8le J. L. Adam#
Versatile multilayer metamaterial nanoparticles with tailored optical constants for force and torque transduction<\/strong>
(* = equal contribution, # = corresponding author)
ACS Nano<\/em> 14<\/strong>, 14895\u221214906 (2020) PDF<\/a><\/strong> SI<\/strong><\/a><\/p>\n\n\n\n

A. Kaczmarczyk, M. He, O. Ordu, J. van Noort#, and N.H. Dekker#
Chromatin fibers stabilize nucleosomes under torsional stress<\/strong>
(# = corresponding author)
Nature Communications<\/em> 11<\/strong>, 126 (2020) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

2019<\/h3>\n\n\n\n

Orkide Ordu, Alexandra Lusser, and Nynke H. Dekker
DNA sequence is a major determinant of tetrasome dynamics<\/strong>
Biophysical Journal<\/em> (2019) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

Seungkyu Ha, Ying Tang, Maarten van Oene, Richard Janissen, Roland Dries, Bel\u00e9n Solano, Aurele Adam, and Nynke H. Dekker
Single-crystal rutile TiO2<\/sub> nanocylinders are highly effective transducers of optical force and torque<\/strong>
ACS Photonics<\/em>, online publication April 22 (2019) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Journal of Virology <\/em>5<\/strong>, 93 (2019), doi: 10.1128\/JVI.02057-18 PDF<\/strong><\/a><\/p>\n\n\n\n

2018<\/h3>\n\n\n\n

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<\/strong>
(* = equal contribution, # = corresponding author)
Cell<\/em> 174<\/strong>, 1188-1199 (2018) (online publication July 26) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Emerging Microbes & Infections<\/em> 7<\/strong>, 111 (2018) (online publication June 21) PDF<\/strong><\/a><\/p>\n\n\n\n

Artur Kaczmarczyk, Thomas B. Brouwer, Chi Pham, Nynke H. Dekker, and John van Noort
Methods for probing chromatin structure with magnetic tweezers<\/strong>
Nanoscale Imaging: Methods and Protocols<\/em>, Methods in Molecular Biology<\/em> 1814<\/strong>, 297-323 (2018) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
(* = equal contribution)
Biophysical Journal<\/em> 114<\/strong>, 1970\u20131979 (2018) (online publication April 24) PDF<\/strong><\/a> Extended PDF<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
Journal of Chemical Physics<\/em> 148<\/strong>, 123323 (2018) PDF<\/strong><\/a><\/p>\n\n\n\n

2017<\/h3>\n\n\n\n

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<\/strong>
Critical Reviews in Biochemistry and Molecular Biology<\/em> 53<\/strong>(1):49-63 (2017) (published online November 7) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Cell Reports<\/em> 21<\/strong>, 1063\u20131076 (2017) PDF<\/a> Extended PDF<\/a><\/strong><\/p>\n\n\n\n

Artur Kaczmarczyk, Abdollah Allahverdi, Thomas Brouwer, Lars Nordenski\u00f6ld, Nynke H. Dekker, and John van Noort
Single-molecule force spectroscopy on H4 tail cross-linked chromatin reveals fiber folding<\/strong>
Journal of Biological Chemistry<\/em> 292<\/strong>(42), 17506\u201317513 (2017) PDF<\/a><\/strong><\/p>\n\n\n\n

Roy de Leeuw, Peter Brazda, M. Charl Moolman, Bel\u00e9n Solano, and Nynke H. Dekker
Measuring in vivo<\/em> protein dynamics throughout the cell cycle using microfluidics<\/strong>
Methods in Molecular Biology,<\/em> online publication August 28 (2017) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nucleic Acids Research<\/em> 45<\/strong>, 5920-5929 (2017) (online publication April 29) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

Maarten M. van Oene, Laura E. Dickinson, Bronwen Cross, Francesco Pedaci, Jan Lipfert, and Nynke H. Dekker
Applying torque to the Escherichia coli<\/em> flagellar motor using magnetic tweezers<\/strong>
Scientific Reports<\/em> 7<\/strong>, 43285 (2017) PDF<\/a><\/strong><\/p>\n\n\n\n

2016<\/h3>\n\n\n\n

O. Ordu, A. Lusser, and N.H. Dekker
Recent insights from single-molecule studies into nucleosome structure and dynamics<\/strong>
Biophysical Reviews<\/em> 8<\/strong>, 33-49 (2016) (online publication October 16) PDF<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
BioRxiv<\/em>, doi: https:\/\/doi.org\/10.1101\/077800 (2016)<\/p>\n\n\n\n

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<\/strong>
Nucleic Acids Research<\/em> 44<\/strong> (13), 6262-6273 (2016) (online publication May 10) PDF<\/a><\/strong> SI
<\/a><\/strong>(* = equal contribution)<\/p>\n\n\n\n

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<\/strong>
Proceedings of the National Academy of Sciences (USA)<\/em> 113<\/strong> (18), 4982\u20134987 (2016) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nanoscale<\/em> 8<\/strong>, 10739-10748 (2016) (online publication April 18) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

B.A. Berghuis, M. Koeber, T. van Laar, and N.H. Dekker
High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers<\/strong>
Methods<\/em> 105<\/strong>, 90-98 (2016) (online publication March 30) PDF<\/a><\/strong><\/p>\n\n\n\n\n\n\n\n

2015<\/h3>\n\n\n\n

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<\/strong>
Biophysical Journal<\/em> 109<\/strong>, 2113\u20132125 (2015) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nucleic Acids Research<\/em> 43<\/strong>, 10421-9 (2015) (online publication October 22) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/sub> tetrasomes to canonical tetrasomes<\/strong>
Plos One<\/em> 10<\/strong>, e0141267 (2015) (online publication October 28) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Current Opinion in Structural Biology<\/em> 34<\/strong>, 116\u2013122 (2015) (online publication October 1) PDF<\/a><\/strong><\/p>\n\n\n\n

M. Charl Moolman*, Jacob W.J. Kerssemakers*, and Nynke H. Dekker
Quantitative analysis of intracellular fluorescent foci in live bacteria<\/strong>
Biophysical Journal<\/em> 109<\/strong>, 883-891 (2015) (online publication September 4)
(* = equal contribution) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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\u2013Ter replication fork barrier<\/strong>
Nature Chemical Biology<\/em> 11<\/strong>, 579\u2013585 (2015) (online publication July 6) PDF<\/strong><\/a> SI<\/strong><\/a> news and views<\/strong><\/a><\/p>\n\n\n\n

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

Jan Lipfert and Nynke H. Dekker
De RNA helix lijkt niet altijd op die van DNA<\/strong>
Nederlands Tijdschrift voor Natuurkunde<\/em> 81<\/strong>(6), 224-227 (2015) (online publication May 28) PDF<\/a> <\/strong>(in Dutch)<\/p>\n\n\n\n

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<\/strong>
Phys. Rev. Lett.<\/em> 114<\/strong>, 218301 (2015) (online publication May 27) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
Cell Reports<\/em> 10<\/strong>(6), 983-992 (2015) (online publication Feb. 12) PDF<\/strong><\/a> Extended PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Cell Reports<\/em> 10<\/strong>, 216\u2013225 (2015) (online publication Jan. 8) PDF<\/strong><\/a> Extended PDF<\/strong><\/a>
(*=equal contribution)<\/p>\n\n\n\n

2014<\/a><\/h3>\n\n\n\n

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<\/strong>
Chemical Reviews<\/em> 115<\/strong> (3), 1449\u20131474 (2015) (online publication Dec. 26, 2014) PDF<\/strong><\/a><\/p>\n\n\n\n

Zhongbo Yu, David Dulin, Jelmer P. Cnossen, Mariana K\u00f6ber, Maarten M. van Oene, Orkide Ordu, Bojk A. Berghuis, Toivo Hensgens, Jan Lipfert, and Nynke H. Dekker
A force calibration standard for magnetic tweezers<\/strong>
Review of Scientific Instruments<\/em> 85<\/strong>(12):123114 (2014) (online publication Dec. 23) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nature Communications<\/em> 5<\/strong>, article number 5820 (2014) (online publication Dec. 18) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

David Dulin, Stephane Barland, Xavier Hachair, and Francesco Pedaci
Efficient Illumination for Microsecond Tracking Microscopy<\/strong>
PLoS One<\/em> 9<\/strong>(9) e107335 (2014) PDF<\/strong><\/a><\/p>\n\n\n\n

J.P. Cnossen, D. Dulin, and N.H. Dekker
An optimized software framework for real-time, high-throughput tracking of spherical beads<\/strong>
Review of Scientific Instruments<\/em> 85<\/strong>, 103712 (2014) PDF<\/strong><\/a><\/p>\n\n\n\n

Fang-Chieh Chou, Jan Lipfert, and Rhiju Das
Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque<\/strong>
PLOS Computational Biology <\/em>10<\/strong>(8), e1003756 (2014) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Proceedings of the National Academy of Sciences (USA)<\/em> 111<\/strong> (43), 15408\u201315413 (2014) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nucleic Acids Research<\/em>, doi: 10.1093\/nar\/gku677 (2014) PDF<\/a><\/strong><\/p>\n\n\n\n

Jan Lipfert, Mina Lee, Orkide Ordu, Jacob Kerssemakers, and Nynke H. Dekker
Magnetic Tweezers for the Measurement of Twist and Torque<\/strong>
Journal of Visual Experiments <\/em>87, e51503, doi: 10.3791\/51503 (2014) preprint<\/a><\/strong><\/p>\n\n\n\n

Nynke H. Dekker
Impact van fysica op ontdekkingen in de biomoleculaire wereld<\/strong>
Nederlands Tijdschrift voor Natuurkunde<\/em>, March (2014) PDF preprint<\/strong><\/a><\/p>\n\n\n\n

2013<\/h3>\n\n\n\n

M. Lee, J. Lipfert, H. S\u00e1nchez, C. Wyman, and N.H. Dekker
Structural and Torsional Properties of the RAD51-dsDNA Nucleoprotein Filament<\/strong>
Nucleic Acids Research<\/em> 41, 7023\u20137030 (2013) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
J. Nanobiotechnology<\/em>, published online April (2013) PDF<\/strong><\/a><\/p>\n\n\n\n

2012<\/h3>\n\n\n\n

D. Dulin, J. Lipfert, M.C. Moolman, and N.H. Dekker
Genomic Processes Studied at the Single-Molecule Level: Introducing the Tools and Applications<\/strong>
Nature Reviews Genetics<\/em>, published online November (2012) PDF<\/strong><\/a><\/p>\n\n\n\n

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<\/strong>
Nanotechnology<\/em> (2012) PDF<\/strong><\/a>
(*=equal contribution)<\/p>\n\n\n\n

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<\/strong>
Nano Letters<\/em>, in press (2012) PDF<\/a> SI<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n

F. Pedaci*, Z. Huang*, M. van Oene, and N.H. Dekker
Calibration of the optical torque wrench<\/strong>
Optics Express<\/em> 20, 3787-3802 (2012) PDF<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n

2011<\/h3>\n\n\n\n

Jan Lipfert, Jacob J. W. Kerssemakers, Maylon Rojer, and Nynke H. Dekker
A method to track rotational motion for use in single-molecule biophysics<\/strong>
Review of Scientific Instruments<\/em> 82, 103707 (2011) PDF<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
Nature Communications<\/em> (2011) PDF<\/a> SI<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n

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<\/strong>
Proceedings of the National Academy of Sciences USA<\/em> (2011) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
Small<\/em> 7, 2217\u20132224 (2011) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

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<\/strong>
ACS Nano <\/em>5, 1418\u20131427 (2011) (online January 31, 2011)  PDF<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n\n\n\n\n

2010<\/h3>\n\n\n\n

F. Pedaci*, Z. Huang*, M. van Oene, S. Barland, and N.H. Dekker
Excitable Particles in an Optical Torque Wrench<\/strong>
Nature Physics<\/em> 7, 259\u2013264 (2011) (online Dec. 19, 2010)
PDF<\/a><\/strong> SI<\/strong><\/a>
(*=equal contribution)<\/p>\n\n\n\n

M. van den Hout, V. Krudde, X.J.A. Janssen, and N.H. Dekker
Distinguishable Populations Report on the Interactions of Single DNA Molecules with Solid-State Nanopores<\/strong>
Biophysical Journal<\/em> 99, 3840-3848 (2010) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

J. Lipfert, J.W.J. Kerssemakers, T. Jager, and N.H. Dekker
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments<\/strong>
Nature Methods<\/em> 7, 977\u2013980 (2010) (online Oct. 17, 2010) PDF<\/strong><\/a> SI (incl. many details)<\/strong><\/a><\/p>\n\n\n\n

D.A. Koster, A. Crut, S. Shuman, M.-A. Bjornsti, and N.H. Dekker
Cellular strategies for regulating DNA supercoiling: a single-molecule perspective<\/strong>
Cell <\/em>142, 519-530 (2010) PDF<\/strong><\/a> SI<\/strong><\/a><\/p>\n\n\n\n

A.J.W. te Velthuis*, J.W.J. Kerssemakers*, J. Lipfert, and N.H. Dekker
Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data<\/strong>
Biophysical Journal <\/em>99, 1292-1302 (2010) PDF<\/strong><\/a> SI<\/strong><\/a>
(*=equal contribution)<\/p>\n\n\n\n

J. Lipfert, S. Klijnhout, and N.H. Dekker
Torsional Sensing of Small-Molecule Binding Using Magnetic Tweezers<\/strong>
Nucleic Acids Research, <\/em>doi:10.1093\/nar\/gkq598 (2010) PDF<\/strong><\/a><\/p>\n\n\n\n

M. van den Hout, A.R. Hall, M.-Y. Wu, H.W. Zandbergen, C. Dekker, and N.H. Dekker
Controlling Nanopore Size, Shape, and Stability<\/strong>
Nanotechnology<\/em> 21, 115304 (2010) PDF<\/a><\/strong><\/p>\n\n\n\n

M. van den Hout, I.D. Vilfan, S. Hage, and N.H. Dekker
Direct Force Measurements on Double-Stranded RNA Molecules in Solid-State Nanopores<\/strong>
Nano Letters<\/em> 10, 701\u2013707 (2010) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

2009<\/h3>\n\n\n\n

G.M. Skinner*, M. van den Hout*, O. Broekmans, C. Dekker, and N.H. Dekker
Distinguishing Nucleic Acids Using Solid-State Nanopores<\/strong>
Nano Letters<\/em> 9 (8), 2953\u20132960 (2009) PDF<\/a><\/strong> SI<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n

J. Lipfert, D. A. Koster, I.D. Vilfan, S. Hage, and N.H. Dekker
Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases<\/strong>
Methods in Molecular Biology<\/em> series entitled \u201cDNA Topoisomerases\u201d (2009) PDF<\/a><\/strong><\/p>\n\n\n\n

I.D. Vilfan, J. Lipfert, D. A. Koster, S.G. Lemay and N.H. Dekker
Magnetic Tweezers for Single-Molecule Experiments<\/strong>
Springer Handbook of Single-Molecule Biophysics<\/em> (2009) PDF<\/a><\/strong><\/p>\n\n\n\n

U.F. Keyser, J. van der Does, C. Dekker, and N.H. Dekker
Biomolecule Analysis and Manipulation: Methods and Protocols<\/em> <\/strong>
published in Methods in Molecular Biology<\/em> 544 (2009). Lee, James Weifu and Foote, Robert S. (Eds.) ISBN: 978-1-934115-40-4. PDF<\/a><\/strong><\/p>\n\n\n\n

J. Lipfert, X. Hao, and N.H. Dekker
Quantitative Modelling and Optimization of Magnetic Tweezers<\/strong>
Biophysical Journal<\/em> 96, 5040-5049 (2009) PDF<\/a> SI<\/a><\/strong><\/p>\n\n\n\n

Ralph M. M Smeets, Nynke H. Dekker, and Cees Dekker
Low-Frequency Noise in Solid-State Nanopores<\/strong>
Nanotechnology<\/em> 20, 095501 (2009) PDF<\/a><\/strong><\/p>\n\n\n\n

Stijn van Dorp, Ulrich F. Keyser, Nynke H. Dekker, Cees Dekker, and Serge G. Lemay
Origin of the Electrophoretic Force on DNA in Solid-State Nanopores<\/strong>
Nature Physics<\/em> 5<\/strong>, 347-351 (2009) PDF<\/a><\/strong><\/p>\n\n\n\n

M.Y. Wu, R.M.M Smeets, M. Zandbergen, U. Ziese, D. Krapf, P.E. Batson, N.H. Dekker, C. Dekker and H.W. Zandbergen
Control of Shape and Material Composition of Solid-State Nanopores<\/strong>
Nano Letters<\/em>, DOI: 10.1021\/nl803613s, (2009) PDF<\/a><\/strong><\/p>\n\n\n\n

R.M.M Smeets*, S.W. Kowalczyk*, A.R. Hall, N.H. Dekker, C. Dekker
Translocation of RecA-coated Double-Stranded DNA Through Solid-State Nanopores<\/strong>
Nano Letters<\/em>, 9 (9): 3089-3095 (2009) PDF<\/a><\/strong>
(*=equal contribution)<\/p>\n\n\n\n

2008<\/a><\/h3>\n\n\n\n

I.D. Vilfan, A. Candelli, S. Hage, A.P. Aalto, M.M. Poranen, D.H. Bamford and N.H. Dekker
Reinitiated Viral RNA-dependent RNA Polymerase Resumes Replication at a Reduced Rate<\/strong>
Nucleic Acids Research<\/em>, doi:10.1093\/nar\/gkn836, (2008) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

A. Crut, D.A. Koster, Z.-X. Huang, S. Hage, N.H. Dekker
Controlling the surface properties of nanostructures for single-molecule studies of polymerases<\/strong>
Nanotechnology<\/em> 19, 465301 (2008) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

M. van den Hout, S. Hage, C. Dekker, and N. H. Dekker
End-Joining Long Nucleic Acid Polymers<\/strong>
Nucleic Acids Research<\/em>, doi:10.1093\/nar\/gkn442, (2008) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

A. Crut, P. Nair, D.A. Koster, S. Shuman, and N.H. Dekker
Dynamics of Phosphodiester Synthesis by DNA Ligase<\/strong>
Proceedings of the National Academy of Sciences USA<\/em>, 105<\/strong>, 6894-6899 (2008) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

D.A. Koster, F. Czerwinski, L. Halby, A. Crut, P. Vekhoff, K. Palle, P.B. Arimondo, N.H. Dekker
Single-molecule observation pf topotecan-mediated TopIB activity at a unique DNA sequence<\/strong>
Nucleic Acids Research<\/em>, 36<\/strong>, 2301-2310 (2008) PDF<\/a><\/strong><\/p>\n\n\n\n

R. Smeets, U. F. Keyser, N. H. Dekker, C. Dekker
Noise in Solid-state Nanopores<\/strong>
Proceedings of the National Academy of Sciences USA<\/em> 105<\/strong>: 417-421 (2008) PDF<\/a><\/strong><\/p>\n\n\n\n

2007<\/h3>\n\n\n\n

I.D. Vilfan, W. Kamping, M. van den Hout, A. Candelli, S. Hage, N.H. Dekker
An RNA toolbox for single-molecule force spectroscopy studies<\/strong>
Nucleic Acids Research<\/em>: doi: 10.1093\/nar\/gkm585 (2007) P<\/a>D<\/a>F<\/a><\/strong><\/p>\n\n\n\n

K. Besteman, S. Hage, N.H. Dekker, S.G. Lemay
The role of tension and twist in single-molecule DNA condensation<\/strong>
Physical Review Letters<\/em> 98<\/strong>: 058103 (2007) PDF<\/a><\/strong><\/p>\n\n\n\n

A. Crut, D.A. Koster, R. Seidel, C.H. Wiggins, N.H. Dekker
Fast dynamics of supercoiled DNA revealed by single-molecule experiments<\/strong>
Proceedings of the National Academy of Sciences USA<\/em> 104<\/strong>: 11957-11962 (2007) PDF<\/a><\/strong><\/p>\n\n\n\n

D.A. Koster, K. Palle, E.S.M. Bot, C. A.M. Bjornsti, N.H. Dekker
Antitumor drugs impede DNA uncoiling by topoisomerase I<\/strong>
Nature<\/em> 448<\/strong>: 213-217 (2007) PDF<\/a><\/strong> SI<\/a><\/strong><\/p>\n\n\n\n

2006<\/h3>\n\n\n\n

F. Moreno-Herrero, R. Seidel, S.M. Johnson, A. Fire, N.H. Dekker
Structural analysis of hyperperiodic DNA from Caenorhabditis elegans<\/strong>
Nucleic Acids Research<\/em> 34<\/strong> (10): 3057-3066 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n

U. F. Keyser, J. van der Does, C. Dekker, and N. H. Dekker
Optical tweezers for force measurements on DNA in nanopores<\/strong>
Review of Scientific Instruments<\/em> 77<\/strong> (10): Art. No. 105105 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n

R.M.M. Smeets, U.F. Keyser, M.Y. Wu, N.H. Dekker, C. Dekker
Nanobubbles in solid-state nanopores<\/strong>
Physical Review Letters<\/em> 97<\/strong> (8): Art. No. 088101 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n

U.F. Keyser, B.N. Koeleman, D. Krapf, R.M.M. Smeets, S.G. Lemay, N.H. Dekker, C. Dekker
Direct force measurements on DNA in a solid-state nanopore<\/strong>
Nature Physics<\/em> 2<\/strong> (7): 473-477 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n

L.K. Stanley, R. Seidel, C. van der Scheer, N.H. Dekker, M.D. Szczelkun and C. Dekker
When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I<\/strong>
EMBO Journal<\/em> 25<\/strong> (10): 2230-2239 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n

D.A. Koster, C. Wiggins, N.H. Dekker
Multiple events on single molecules: unbiased estimation in single-molecule biophysics<\/strong>
Proceeedings of the National Academy of Science USA<\/em> 103<\/strong> (6): 1750-1755 (2006) PDF<\/a> <\/strong>SI<\/strong><\/a><\/p>\n\n\n\n

R.M.M. Smeets, U.F. Keyser, D. Krapf, M.Y. Wu, N.H. Dekker, C. Dekker
Salt dependence of ion transport and DNA translocation through solid-state nanopores.<\/strong>
Nano Letters<\/em> 6<\/strong> (1): 89-95 (2006) PDF<\/strong><\/a><\/p>\n\n\n\n\n\n\n\n

2005<\/h3>\n\n\n\n

F. Moreno-Herrero, L. Holtzer, D. Koster, S. Shuman, C. Dekker, and N.H. Dekker
Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion<\/strong>
Nucleic Acids Research<\/em> 33<\/strong> (18): 5945-5953 (2005) PDF<\/strong><\/a><\/p>\n\n\n\n

R. Seidel, J. G. P. Bloom, J. van Noort, C. F. Dutta, N. H. Dekker, K. Firman, M. D. Szczelkun, and C. Dekker
Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I<\/strong>
EMBO Journal<\/em> 24<\/strong> (23): 4188-4197 (2005) PDF<\/a><\/strong><\/p>\n\n\n\n

U.F. Keyser, D. Krapf, B. N. Koeleman, R. M. M. Smeets, N. H. Dekker, C. Dekker
Nanopore tomography of a laser focus<\/strong>
Nano Letters<\/em> 5<\/strong> (11): 2253-2256 (2005) PDF<\/a><\/strong><\/p>\n\n\n\n

T. van der Heijden, J. van Noort, H. van Leest, R. Kanaar, C. Wyman, N.H. Dekker, C. Dekker
Torque-limited RecA polymerization on dsDNA<\/strong>
Nucleic Acids Research<\/em> 33<\/strong> (7): 2099-2105 (2005) PDF<\/a><\/strong><\/p>\n\n\n\n

D.A. Koster, V. Croquette, C. Dekker, S. Shuman, and N.H. Dekker
Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB<\/strong>
Nature<\/em> 434<\/strong> (7033): 671-674 (2005) PDF<\/a><\/strong><\/p>\n\n\n\n

J.A. Abels, F. Moreno-Herrero, T. van der Heijden, C. Dekker, and N.H. Dekker
Single-Molecule Measurements of the Persistence Length of double-stranded RNA<\/strong>
Biophysical Journal<\/em> 88<\/strong> (4): 2737-2744 (2005) PDF<\/a><\/strong><\/p>\n\n\n\n

2004<\/h3>\n\n\n\n

N. H. Dekker, J. A. Abels, P. T. M. Veenhuizen, and C. Dekker
Joining of Long Double-stranded RNA Molecules through Controlled Overhangs<\/strong>
Nucleic Acids Research<\/em> 32<\/strong> (18): Art. No. e140 (2004) PDF<\/a><\/strong><\/p>\n\n\n\n

R. Seidel, J. van Noort, C. van der Scheer, J. G. P. Bloom, N. H. Dekker, C. F. Dutta, A. Blundell, T. Robinson, K. Firman, and C. Dekker
Real-Time Observation of DNA Translocation by the Type I Restriction-Modification Enzyme EcoR124I<\/strong>
Nature Structural and Molecular Biology<\/em> (2004) PDF<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

2024 Daniel Ram\u00edrez Montero, Humberto S\u00e1nchez, Edo van Veen, Theo van Laar, Bel\u00e9n Solano, John F.X. Diffley, and Nynke H. DekkerA hybrid ensemble and single-molecule assay to image the motion of fully reconstituted CMGsubmitted (2024) Louis Kuijpers, Wouter van den Braak, Abbas Freydoonian, Nynke H. Dekker, and Leo van der PolOptimization of enterovirus-like particle production and […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/pages\/55"}],"collection":[{"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=55"}],"version-history":[{"count":170,"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/pages\/55\/revisions"}],"predecessor-version":[{"id":2434,"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=\/wp\/v2\/pages\/55\/revisions\/2434"}],"wp:attachment":[{"href":"https:\/\/nynkedekkerlab.tudelft.nl\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=55"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}