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) PDF SI

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) PDF

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) PDF

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) PDF

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) PDF SI

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) PDF SI news and views

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) PDF

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) PDF (in 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) PDF SI

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) PDF Extended PDF

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) PDF Extended PDF
(*=equal contribution)


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) PDF

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) PDF

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) PDF SI

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

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) PDF

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) PDF

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) PDF SI

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) PDF

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) preprint

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


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) PDF

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) PDF


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) PDF

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) PDF
(*=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) PDF SI
(*=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) PDF
(*=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) PDF

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) PDF SI
(*=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) PDF SI

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) PDF SI

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)  PDF
(*=equal contribution)