Publications

publications

2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004

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
Biophysical Journal, submitted (2017)

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, submitted (2017)

R. Janissen*, M. Arens*, N. Vtyurina*, B. Eslami-Mossallam, A. Gritsenko, D. de Ridder, I. Artsimovitch, N.H. Dekker, E. A. Abbondanzieri, and A. S. Meyer
Transcriptional regulation is independent of Dps-driven reorganization of DNA
(* = equal contribution)
Cell, submitted (2017)

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, in press (2017)

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, in press (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, in press (2017)

Measuring in vivo protein dynamics throughout the cell cycle using microfluidics
Roy de Leeuw, Peter Brazda, M. Charl Moolman, Belen Solano, and Nynke H. Dekker
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, online publication April 29 (2017) PDF

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, online publication 2017 PDF

2016 back to top

O. Ordu, A. Lusser, and N.H. Dekker
Recent insights from single-molecule studies into nucleosome structure and dynamics
Biophysical Reviews, online publication October 16 (2016) 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: 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, online publication May 10 (2016) 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) (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, advance online publication April 18 (2016) PDF

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, online publication March 30 (2016) PDF

2015 back to top

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, online publication October 22 (2015) 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, online publication October 28 (2015) 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, online publication October 1 (2015) PDF

M. Charl Moolman*, Jacob W.J. Kerssemakers*, and Nynke H. Dekker
Quantitative analysis of intracellular fluorescent foci in live bacteria
Biophysical Journal, online publication September 4 (2015)
(* = 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, online publication July 6 (2015) 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, published July 1 (2015) PDF

Jan Lipfert and Nynke H. Dekker
De RNA helix lijkt niet altijd op die van DNA
Nederlands Tijdschrift voor Natuurkunde, online publication May 28 (2015) 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., online publication May 27 (2015) 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, online publication Feb. 12 (2015) 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, online publication Jan. 8 (2015) PDF Extended PDF
(*=equal contribution)

2014 back to top

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, 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, online publication Dec. 23 (2014) 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, online publication Dec. 18 (2014) 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

2013 back to top

M. Lee, J. Lipfert, H. Sanchez, 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

2012 back to top

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)

2011 back to top

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)

2010 back to top

F. Pedaci*, Z. Huang*, M. van Oene, S. Barland, and N.H. Dekker
Excitable Particles in an Optical Torque Wrench
Nature Physics 7, 259–264 (2011) (online Dec. 19, 2010)
PDF SI
(*=equal contribution)

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
Biophysical Journal 99, 3840-3848 (2010) PDF SI

J. Lipfert, J.W.J. Kerssemakers, T. Jager, and N.H. Dekker
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
Nature Methods 7, 977–980 (2010) (online Oct. 17, 2010) PDF SI (incl. many details)

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

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
Biophysical Journal 99, 1292-1302 (2010) PDF SI
(*=equal contribution)

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

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
Nanotechnology 21, 115304 (2010) PDF

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
Nano Letters 10, 701–707 (2010) PDF SI

2009 back to top

G.M. Skinner*, M. van den Hout*, O. Broekmans, C. Dekker, and N.H. Dekker
Distinguishing Nucleic Acids Using Solid-State Nanopores
Nano Letters 9 (8), 2953–2960 (2009) PDF SI
(*=equal contribution)

J. Lipfert, D. A. Koster, I.D. Vilfan, S. Hage, and N.H. Dekker
Single-Molecule Magnetic Tweezers Studies of Type IB Topoisomerases
Methods in Molecular Biology series entitled “DNA Topoisomerases” (2009) PDF

I.D. Vilfan, J. Lipfert, D. A. Koster, S.G. Lemay and N.H. Dekker
Magnetic Tweezers for Single-Molecule Experiments
Springer Handbook of Single-Molecule Biophysics (2009) PDF

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

J. Lipfert, X. Hao, and N.H. Dekker
Quantitative Modelling and Optimization of Magnetic Tweezers
Biophysical Journal 96, 5040-5049 (2009) PDF SI

Ralph M. M Smeets, Nynke H. Dekker, and Cees Dekker
Low-Frequency Noise in Solid-State Nanopores
Nanotechnology 20, 095501 (2009) PDF

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

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
Nano Letters, DOI: 10.1021/nl803613s, (2009) PDF

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
Nano Letters, 9 (9): 3089-3095 (2009) PDF
(*=equal contribution)

2008 back to top

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
Nucleic Acids Research, doi:10.1093/nar/gkn836, (2008) PDF SI

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
Nanotechnology 19, 465301 (2008) PDF SI

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

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

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
Nucleic Acids Research, 36, 2301-2310 (2008) PDF

R. Smeets, U. F. Keyser, N. H. Dekker, C. Dekker
Noise in Solid-state Nanopores
Proceedings of the National Academy of Sciences USA 105: 417-421 (2008) PDF

2007 back to top

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
Nucleic Acids Research: doi: 10.1093/nar/gkm585 (2007) PDF

K. Besteman, S. Hage, N.H. Dekker, S.G. Lemay
The role of tension and twist in single-molecule DNA condensation
Physical Review Letters 98: 058103 (2007) PDF

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

D.A. Koster, K. Palle, E.S.M. Bot, C. A.M. Bjornsti, N.H. Dekker
Antitumor drugs impede DNA uncoiling by topoisomerase I
Nature 448: 213-217 (2007) PDF SI

2006 back to top

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

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

R.M.M. Smeets, U.F. Keyser, M.Y. Wu, N.H. Dekker, C. Dekker
Nanobubbles in solid-state nanopores
Physical Review Letters 97 (8): Art. No. 088101 (2006) PDF

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
Nature Physics 2 (7): 473-477 (2006) PDF

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
EMBO Journal 25 (10): 2230-2239 (2006) PDF

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

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.
Nano Letters 6 (1): 89-95 (2006) PDF

2005 back to top

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
Nucleic Acids Research 33 (18): 5945-5953 (2005) PDF

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
EMBO Journal 24 (23): 4188-4197 (2005) PDF

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

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
Nucleic Acids Research 33 (7): 2099-2105 (2005) PDF

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
Nature 434 (7033): 671-674 (2005) PDF

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
Biophysical Journal 88 (4): 2737-2744 (2005) PDF

2004 back to top

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

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
Nature Structural and Molecular Biology (2004) PDF