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)
(*=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


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

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
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)


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


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


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