Publications

2019

A single-molecule view on cellular and viral RNA synthesis
E. Ostrofet, F. Stal Papini, A.M. Malinen, D. Dulin
Chapter in Springer book “Biophysics of RNA-Protein Interactions: From Single Molecules to Biological Systems”in press

High-yield fabrication of DNA and RNA scaffolds for single molecule force and torque spectroscopy experiments.
F. Stal Papini*, M. Seifert*, D. Dulin
*: equal contribution
BioRxiv  doi: https://doi.org/10.1101/661330

 

2018

Correction-free force calibration for magnetic tweezers experiments
E. Ostrofet, F. Stal Papini, D. Dulin
Scientific Reports8:15920, October 29, 2018

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria
D. Dulin*, D.L.V. Bauer, A.M. Malinen, J.J.W. Bakermans, M. Kaller, Z. Morichaud, I. Petushkov, M. Depken, K. Brodolin, A. Kulbachinskiy and A.N. Kapanidis*
Nature Communications, 9, 1478, April 16, 2018
BioRxiv, doi: https://doi.org/10.1101/199307
(* : corresponding authors)

 

2017

Signatures of Nucleotide Analogue Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers
D. Dulin, J.J. Arnold, T. van Laar, H.-S. Oh, C. Lee, D.A. Harki, M. Depken, C.E. Cameron, and N.H. Dekker
Cell Reports, 21 (4), 1063-1076, October 24, 2017

Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single molecule fluorescence microscopy
O. Bugaud, N. Barbier, H. Chommy, N. Fiszman, A. Le Gall, D. Dulin, M. Saguy, N. Westbrook, K. Perronet and O. Namy
RNA, 23, 1626-1635, August 2, 2017

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers
F. Kriegel, N. Ermann, R. Forbes, D. Dulin, N.H. Dekker and J. Lipfert
Nucl. Acids Res., 45 (10), 5920-5929

 

2016  

Real-time observation of replicative helicase assembly onto single-stranded DNA
D. Dulin, Z. Yu, T.J. Cui, B.A. Berghuis, M. Depken and N.H. Dekker
BioRxiv, doi: https://doi.org/10.1101/077800

Hysteresis in DNA compaction by Dps is described by an Ising model
N.N. Vtyurina, D. Dulin, M. Docter, A. Meyer, N.H. Dekker and E.A. Abbondanzieri
PNAS, 2016 May 3, Vol. 113, 4982-4987

 

2015

High Spatiotemporal Resolution Magnetic Tweezers : Calibration and Applications to DNA Dynamics
D. Dulin*, T.J. Cui, J.P. Cnossen, M.W. Docter, J. Lipfert and N.H. Dekker*
Biophys. J., 2015 November 15, Vol. 109, 2113-2125  (* : corresponding authors)

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site
D. Dulin, I.D. Vilfan, B.A. Berghuis, M. Poranen, M. Depken and N.H. Dekker
Nucl. Acids Res., 2015 October 22, 43 (21), 10421-10429

Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments
D. Dulin, B.A. Berghuis, M. Depken and N.H. Dekker
Curr. Op. Struct. Biol., 2015 October 1, Vol. 34, 116-122

Strand separation suffices to establish a sustained lock at the Tus-Ter replication fork barrier
B.A. Berghuis, D. Dulin, Z.-Q. Xu, T. van Laar, B. Cross, R. Janissen, S. Jergic, N. Dixon, M. Depken and N.H. Dekker
Nat. Chem. Biol., 2015 August 1, Vol. 11, 579-585

Biological magnetometry : Torque on superparamagnetic beads in magnetic fields
M.M. van Oene, L.E. Dickinson, F. Pedaci, M. Kober, D. Dulin, J. Lipfert and N.H. Dekker
Phys. Rev. Lett., Vol. 114, 218301

Elongation-competent pauses govern the fidelity of a viral RNA-dependent RNA polymerase
D. Dulin, I.D. Vilfan, B.A. Berghuis, S. Hage, D. Bamford, M. Poranen, M. Depken and N.H. Dekker
Cell Reports, 2015 February 17, Vol. 10, 983-992

 

2014

A force calibration standard for magnetic tweezers
Z. Yu, D. Dulin, J.P. Cnossen, M. Köber, M. van Oene, O. Ordu, B.A. Berghuis, T. Hensgens, J. Lipfert and N.H. Dekker
Rev. Sci. Inst., Vol. 85, 123114

An optimized software framework for real-time, high-throughput tracking of spherical beads
J.P. Cnossen, D. Dulin and N.H. Dekker
Rev. Sci. Inst., 2014 October, Vol. 85, 103712

Double-Stranded RNA under Force and Torque : Similarities to and Striking Differences from Double- Stranded DNA
J. Lipfert, G.M. Skinner, J. M. Keegstra, T. Hensgens, T. Jager, D. Dulin, M. Köber, Z. Yu, S. P. Donkers, F.-C. Chou, R. Das and N.H. Dekker
PNAS, Vol. 111, 2014 October 28, 15408-15413

Efficient illumination for microsecond tracking microscopy
D. Dulin, S. Barland, X. Hachair and F. Pedaci
PLoS One, Vol. 9, e107335

Invincible DNA tethers : covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments
R. Janissen, B.A. Berghuis, D. Dulin, M. Wink, T. van Laar and N.H. Dekker
Nucl. Acids Res., Vol. 42, e137

 

2012

Studying genomic processes at the single-molecule level : introducing the tools and applications
D. Dulin, J. Lipfert, C.M. Moolman, and N.H. Dekker
Nat. Rev. Gen., 2012 October 30, Vol. 14, 9-22. 

 

2011

Improved Photon Yield from a Green Dye with a Reducing and Oxidizing System
A. Le Gall#, D. Dulin#, G. Clavier, R. Meallet-Renault, P. Bouyer, K. Perronet, and N. Westbrook
Chem. Phys. Chem., Vol. 12, Iss. 9, pp. 1657 (# : equal contribution)

 

2010

Simultaneous calibration of optical tweezers spring constant and position detector response
A. Le Gall, K. Perronet, D. Dulin, A. Villing, P. Bouyer, K. Visscher and N. Westbrook
Opt. Exp., Vol. 18, Iss. 25, pp. 26469

Reduced photobleaching of BODIPY-FL
D. Dulin, A. Le Gall, K. Perronet, N. Soler, D. Fourmy, S. Yoshizawa, P. Bouyer and N. Westbrook
Proceedings of HBSM 2009, Physics Procedia Vol. 3, Iss. 4, pp. 1563

A single-molecule view on cellular and viral RNA synthesis
E. Ostrofet, F. Stal Papini, A.M. Malinen, D. Dulin
Chapter in Springer book “Biophysics of RNA-Protein Interactions: From Single Molecules to Biological Systems”, in press

 

High-yield fabrication of DNA and RNA scaffolds for single molecule force and torque spectroscopy experiments.
F. Stal Papini*, M. Seifert*, D. Dulin
*: equal contribution
BioRxiv  doi: https://doi.org/10.1101/661330

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