An up to date publication list can be found on Google Scholar.
2025
The 2’-endo conformation of arabinose-CTP and arabinose-UTP inhibit viral polymerases by inducing long pauses
Z. Xiao*, A. Das*, A. Jain*, T. K. Anderson, C. E. Cameron, J. J. Arnold#, D. Dulin#, R. N. Kirchdoerfer#
*: equal contribution
#: corresponding authors
BioRxiv https://doi.org/10.1101/2025.08.26.672356
Entropy-based super-resolution imaging in waveguide-based TIRF microscopy—an experimental and numerical study
C. Lu, M. Talebi Khoshmehr, M.S. Feiz, M.M. Dashtabi, D. Dulin, B. Imran Akca
Optics Express 33 (14), 29295-29307 https://doi.org/10.1364/OE.546872
Template switching by coronavirus polymerase requires helicase activity and is stimulated by remdesivir
and molnupiravir
A. Rakib, A. Das, S. C. Bera, P. P. B. America, M. Klein, T. K. Anderson, J. C. Marecki, B. Wang, E. Bogers, J. Y. Feng, J. P. Bilello, F. S. Papini, Q. Smitskamp, J. J. Arnold, I. Artsimovitch, R. N. Kirchdoerfer, C. E. Cameron, K. D. Raney, D. Dulin
BioRxiv https://doi.org/10.1101/2025.10.03.680419
Integrative Structure of Norovirus NS3 Suggests a Role in RNA Transport
M. Haas, J. T. Mills, C. Kelley, A. Das, H. Hof, C. Niemel, T. Donselaar, I. Drulyte, F.J.M. van Kuppeveld, D. Dulin, J. Snijder, M.R. Herod, and D.L. Hurdiss
BioRxiv https://doi.org/10.1101/2025.06.17.659504
The coronavirus helicase synergizes with the viral RNA polymerase to enable rapid RNA synthesis through duplex RNA
P. America*, S. C. Bera*, A. Das, T. K. Anderson, J. C. Marecki, F. S. Papini, J. J. Arnold, R. N. Kirchdoerfer, C. E. Cameron, K. D. Raney, M. Depken#, D. Dulin#
*: equal contribution
#: corresponding authors
BioRxiv doi: https://doi.org/10.1101/2025.03.05.641625
A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent
M. Klein*, A. Das*, S. C. Bera*, T. K. Anderson, D. Kocincova, H. W. Lee, B. Wang, F. S. Papini, J. C. Marecki, J. J. Arnold, C. E. Cameron, K. D. Raney, I. Artsimovitch, M. Götte, R. N. Kirchdoerfer, M. Depken#, D. Dulin#
*: equal contribution
#: corresponding authors
BioRxiv doi: https://doi.org/10.1101/2025.01.10.632299
Nucleic Acids Research, 53(10), 10 June 2025, gkaf450, https://doi.org/10.1093/nar/gkaf450
2024
Single-molecule magnetic tweezers reveals that TAV2b-derived peptides underwind and stabilize double-stranded RNA
Z. M. Rashid, S. Quack, M. Klein, Q. Smitskamp, P. P. B. America, M. A. Albers, J. Paulus, T. N. Grossmann, D. Dulin
BioRxiv doi: https://doi.org/10.1101/2024.09.05.611413
An alternative mechanism for activation of innate immune signaling by MDA5
S. Quack, S.Maity, P. P. B. America, M. Klein, A. Herrero del Valle, R. Singh, Q. Smitskamp, F. S. Papini, C. P. Broedersz, W. H. Roos, Y. Modis, D. Dulin
BioRxiv doi: https://doi.org/10.1101/2024.08.27.609867
Temperature-dependent twist of double-stranded RNA probed by magnetic tweezers experiments and molecular dynamics simulations
H. Dohnalova*, M. Seifert*, E. Matouskova, M. Klein, F. S. Papini, J. Lipfert, D. Dulin#, F. Lankas#
*: equal contribution
#: corresponding authors
BioRxiv doi: https://doi.org/10.1101/2023.05.31.543084
J. Phys. Chem. B 2024, 128, 664−675
2023
Surface Functionalization, Nucleic Acid Tether Characterization, and Force Calibration for a Magnetic Tweezers Assay
S. Quack, D. Dulin
Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis . Methods in Molecular Biology, vol 2694. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3377-9_19
An Introduction to Magnetic Tweezers
D. Dulin
Heller, I., Dulin, D., Peterman, E.J. (eds) Single Molecule Analysis . Methods in Molecular Biology, vol 2694. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3377-9_18
Interfering with nucleotide excision by the coronavirus 3′-to-5′ exoribonuclease
R. Chinthapatla, M. Sotoudegan, P. Srivastava , T. K. Anderson, I. M. Moustafa, K. T. Passow, S. A. Kennelly, R. Moorthy, D. Dulin, J. Y. Feng, D. A. Harki, R. N. Kirchdoerfer, C. E. Cameron, J. J. Arnold
Nucleic Acids Research, 51(1): 315–336, January 2023
2022
Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter
S.C. Bera*, P. P. B. America*, S. Maatsola, M. Seifert, E. Ostrofet, J. Cnossen, M. Spermann, F.S. Papini, M. Depken, A.M. Malinen, D. Dulin
*: equal contribution
Nucleic Acids Research, 50(13):7511-7528, July 2022.
BioRxiv doi: https://doi.org/10.1101/2021.10.13.464252
2021
Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single molecule perspective
M. Seifert*, S.C. Bera*, P. van Nies, R.N. Kirchdoerfer, A. Shannon, T.T.N. Le, X. Meng, H. Xia, J. M. Wood, L. D. Harris, F.S. Papini, J.J. Arnold, S.C. Almo, T.L. Grove, P.-Y. Shi, Y. Xiang, B. Canard, M. Depken, C.E. Cameron, and D. Dulin.
*: equal contribution
eLife, 2021; 10:e70968.
BioRxiv doi: https://doi.org/10.1101/2020.08.06.240325
The nucleotide addition cycle of the SARS-CoV-2 polymerase
S.C. Bera*, M. Seifert*, R.N. Kirchdoerfer, P. van Nies, Y. Wubulikasimu, S. Quack, F.S. Papini, J.J. Arnold, B. Canard, C.E. Cameron, M. Depken, D. Dulin.
*: equal contribution
Cell Reports, 36, 109650, August 2021.
BioRxiv https://doi.org/10.1101/2021.03.27.437309
2020
Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases
M. Seifert, P. van Nies, F. S. Papini, J.J. Arnold, M.M. Poranen, C.E. Cameron, M. Depken, D. Dulin
BioRxiv doi: https://doi.org/10.1101/661330
Nucleic Acids Research, gkaa233, April 2020.
High spatiotemporal resolution data from a custom magnetic tweezers instrument
E. Ostrofet, F. S. Papini, D. Dulin
Data in Brief, 105397, March 2020
2019
A single-molecule view on cellular and viral RNA synthesis
E. Ostrofet, F. S. Papini, A.M. Malinen, D. Dulin
In: Joo C., Rueda D. (eds) Biophysics of RNA-Protein Interactions. Biological and Medical Physics, Biomedical Engineering. Springer, New York, NY.
High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments.
F. S. Papini*, M. Seifert*, D. Dulin
*: equal contribution
BioRxiv doi: https://doi.org/10.1101/661330
Nucleic Acids Research, gkz851, October 2019
2018
Correction-free force calibration for magnetic tweezers experiments
E. Ostrofet, F. S. Papini, D. Dulin
Scientific Reports, 8:15920, 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
David Dulin lab 