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Interdisciplinary Center for Clinical Research (IZKF)
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Interdisciplinary Center for Clinical Research (IZKF)

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      • RNA virus replication
      • Mitochondrial Transcription
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  2. Publications

Publications

In page navigation: Publications

    Publications

     
    An up to date publication list can be found on Google Scholar.

     

    2020

    Signatures and mechanisms of efficacious therapeutic ribonucleotides against SARS-CoV-2 revealed by analysis of its replicase using magnetic tweezers 

    M. Seifert*, S.C. Bera*, P. van Nies, R.N. Kirchdoerfer, A. Shannon, T.-T.-N. Le, T.L. Grove, F.S. Papini, J.J. Arnold, S.C. Almo, B. Canard, M. Depken, C.E. Cameron, D. Dulin
    *equal contribution
    BioRxiv doi: https://doi.org/10.1101/2020.08.06.240325
    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

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