1. 2013
  2. Backtracking and other off-path pauses control the dynamic of viral RNA dependent RNA polymerases

    Dulin, D., Vilfan, ID., Berghuis, BA., Hage, S., Bamford, D., Poranen, M., Depken, SM. & Dekker, NH., 2013, In : Biophysical Journal. 104, 2, p. 364A-364A

    Research output: Contribution to journalArticleScientificpeer-review

  3. Intermittent transcription dynamics for the rapid production of long transcripts of high fidelity

    Depken, SM., Parrondo, JMR. & Grill, SW., 2013, In : Cell Reports. 5, 2, p. 521-530 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Irregular transcription dynamics for rapid production of long transcripts of high-fidelity

    Depken, SM., Parrondo, JMR. & Grill, SW., 2013, In : Cell Reports. 5, 2, p. 521-530 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. RAD51-Nucleoprotein filament assembly quantified at the single-molecule level

    Candelli, A., Holhausen, JT., Depken, SM., Franker, MM., Maman, J., Pellegrini, L., Modesti, M., Wyman, C., Wuite, GJL. & Peterman, EJG., 2013, In : Biophysical Journal. 104, 2, p. 369A-369A

    Research output: Contribution to journalArticleScientificpeer-review

  6. Stress-enhanced gelation: A dynamic nonlinearity of elasticity

    Yao, NY., Broedersz, CP., Depken, SM., Becker, DJ., Pollak, MR., Mackintosh, FC. & Weitz, DA., 2013, In : Physical Review Letters. 110, 1, p. 1-5 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. 2014
  8. Visualization and quantification of RAD51-filament formation at single-monomer resolution

    Candelli, A., Holthausen, JT., Depken, SM., Brouwer, I., Franker, MM., Marchetti, M., Heller, I., Bernard, S., Garcin, EB., Modesti, M., Wyman, C., Wuite, GJL. & Peterman, EJG., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 42, p. 15090-15095 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  9. 2015
  10. Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site

    Dulin, D., Vilfan, I. D., Berghuis, B. A., Poranen, M. M., Depken, M. & Dekker, N. H., 2015, In : Nucleic Acids Research. 43, 21, p. 10421-10429 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Elongation-competent pauses govern the fidelity of a viral RNA-dependent RNA polymerase

    Dulin, D., Vilfan, ID., Berghuis, BA., Hage, S., Bamford, D., Poranen, M., Depken, SM. & Dekker, NH., 2015, In : Cell Reports. 10, 6, p. 983-992 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Slow unloading leads to DNA-bound B2 sliding clamp accumulation in live Escherichia coli cells

    Moolman, MC., Tiruvadi Krishnan, S., Kerssemakers, JWJ., van den Berg, AA., Tulinski, P., Depken, SM., Reyes-Lamothe, R., Sherratt, DJ. & Dekker, NH., 2015, In : Nature Communications. 5, p. 1-11 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier

    Berghuis, B. A., Dulin, D., Xu, Z. Q., Van Laar, T., Cross, B., Janissen, R., Jergic, S., Dixon, N. E., Depken, M. & Dekker, N. H., 2015, In : Nature Chemical Biology. 11, p. 579-585 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. Strand separation suffices to establish a long-lived, foolproof DNA-protein lock at the TusTer replication fork barrier

    Berghuis, BA., Dulin, D., Xu, ZQ., van Laar, T., Cross, B., Janissen, R., Jergic, S., Dixon, NE., Depken, SM. & Dekker, NH., 2015, In : Nature Chemical Biology. 11, 8, p. 579-585 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments

    Dulin, D., Berghuis, BA., Depken, SM. & Dekker, NH., 2015, In : Current Opinion in Structural Biology. 34, p. 116-122 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. 2016
  17. Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

    Künne, T., Kieper, S. N., Bannenberg, J. W., Vogel, A. I. M., Miellet, W. R., Klein, M., Depken, M., Suarez-Diez, M. & Brouns, S. J. J., 1 Sep 2016, In : Molecular Cell. 63, 5, p. 852-864 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  18. 2017
  19. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes

    van den Berg, A. & Depken, M., 2017, In : Nucleic Acids Research. 45, 13, p. 7623-7632

    Research output: Contribution to journalArticleScientificpeer-review

  20. Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers

    Dulin, D., Arnold, J. J., van Laar, T., Oh, H. S., Lee, C., Perkins, A. L., Harki, D. A., Depken, M., Cameron, C. E. & Dekker, N. H., 2017, In : Cell Reports. 21, 4, p. 1063-1076 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Why Argonaute is needed to make microRNA target search fast and reliable

    Klein, M., Chandradoss, S. D., Depken, M. & Joo, C., 2017, In : Seminars in Cell and Developmental Biology. 65, p. 20-28

    Research output: Contribution to journalArticleScientificpeer-review

  22. Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity

    Hoekstra, T. P., Depken, M., Lin, S. N., Cabanas-Danés, J., Gross, P., Dame, R. T., Peterman, E. J. G. & Wuite, G. J. L., 28 Feb 2017, In : Biophysical Journal. 112, 4, p. 575-583 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Designing nucleosomal force sensors

    Tompitak, M., De Bruin, L., Eslami Mosallam, B. & Schiessel, H., 8 May 2017, In : Physical Review E. 95, 5, 6 p., 052402.

    Research output: Contribution to journalArticleScientificpeer-review

  24. What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments

    Berghuis, B., Raducanu, V-S., Elshenawy, M. M., Jergic, S., Depken, M., Dixon, NE., Hamdan, S. M. & Dekker, N., 6 Nov 2017, In : Critical Reviews in Biochemistry and Molecular Biology. p. 1-15 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  25. 2018
  26. Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules

    Klein, M., Eslami Mosallam, B., Gonzalez Arroyo, D. W. & Depken, M., 2018, In : Cell Reports. 22, 6, p. 1413-1423

    Research output: Contribution to journalArticleScientificpeer-review

  27. Kinetic analysis methods applied to single motor protein trajectories

    Nord, A. L., Pols, A. F., Depken, M. & Pedaci, F., 2018, In : Physical Chemistry Chemical Physics. 20, 27, p. 18775-18781 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  28. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria

    Dulin, D., Bauer, D. L. V., Malinen, A. M., Bakermans, J. J. W., Kaller, M., Morichaud, Z., Petushkov, I., Depken, M., Brodolin, K., Kulbachinskiy, A. & Kapanidis, A. N., 16 Apr 2018, In : Nature Communications. 9, 1, 1478.

    Research output: Contribution to journalArticleScientificpeer-review

  29. 2019
  30. Argonaute bypasses cellular obstacles without hindrance during target search

    Cui, T., Klein, M., Hegge, J. W., Chandradoss, S. D., van der Oost, J., Depken, M. & Joo, C., 2019, In : Nature Communications. 10, 1, 11 p., 4390.

    Research output: Contribution to journalArticleScientificpeer-review

  31. Erratum: Kinetic analysis methods applied to single motor protein trajectories (Physical Chemistry Chemical Physics (2018) 20 (18775-18781) DOI: 10.1039/c8cp03056a)

    Nord, A. L., Pols, A. F., Depken, M. & Pedaci, F., 2019, In : Physical Chemistry Chemical Physics. 21, 22, 1 p.

    Research output: Contribution to journalComment/Letter to the editorScientific

  32. 2020
  33. A Unifying Mechanistic Model of Bacterial Transcription with Three Interconnected Pause States and Non-Diffusive Backtrack Recovery

    Janissen, R., Eslami-Mossallam, B., Artsimovitch, I., Depken, M. & Dekker, N. H., 2020, (In preparation) In : Biophysical Journal. 118, 3, p. 543A-543A

    Research output: Contribution to journalMeeting AbstractScientific

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