BN/Martin Depken Lab

Research Output

  • 24 Article
  • 3 Dissertation (TU Delft)
  • 1 Meeting Abstract
  • 1 Comment/Letter to the editor
2020

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

Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases

Seifert, M., van Nies, P., Papini, F. S., Arnold, J. J., Poranen, M. M., Cameron, C. E., Depken, M. & Dulin, D., 2020, In : Nucleic Acids Research. 48, 10, p. 5591-5602

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Downloads (Pure)
2019

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

Open Access
File
3 Citations (Scopus)
29 Downloads (Pure)

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

Right place, Right Time: Modeling the search time and specificity of Cas9 and Argonaute

Klein, M., 2019, 191 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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25 Downloads (Pure)
Open Access
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42 Downloads (Pure)
2018

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

Open Access
File
31 Citations (Scopus)
58 Downloads (Pure)

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

Open Access
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14 Downloads (Pure)

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

Open Access
File
20 Citations (Scopus)
19 Downloads (Pure)
2017

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

Open Access
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4 Citations (Scopus)
14 Downloads (Pure)

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

Open Access
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7 Citations (Scopus)
17 Downloads (Pure)

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

Open Access
File
15 Citations (Scopus)
26 Downloads (Pure)

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

5 Citations (Scopus)
Open Access
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36 Downloads (Pure)

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

Open Access
File
2 Citations (Scopus)
30 Downloads (Pure)

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

Open Access
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21 Citations (Scopus)
37 Downloads (Pure)
2016

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

Open Access
File
61 Citations (Scopus)
147 Downloads (Pure)
2015

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 Citations (Scopus)

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

34 Citations (Scopus)

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

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

Open Access
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16 Citations (Scopus)
13 Downloads (Pure)

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

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

Open Access
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17 Citations (Scopus)
18 Downloads (Pure)
2014

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

Open Access
36 Citations (Scopus)
2013

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

Open Access

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

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

Open Access
19 Citations (Scopus)

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

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

Open Access
29 Citations (Scopus)