S.M. Depken

Search results

• 2024

  Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a

  Olivi, L., Bagchus, C., Pool, V., Bekkering, E., Speckner, K., Offerhaus, H., Wu, W. Y., Depken, M., Martens, K. J. A., Staals, R. H. J. & Hohlbein, J., 2024, In: Nucleic Acids Research. 52, 9, p. 5241-5256 16 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • flexibility 100%
  • efficiency 100%
  • nucleases 100%
  • Nuclease 100%
  • Cas9 100%
  28 Downloads (Pure)
• 2023

  Mechanism of assembly of an elongation-competent SARS-CoV-2 replication transcription complex

  Klein, M., Bera, S. C., Anderson, T. K., Wang, B., Papini, F. S., Arnold, J. J., Cameron, C. E., Depken, M., Dulin, D. & More Authors, 2023, In: Biophysical journal. 122, 3 S1, p. 171a

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
  16 Downloads (Pure)
• 2022

  A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity

  Eslami-Mossallam, B., Klein, M., Smagt, C. V. D., Sanden, K. V. D., Jones, S. K., Hawkins, J. A., Finkelstein, I. J. & Depken, M., 2022, In: Nature Communications. 13, 1, 10 p., 1367.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • kinetics 100%
  • rna 100%
  • cleavage 100%
  • classification 100%
  • CRISPR 100%
  13 Citations (Scopus)

  45 Downloads (Pure)

• High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription

  Janissen, R., Eslami-Mossallam, B., Artsimovitch, I., Depken, M. & Dekker, N. H., 2022, In: Cell Reports. 39, 4, p. 110749 1 p., 110749.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • rna 100%
  • recovery 100%
  • transcription 100%
  • molecules 100%
  • Transcription 100%
  13 Citations (Scopus)

  45 Downloads (Pure)

• Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter

  Bera, S. C., America, P. P. B., Maatsola, S., Seifert, M., Ostrofet, E., Cnossen, J., Spermann, M., Depken, M., Dulin, D. & More Authors, 2022, In: Nucleic Acids Research. 50, 13, p. 7511-7528

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Promoter Region 100%
  • Complex Formation 100%
  • RNA Polymerase 100%
  • Consensus 100%
  • stabilization 100%
  4 Citations (Scopus)

  55 Downloads (Pure)

• Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity

  Fu, R., He, W., Dou, J., Villarreal, O. D., Bedford, E., Wang, H., Hou, C., Zhang, L., Depken, M. & More Authors, 2022, In: Nature Communications. 13, 1, 15 p., 474.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • Allele 100%
  • CRISPR/Cas9 100%
  • Decomposition 100%
  • specificity 100%
  • decomposition 100%
  19 Citations (Scopus)

  87 Downloads (Pure)
• 2021

  Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective

  Seifert, M., Bera, S. C., van Nies, P., Kirchdoerfer, R. N., Shannon, A., Le, T. T. N., Meng, X., Depken, M., Dulin, D. & More Authors, 2021, In: eLife. 10, 26 p., e70968.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • polymerases 100%
  • inhibition 100%
  • nucleotides 100%
  • molecules 100%
  • coronaviruses 83%
  41 Citations (Scopus)

  112 Downloads (Pure)

• The nucleotide addition cycle of the SARS-CoV-2 polymerase

  Bera, S. C., Seifert, M., Kirchdoerfer, R. N., van Nies, P., Wubulikasimu, Y., Quack, S., Papini, F. S., Depken, M., Dulin, D. & More Authors, 2021, In: Cell Reports. 36, 9, 23 p., 109650.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • RNA 100%
  • Cycle 100%
  • Addition 100%
  • Nucleotide 100%
  • Polymerase 100%
  12 Citations (Scopus)

  69 Downloads (Pure)
• 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: Biophysical Journal. 118, 3, p. 543A-543A

  Research output: Contribution to journal › Meeting Abstract › Scientific

• 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • rna 100%
  • rna polymerases 100%
  • activation energy 100%
  • Show 100%
  • RNA 100%
  20 Citations (Scopus)

  52 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • proteins 100%
  • nucleic acids 100%
  • bypasses 100%
  • Argonaute 100%
  • Acid 100%
  12 Citations (Scopus)

  98 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 journal › Comment/Letter to the editor › Scientific

  • proteins 100%
  • kinetics 100%
  • trajectories 100%
  • information 100%
  • physical chemistry 100%
• 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • calcium sulfides 100%
  • kinetics 100%
  • specificity 100%
  • nucleases 100%
  • hybridization 100%
  78 Citations (Scopus)

  161 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • proteins 100%
  • kinetics 100%
  • trajectories 100%
  • motors 100%
  • Kinetics 100%
  2 Citations (Scopus)

  50 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • control 100%
  • rna 100%
  • bacteria 100%
  • branching ratio 100%
  • transcription 100%
  43 Citations (Scopus)

  59 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • polymerases 100%
  • nucleosomes 100%
  • density 100%
  • genes 100%
  • Density 100%
  10 Citations (Scopus)

  62 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • nucleotides 100%
  • rna 100%
  • rna polymerases 100%
  • Nucleoside Analogues 100%
  • Ribonucleotides 42%
  43 Citations (Scopus)

  72 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 journal › Article › Scientific › peer-review

  • T7 DNA Polymerase 100%
  • dna polymerases 100%
  • Bacteriophage T7 66%
  • Enterobacteria Phage T7 66%
  • kinetics 40%
  28 Citations (Scopus)

• 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • Experiment 100%
  • Helicase 100%
  • Molecule 100%
  • interactions 100%
  • comparative evaluations 100%
  13 Citations (Scopus)

  68 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 journal › Article › Scientific › peer-review

  Open Access

  File

  • proteins 100%
  • dynamics 100%
  • messenger-rna 100%
  • specificity 100%
  • resolution 100%
  32 Citations (Scopus)

  94 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 Sept 2016, In: Molecular Cell. 63, 5, p. 852-864 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

  • CRISPR Adaptation 100%
  • Cas1 100%
  • Target DNA 100%
  • 2-complex 100%
  • DNA Degradation 100%
  93 Citations (Scopus)

  211 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 journal › Article › Scientific › peer-review

  • Initiation Site 100%
  • RNA-dependent RNA Polymerase (RdRP) 100%
  • Viral RNA-dependent RNA Polymerase 100%
  • Models 100%
  • Throughput 100%
  25 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 journal › Article › Scientific › peer-review

  54 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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review

  Open Access

  File

  • Protein 100%
  • Replisome 100%
  • Protein-Protein Interaction 100%
  • proteins 100%
  • barriers 100%
  27 Citations (Scopus)

  54 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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review

  Open Access

  File

  • Reaction Pathway 100%
  • Single-molecule Force Spectroscopy 100%
  • Modern Approaches 100%
  • Spectroscopy 100%
  • Molecule 100%
  26 Citations (Scopus)

  76 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 journal › Article › Scientific › peer-review

  Open Access
  60 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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review

  Open Access
  20 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 journal › Article › Scientific › peer-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 journal › Article › Scientific › peer-review

  Open Access
  48 Citations (Scopus)