BN/Nynke Dekker Lab

Research Output

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

Chromatin fibers stabilize nucleosomes under torsional stress

Kaczmarczyk, A., Meng, H., Ordu, O., Noort, J. V. & Dekker, N. H., 2020, In : Nature Communications. 11, 1, 126.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2 Citations (Scopus)
40 Downloads (Pure)

Conformational flexibility and oligomerization of BRCA2 regions induced by RAD51 interaction

Sidhu, A., Grosbart, M., Sánchez, H., Verhagen, B., van der Zon, N. L. L., Ristić, D., van Rossum-Fikkert, S. E. & Wyman, C., 2020, In : Nucleic Acids Research. 48, 17, p. 9649-9659

Research output: Contribution to journalArticleScientificpeer-review

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1 Downloads (Pure)

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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1 Citation (Scopus)
4 Downloads (Pure)

Visualizing response to DNA damage in bacteria

Deb Roy, S., 2020, 155 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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8 Downloads (Pure)
2019

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Wu, F., Swain, P., Kuijpers, L., Zheng, X., Felter, K., Guurink, M., Solari, J., Jun, S., Dekker, C. & More Authors, 2019, In : Current Biology. 29, 13, p. 2131-2144.e4

Research output: Contribution to journalArticleScientificpeer-review

10 Citations (Scopus)

DNA Sequence Is a Major Determinant of Tetrasome Dynamics

Ordu, O., Lusser, A. & Dekker, N. H., 2019, In : Biophysical Journal. 117, 11, p. 2217-2227 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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1 Downloads (Pure)

Predicting Intraserotypic Recombination in Enterovirus 71

Woodman, A., Lee, K. M., Janissen, R., Gong, Y. N., Dekker, N. H., Shih, S. R. & Cameron, C. E., 2019, In : Journal of virology. 93, 4, 15 p., e0205718.

Research output: Contribution to journalArticleScientificpeer-review

8 Citations (Scopus)

Single-Crystal Rutile TiO 2 Nanocylinders are Highly Effective Transducers of Optical Force and Torque

Ha, S., Tang, Y., Van Oene, M. M., Janissen, R., Dries, R. M., Solano, B., Adam, A. J. L. & Dekker, N. H., 2019, In : ACS Photonics. 6, 5, p. 1255-1265 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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4 Citations (Scopus)
76 Downloads (Pure)
2018
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26 Downloads (Pure)

Discovery of Enterovirus A71-like nonstructural genomes in recent circulating viruses of the Enterovirus A species

Lee, K. M., Gong, Y. N., Hsieh, T. H., Woodman, A., Dekker, N. H., Cameron, C. E. & Shih, S. R., 1 Dec 2018, In : Emerging Microbes and Infections. 7, 1, 111.

Research output: Contribution to journalArticleScientificpeer-review

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

Dissecting the Nucleosome: Single-Molecule Studies of Subnucleosomal Structure and Dynamics

Ordu, O., 2018, 209 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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50 Downloads (Pure)

Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription

Janissen, R., Arens, M. M. A., Vtyurina, N. N., Rivai, Z., Sunday, N. D., Eslami-Mossallam, B., Gritsenko, A. A., Laan, L., de Ridder, D., Artsimovitch, I., Dekker, N. H., Abbondanzieri, E. A. & Meyer, A. S., 2018, In : Cell. 174, 5, p. 1188-1199.e14 27 p.

Research output: Contribution to journalArticleScientificpeer-review

18 Citations (Scopus)

High-Speed Magnetic Tweezers Studies of the E-coli Replisome

Leachman, S. M. & Dekker, N. H., 2018, In : Biophysical Journal. 114, 3, p. 85A-85A

Research output: Contribution to journalMeeting AbstractScientific

Imaging of DNA and protein by SFM and combined SFM-TIRF microscopy

Grosbart, M., Ristić, D., Sánchez, H. & Wyman, C., 2018, Methods in Molecular Biology. Springer, Vol. 1665. p. 259-280 22 p. (Methods in Molecular Biology; vol. 1665).

Research output: Chapter in Book/Conference proceedings/Edited volumeChapterScientificpeer-review

2 Citations (Scopus)

Luminescence Properties of Self-Aggregating TbIII-DOTA-Functionalized Calix[4]arenes

Mayer, F., Tiruvadi Krishnan, S., Schuhle, DT., Eliseeva, S. V., Petoud, S., Toth, E. & Djanashvili, K., 30 Jan 2018, In : Frontiers in Chemistry. 6, 9 p., 1.

Research output: Contribution to journalArticleScientificpeer-review

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

Modification of the histone tetramer at the H3-H3 interface impacts tetrasome conformations and dynamics

Ordu, O., Kremser, L., Lusser, A. & Dekker, N. H., 2018, In : Journal of Chemical Physics. 148, 12, 11 p., 123323.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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6 Citations (Scopus)
39 Downloads (Pure)

Probing chromatin structure with magnetic tweezers

Kaczmarczyk, A., Brouwer, T. B., Pham, C., Dekker, N. H. & van Noort, J., 1 Jan 2018, Methods in Molecular Biology. Springer, Vol. 1814. p. 297-323 (Methods in Molecular Biology; vol. 1814).

Research output: Chapter in Book/Conference proceedings/Edited volumeChapterScientificpeer-review

4 Citations (Scopus)

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance

van Oene, M. M., Ha, S., Jager, T., Lee, M., Pedaci, F., Lipfert, J. & Dekker, N. H., 24 Apr 2018, In : Biophysical Journal. 114, 8, p. 1970-1979 10 p.

Research output: Contribution to journalArticleScientificpeer-review

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

The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF)

Sidhu, A., Ristic, D., Sánchez, H. & Wyman, C., 2018, Methods in Enzymology. Spies, M. & Malkova, A. (eds.). Academic Press, Vol. 600. p. 347-374 28 p. (Methods in Enzymology; vol. 600).

Research output: Chapter in Book/Conference proceedings/Edited volumeChapterScientific

2017

Applying torque to the Escherichia coli flagellar motor using magnetic tweezers

Van Oene, M. M., Dickinson, L. E., Cross, B., Pedaci, F., Lipfert, J. & Dekker, N. H., 2017, In : Scientific Reports. 7, 11 p., 43285.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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9 Citations (Scopus)
43 Downloads (Pure)

InP Nanowire Biosensor with Tailored Biofunctionalization: Ultrasensitive and Highly Selective Disease Biomarker Detection

Janissen, R., Sahoo, P. K., Santos, C. A., Da Silva, A. M., Von Zuben, A. A. G., Souto, D. E. P., Costa, A. D. T., Celedon, P., Zanchin, N. I. T., Almeida, D. B., Oliveira, D. S. & More Authors, 2017, In : Nano Letters. 17, 10, p. 5938-5949

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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31 Citations (Scopus)
96 Downloads (Pure)

Measuring in vivo protein dynamics throughout the cell cycle using microfluidics

de Leeuw, R., Brazda, P., Moolman, M. C., Kerssemakers, J. W. J., Solano Hermosilla, B. P. & Dekker, N. H., 2017, The Bacterial Nucleoid : methods and Protocols. Espéli, O. (ed.). Springer, Vol. 1624. p. 237-252 16 p. (Methods in Molecular Biology; vol. 1624).

Research output: Chapter in Book/Conference proceedings/Edited volumeChapterScientific

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers

Kriegel, F., Ermann, N., Forbes, R., Dulin, D., Dekker, N. H. & Lipfert, J., 2017, In : Nucleic Acids Research. 45, 10, p. 5920-5929 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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15 Citations (Scopus)
23 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
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16 Citations (Scopus)
26 Downloads (Pure)

Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding

Kaczmarczyk, A., Allahverdi, A., Brouwer, T. B., Nordenskiöld, L., Dekker, N. H. & Van Noort, J., 2017, In : Journal of Biological Chemistry. 292, 42, p. 17506-17513 8 p.

Research output: Contribution to journalArticleScientificpeer-review

13 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
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2 Citations (Scopus)
30 Downloads (Pure)
2016
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12 Downloads (Pure)

High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers

Berghuis, B. A., Köber, M., van Laar, T. & Dekker, N. H., 1 Aug 2016, In : Methods. 105, p. 90-98

Research output: Contribution to journalArticleScientificpeer-review

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

Hysteresis in DNA compaction by Dps is described by an ising model

Vtyurina, N. N., Dulin, D., Docter, M. W., Meyer, A. S., Dekker, N. H. & Abbondanzieri, E. A., 3 May 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 18, p. 4982-4987 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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11 Citations (Scopus)
30 Downloads (Pure)

In vivo investigations of E. coli chromosomal replication using single-molecule imaging

Tiruvadi Krishnan, S., 2016, 169 p.

Research output: ThesisDissertation (TU Delft)

Open Access
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72 Downloads (Pure)

Nanowire arrays as cell force sensors to investigate adhesin-enhanced holdfast of single cell bacteria and biofilm stability

Sahoo, P. K., Janissen, R., Monteiro, M. P., Cavalli, A., Murillo, D. M., Merfa, M. V., Cesar, C. L., Carvalho, H. F., De Souza, A. A., Bakkers, E. P. A. M. & Cotta, M. A., 2016, In : Nano Letters: a journal dedicated to nanoscience and nanotechnology. 16, 7, p. 4656-4664 9 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Recent insights from single-molecule studies into nucleosome structure and dynamics

Ordu, O., Lusser, A. & Dekker, N., 2016, In : Biophysical Reviews. 8, Supplement 1, p. 33-49 17 p.

Research output: Contribution to journalArticleScientificpeer-review

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

The progression of replication forks at natural replication barriers in live bacteria

Moolman, M. C., Tiruvadi Krishnan, S., Kerssemakers, J. W. J., De Leeuw, R., Lorent, V., Sherratt, D. J. & Dekker, N. H., 2016, In : Nucleic Acids Research. 44, 13, p. 6262-6273 12 p.

Research output: Contribution to journalArticleScientificpeer-review

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

Tunable top-down fabrication and functional surface coating of single-crystal titanium dioxide nanostructures and nanoparticles

Dekker, N., Ha, S., Janissen, R., Ussembayev, Y., van Oene, M. & Solano Hermosilla, B., 18 Apr 2016, In : Nanoscale.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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6 Citations (Scopus)
20 Downloads (Pure)
2015

A force calibration standard for magnetic tweezers

Yu, Z., Dulin, D., Cnossen, JP., Kober, M., van Oene, MM., Ordu, O., Berghuis, BA., Hensgens, T., Lipfert, J. & Dekker, NH., 2015, In : Review of Scientific Instruments. 85, p. 1-10 10 p.

Research output: Contribution to journalArticleScientificpeer-review

A singular perpective on chromosomal replication

Moolman, MC., 2015, Delft. 155 p.

Research output: ThesisDissertation (TU Delft)

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)

Biological magnetometry: The torque on superparamagnetic beads in magnetic fields

van Oene, MM., Dickinson, LE., Pedaci, F., Köber, M., Dulin, D., Lipfert, J. & Dekker, NH., 2015, In : Physical Review Letters. 114, p. 1-6 6 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
39 Citations (Scopus)

Comparing the assembly and handedness dynamics of (H3.3-H4)(2) Tetrasomes to canonical tetrasomes

Vlijm, R., Lee, M., Ordu, O., Boltengagen, A., Lusser, A., Dekker, NH. & Dekker, C., 2015, In : PLoS ONE. 10, 10, p. 1-14 14 p.

Research output: Contribution to journalArticleScientificpeer-review

10 Citations (Scopus)

De RNA helix lijkt niet altijd op die van DNA

Lipfert, J. & Dekker, NH., 2015, In : Nederlands Tijdschrift voor Natuurkunde. 62015, p. 224-227 4 p.

Research output: Contribution to journalArticleScientificpeer-review

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)

Essential validation methods for E.coli strains created by chromosomal engineering

Tiruvadi Krishnan, S., Moolman, MC., van Laar, T., Meyer, AS. & Dekker, NH., 2015, In : Journal of Biological Engineering. 9, 11, p. 1-14 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Essential validation methods for E. coli strains created by chromosome engineering

Tiruvadi Krishnan, S., Moolman, M. C., van Laar, T., Meyer, A. S. & Dekker, N. H., 2015, In : Journal of Biological Engineering. 9, 1, 14 p., 11.

Research output: Contribution to journalArticleScientificpeer-review

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

Freely orbiting magnatic tweezers to directly monitor changes in the twist of nucleic acids (vol.2, 439, 2011)

Lipfert, J., Wiggin, MJ., Kerssemakers, JWJ., Pedaci, F. & Dekker, NH., 2015, In : Nature Communications. 6, p. 1-1 1 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
2 Citations (Scopus)

High spatiotemporal-resolution magnetic tweezers: Calibration and applications for DNA Dynamics

Dulin, D., Cui, TJ., Cnossen, JP., Docter, MW., Lipfert, J. & Dekker, NH., 2015, In : Biophysical Journal. 109, 10, p. 2113-2125 13 p.

Research output: Contribution to journalArticleScientificpeer-review

36 Citations (Scopus)

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes

Vlijm, R., Lee, M., Lipfert, J., Lusser, A., Dekker, C. & Dekker, NH., 2015, In : Cell Reports. 10, 2, p. 216-225 10 p.

Research output: Contribution to journalArticleScientificpeer-review

26 Citations (Scopus)

Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria

Moolman, M. C., Kerssemakers, J. W. J. & Dekker, N. H., 2 Sep 2015, In : Biophysical Journal. 109, 5, p. 883-891 9 p.

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

Quantitative analysis of intra-cellular fluorescent foci in live bacteria

Moolman, MC., Kerssemakers, JWJ. & Dekker, NH., 2015, In : Biophysical Journal. 109, 5, p. 883-891 9 p.

Research output: Contribution to journalArticleScientificpeer-review