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Eeftens, J.M. (author), Katan, A.J. (author), Kschonsak, Marc (author), Hassler, Markus (author), de Wilde, L. (author), Dief, Essam M. (author), Haering, Christian H. (author), Dekker, C. (author)Structural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe...journal article 2016
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Gaio, N. (author), van Meer, B. (author), Quiros Solano, W.F. (author), Bergers, L. (author), van de Stolpe, A. (author), Mummery, CL (author), Sarro, Pasqualina M (author), Dekker, R. (author)Organ-on-Chips (OOCs) are micro-fabricated devices which are used to culture cells in order to mimic functional units of human organs. The devices are designed to simulate the physiological environment of tissues in vivo. Cells in some types of OOCs can be stimulated in situ by electrical and/or mechanical actuators. These actuations can mimic...journal article 2016
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Fayezioghani, A. (author), Dekker, R. (author), Sluys, Lambertus J. (author)Corrosion is a phenomenon observed in structural components in corrosive environments such as pipelines, bridges, aircrafts, turbines, etc. The computational model of corrosion should enjoy two features: a) accurately considering the electrochemistry of corrosion and b) properly dealing with the moving interface between solid and electrolyte....journal article 2022
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Ganji, M. (author), Shaltiel, Indra A. (author), Bisht, Shveta (author), Kim, E. (author), Kalichava, A. (author), Haering, Christian H. (author), Dekker, C. (author)It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a...journal article 2018
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van Oene, M.M. (author), Ha, S. (author), Jager, T. (author), Lee, M. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and...journal article 2018
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Pradhan, B. (author), Barth, R. (author), Kim, E. (author), van Laar, T. (author), Yang, W.W.W. (author), Ryu, J.K. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no...journal article 2022
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Lee, Kuo Ming (author), Gong, Yu Nong (author), Hsieh, Tzu Hsuan (author), Woodman, Andrew (author), Dekker, N.H. (author), Cameron, Craig E. (author), Shih, Shin Ru (author)Enterovirus A71 (EV-A71) is an important nonpolio enterovirus that causes severe neurological complications. In 1998, Taiwan experienced an EV-A71 outbreak that caused 78 deaths. Since then, periodic epidemics of EV-A71 associated with newly emerging strains have occurred. Several of these strains are known to be recombinant; however, how...journal article 2018
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Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological NanoporeRestrepo Perez, L. (author), Huang, Gang (author), Bohländer, Peggy R. (author), Worp, N.M. (author), Eelkema, R. (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author)While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in...journal article 2019
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Japaridze, A. (author), Gogou, C. (author), Kerssemakers, J.W.J. (author), Nguyen, Huyen My (author), Dekker, C. (author)The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move...journal article 2020
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Verschueren, D.V. (author), Shi, X. (author), Dekker, C. (author)Single-molecule sensing technologies aim to detect and characterize single biomolecules, but generally need labeling while the measurement times and throughput are severely restricted by a lack of positional control over the molecule. Here, a plasmonic nanopore biosensor is reported where single molecules can be electrophoretically delivered...journal article 2019
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Størkersen, Kristine (author), Thorvaldsen, Trine (author), Kongsvik, Trond (author), Dekker, S.W.A. (author)Over the past decades, government safety management regulation has been driven by deregulation, simplification and organization-level regimes of inspection. So-called functional rule-making requires organizations to implement safety management systems appropriate for their operations. The paradox that seems to have arisen is that...journal article 2020
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Smith, Kathleen Beth (author), Wehrli, Monika (author), Japaridze, A. (author), Assenza, Salvatore (author), Dekker, C. (author), Mezzenga, Raffaele (author)The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by...journal article 2020
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Kim, E. (author), Kerssemakers, J.W.J. (author), Shaltiel, Indra A. (author), Haering, Christian H. (author), Dekker, C. (author)Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA<sup>1</sup>. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to...journal article 2020
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Kuijpers, L.C. (author), van Laar, T. (author), Janissen, R. (author), Dekker, N.H. (author)Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing...journal article 2022
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Kaczmarczyk, A.P. (author), Meng, He (author), Ordu, O. (author), Noort, John van (author), Dekker, N.H. (author)Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of...journal article 2020
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Last, M.G.F. (author), Deshpande, S.R. (author), Dekker, C. (author)Membraneless organelles formed by liquid-liquid phase separation are dynamic structures that are employed by cells to spatiotemporally regulate their interior. Indeed, complex coacervation-based phase separation is involved in a multitude of biological tasks ranging from photosynthesis to cell division to chromatin organization, and more....journal article 2020
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Verschueren, D.V. (author), Pud, S. (author), Shi, X. (author), de Angelis, L. (author), Kuipers, L. (author), Dekker, C. (author)Solid-state nanopores are single-molecule sensors that hold great potential for rapid protein and nucleic-acid analysis. Despite their many opportunities, the conventional ionic current detection scheme that is at the heart of the sensor suffers inherent limitations. This scheme intrinsically couples signal strength to the driving voltage,...journal article 2018
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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...journal article 2018
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- Lipfert, J. (author), van Oene, M.M. (author), Lee, M. (author), Pedaci, F. (author), Dekker, N.H. (author) journal article 2015
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Dekker, S.W.A. (author), Tooma, Michael (author)The shortcomings of incident-based metrics for worker safety such as total recordable incident frequency rate (TRIFR) are well documented. In particular, a low TRIFR is no assurance against legal liability. There is considerable overlap between the literature on safety as the presence of capacities to make things go well, and jurisprudence in...journal article 2022