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van Oene, M.M. (author), Dickinson, L.E. (author), Cross, B. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)
The bacterial flagellar motor of Escherichia coli is a nanoscale rotary engine essential for bacterial propulsion. Studies on the power output of single motors rely on the measurement of motor torque and rotation under external load. Here, we investigate the use of magnetic tweezers, which in principle allow the application and active control...
journal article 2017
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Dulin, D. (author), Arnold, Jamie J. (author), van Laar, T. (author), Oh, Hyung Suk (author), Lee, Cheri (author), Perkins, Angela L. (author), Harki, Daniel A. (author), Depken, S.M. (author), Cameron, Craig E. (author), Dekker, N.H. (author)
RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral...
journal article 2017
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Eeftens, J.M. (author), Bisht, Shveta (author), Kerssemakers, J.W.J. (author), Kschonsak, Marc (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a conserved member of the SMC protein family of ring-shaped multi-subunit protein complexes, is essential for structuring and compacting chromosomes. Despite its key role, its molecular mechanism has remained largely unknown. Here, we employ single-molecule magnetic tweezers to measure, in real time, the compaction of individual...
journal article 2017
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Joshi, S. (author), Bagani, R. (author), Beckers, Lucas (author), Dekker, R. (author)
This paper reports the use of rubber—Polybutadiene as an intermediate adhesive layer for improving the adhesion between polyimide (PI) and silicone polydimethylsiloxane (PDMS) which is required for a reliable fabrication of flexible/stretchable body patches for various applications. The adhesive bond initiated by the butyl rubber (BR), apart...
conference paper 2017
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Kluba, M.M. (author), Arslan, A. (author), Stoute, R. (author), Muganda, James (author), Dekker, R. (author)
This paper presents a new method for the CMOS compatible fabrication of microchannels integrated into a silicon substrate. In a single-step DRIE process (Deep Reactive Ion Etching) a network of microchannels with High Aspect Ratio (HAR) up to 10, can be etched in a silicon substrate through a mesh mask. In the same single etching step,...
conference paper 2017
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Caspi, Y. (author), Dekker, C. (author)
The bacterial Min protein system provides a major model system for studying reaction-diffusion processes in biology. Here we present the first in vitro study of the Min system in fully confined three-dimensional chambers that are lithography-defined, lipid-bilayer coated and isolated through pressure valves. We identify three typical...
journal article 2016
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Plesa, C. (author), Verschueren, D.V. (author), Pud, S. (author), van der Torre, J. (author), Ruitenberg, J.W. (author), Witteveen, M.J. (author), Jonsson, P.M. (author), Grosberg, Alexander Y. (author), Rabin, Yitzhak (author), Dekker, C. (author)
Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single...
journal article 2016
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Berghuis, B.A. (author), Köber, M. (author), van Laar, T. (author), Dekker, N.H. (author)
Recent advances in high-throughput single-molecule magnetic tweezers have paved the way for obtaining information on individual molecules as well as ensemble-averaged behavior in a single assay. Here we describe how to design robust high-throughput magnetic tweezers assays that specifically require application of high forces (>20. pN) for...
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, P.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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Ganji, M. (author), Kim, S.H. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
DNA supercoiling crucially affects cellular processes such as DNA replication, gene expression, and chromatin organization. However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack of convenient experimental tools to probe these phenomena. Here, we report a...
journal article 2016
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Wu, F. (author), Halatek, Jacob (author), Reiter, Matthias (author), Kingma, Enzo (author), Frey, Erwin (author), Dekker, C. (author)
Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during...
journal article 2016
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Wiktor, J.M. (author), Lesterlin, Christian (author), Sherratt, David J. (author), Dekker, C. (author)
Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein,...
journal article 2016
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Vtyurina, N. (author), Dulin, D. (author), Docter, M.W. (author), Meyer, A.S. (author), Dekker, N.H. (author), Abbondanzieri, E. (author)
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively...
journal article 2016
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Dekker, N.H. (author), Ha, S. (author), Janissen, R. (author), Ussembayev, Y. (author), van Oene, M.M. (author), Solano Hermosilla, B.P. (author)
Titanium dioxide (TiO2) is a key component of diverse optical and electronic applications that exploit its exceptional material properties. In particular, the use of TiO2 in its single-crystalline phase can offer substantial advantages over its amorphous and polycrystalline phases for existing and yet-to-be-developed applications. However, the...
journal article 2016
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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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Hol, F.J.H. (author), Rotem, Or (author), Jurkevitch, Edouard (author), Dekker, C. (author), Koster, D. (author)
Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and...
journal article 2016
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Sudol, W. (author), Dirksen, P. (author), Henneken, V.A. (author), Dekker, R. (author), Louwerse, M.C. (author)
A large aperture CMUT transducer array is formed of a plurality of adjacently located tiles of CMUT cells. The adjacent edges of the tiles are formed by an anisotropic etch process, preferably a deep reactive ion etching process which is capable of cutting through the die and its substrate while maintaining vertical edges in close proximity to...
patent 2016
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), de Leeuw, R. (author), Lorent, V.J.F. (author), Sherratt, David J. (author), Dekker, N.H. (author)
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood....
journal article 2016
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Dekker, S.H. (author), Wurzel, G. (author), Alderliesten, R.C. (author)
Fatigue life is a random variable. The reliability of a conservative fatigue life prediction for a component in the helicopter dynamic system thus needs to be substantiated. A standard analytical substantiation method uses averaged manoeuvre loads instead of seeing manoeuvre loads as a random variable whose distribution is estimated with limited...
journal article 2016
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Joshi, S. (author), Savov, A.M. (author), Dekker, R. (author)
This paper focuses on the implementation of a new technique for the fabrication of stretchable electronic patches that can be used for medical applications. The technique is based on the Electronics on Plastics by Laser Release (EPlaR) technology which enables a one-step release of a stack of flexible/stretchable layers incorporating the active...
journal article 2016
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