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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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Ketterer, Philip (author), Ananth, A.N. (author), Laman Trip, J.D.S. (author), Mishra, Ankur (author), Bertosin, Eva (author), Ganji, M. (author), van der Torre, J. (author), Onck, Patrick (author), Dietz, Hendrik (author), Dekker, C. (author)
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling...
journal article 2018
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Caneva, S.L. (author), Gehring, P. (author), García-Suárez, Víctor M. (author), García-Fuente, Amador (author), Stefani, D. (author), Olavarria Contreras, I.J. (author), Ferrer, Jaime (author), Dekker, C. (author), van der Zant, H.S.J. (author)
The ability to detect and distinguish quantum interference signatures is important for both fundamental research and for the realization of devices such as electron resonators<sup>1</sup>, interferometers<sup>2</sup> and interference-based spin filters<sup>3</sup>. Consistent with the principles of subwavelength optics, the wave nature of...
journal article 2018
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Savov, A.M. (author), Joshi, S. (author), Shafqat, Salman (author), Hoefnagels, Johan (author), Louwerse, M.C. (author), Stoute, R. (author), Dekker, R. (author)
A device for studying the mechanical and electrical behavior of free-standing micro-fabricated metal structures, subjected to a very large deformation, is presented in this paper. The free-standing structures are intended to serve as interconnects in high-density, highly stretchable electronic circuits. For an easy, damage-free handling and...
journal article 2018
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Caspi, Y. (author), Dekker, C. (author)
Cell division in most prokaryotes is mediated by the well-studied fts genes, with FtsZ as the principal player. In many archaeal species, however, division is orchestrated differently. The Crenarchaeota phylum of archaea features the action of the three proteins, CdvABC. This Cdv system is a unique and less-well-studied division mechanism that...
journal article 2018
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Deshpande, S.R. (author), Spoelstra, W.K. (author), van Doorn, M.C. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Liposomes, self-assembled vesicles with a lipid-bilayer boundary similar to cell membranes, are extensively used in both fundamental and applied sciences. Manipulation of their physical properties, such as growth and division, may significantly expand their use as model systems in cellular and synthetic biology. Several approaches have been...
journal article 2018
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Fanalista, F. (author), Deshpande, S.R. (author), Lau, A.W.H.R. (author), Pawlik, G. (author), Dekker, C. (author)
Recently, both the cellular and synthetic biology communities have expressed a strong interest in coacervates, membrane‐less liquid droplets composed of densely packed multivalent molecules that form as a result of spontaneous phase separation. Here, it is studied how FtsZ, a protein that plays a key role in the bacterial division process,...
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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Wiktor, J.M. (author), van der Does, M. (author), Büller, L.A. (author), Sherratt, David J. (author), Dekker, C. (author)
The formation of 3 single-stranded DNA overhangs is a first and essential step during homology-directed repair of double-stranded breaks (DSB) of DNA, a task that in Escherichia coli is performed by RecBCD. While this protein complex has been well characterized through in vitro single-molecule studies, it has remained elusive how end...
journal article 2018
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Verschueren, D.V. (author), Yang, W.W.W. (author), Dekker, C. (author)
We report a simple and scalable technique for the fabrication of nanopore arrays on freestanding SiN and graphene membranes based on electron-beam lithography and reactive ion etching. By controlling the dose of the single-shot electron-beam exposure, circular nanopores of any size down to 16 nm in diameter can be fabricated in both materials...
journal article 2018
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Joshi, S. (author), Savov, A.M. (author), Shafqat, Salman (author), Dekker, R. (author)
The authors found that oxygen plasma etching of polyimide (PI) with aluminum (Al) as a hard-etch mask results in lightly textured arbitrary shaped “fur-like” residues. Upon investigation, the presence of Al was detected in these residues. Ruling out several causes of metal contamination that were already reported in literature, a new theory for...
journal article 2018
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Shi, X. (author), Verschueren, D.V. (author), Dekker, C. (author)
Plasmon resonance biosensors provide ultimate sensitivity at the single-molecule level. This sensitivity is, however, associated with a nanometer-sized confined hotspot, and molecular transport toward the sensor relies on inefficient diffusion. Here, we combine a plasmonic nanoantenna with a solid-state nanopore and demonstrate that single...
journal article 2018
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Yang, W.W.W. (author), Restrepo Perez, L. (author), Bengtson, M.L. (author), Heerema, S.J. (author), Birnie, A.T.F. (author), van der Torre, J. (author), Dekker, C. (author)
Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the...
journal article 2018
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Ordu, O. (author), Kremser, Leopold (author), Lusser, Alexandra (author), Dekker, N.H. (author)
Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of...
journal article 2018
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Heerema, S.J. (author), Vicarelli, L. (author), Pud, S. (author), Schouten, R.N. (author), Zandbergen, H.W. (author), Dekker, C. (author)
Many theoretical studies predict that DNA sequencing should be feasible by monitoring the transverse current through a graphene nanoribbon while a DNA molecule translocates through a nanopore in that ribbon. Such a readout would benefit from the special transport properties of graphene, provide ultimate spatial resolution because of the single...
journal article 2018
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Ananth, A.N. (author), Mishra, Ankur (author), Frey, Steffen (author), Dwarkasing, A. (author), Versloot, Roderick (author), van der Giessen, Erik (author), Görlich, Dirk (author), Onck, Patrick (author), Dekker, C. (author)
Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through...
journal article 2018
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van Driel, B.A. (author), van den Berg, K. J. (author), Smout, M. (author), Dekker, N. (author), Kooyman, P.J. (author), Dik, J. (author)
This study reports on the effect of artists’ paint formulation on degradation rates of TiO2-based oil paints. Titanium white oil paint exists in a multitude of different recipes, and the effect of the formulation on photocatalytic binder<br/>degradation kinetics is unknown. These formulations contain, among others, one or both titanium dioxide...
journal article 2018
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Quiros Solano, W.F. (author), Gaio, N. (author), Stassen, O.M.J.A. (author), Arik, Y.B. (author), Silvestri, C. (author), Van Engeland, N.C.A. (author), Van der Meer, A. (author), Passier, R. (author), Sahlgren, C.M. (author), Bouten, C.V.C. (author), van den Berg, A. (author), Dekker, R. (author), Sarro, P.M. (author)
We present a novel and highly reproducible process to fabricate transferable porous PDMS membranes for PDMS-based Organs-on-Chips (OOCs) using microelectromechanical systems (MEMS) fabrication technologies. Porous PDMS membranes with pore sizes down to 2.0 μm in diameter and a wide porosity range (2–65%) can be fabricated. To overcome issues...
journal article 2018
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Chorus, C.G. (author), Dekker, Thijs (author)
This paper is the first to develop a measure of consumer surplus for the Random Regret Minimisation (RRM) model. Following a not so well-known approach proposed two decades ago, we measure (changes in) consumer surplus by studying (changes in) observed behaviour, i.e. the choice probability, in response to price (changes). We interpret the...
journal article 2018
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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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