Searched for: author:"Dekker, C."
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Deshpande, S.R. (author), Brandenburg, Frank (author), Lau, A.W.H.R. (author), Last, M.G.F. (author), Spoelstra, W.K. (author), Reese, L. (author), Wunnava, Sreekar (author), Dogterom, A.M. (author), Dekker, C. (author)
Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell biology, as it forms numerous membraneless organelles in cells. Coacervates play an indispensable role in regulating intracellular biochemistry, and their dysfunction is associated with several diseases. Understanding of the LLPS dynamics would...
journal article 2019
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Al Nahas, K. (author), Cama, J. (author), Schaich, M. (author), Hammond, K. (author), Deshpande, S.R. (author), Dekker, C. (author), Ryadnov, M. G. (author), Keyser, UF (author)
The spread of bacterial resistance against conventional antibiotics generates a great need for the discovery of novel antimicrobials. Polypeptide antibiotics constitute a promising class of antimicrobial agents that favour attack on bacterial membranes. However, efficient measurement platforms for evaluating their mechanisms of action in a...
journal article 2019
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Kabiri, Y. (author), Ravelli, Raimond B.G. (author), Lehnert, Tibor (author), Qi, Haoyuan (author), Katan, A.J. (author), Roest, Natascha (author), Kaiser, Ute (author), Dekker, C. (author), Peters, Peter J. (author), Zandbergen, H.W. (author)
Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form...
journal article 2019
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Zhao, Shidi (author), Restrepo Perez, L. (author), Soskine, Misha (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author), Aksimentiev, A. (author)
Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations....
journal article 2019
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Kabiri, Y. (author), Angelin, Alessandro (author), Ahmed, Ishtiaq (author), Mutlu, Hatice (author), Bauer, Jens (author), Niemeyer, Christof M. (author), Zandbergen, H.W. (author), Dekker, C. (author)
Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR...
journal article 2019
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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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Wiktor, J.M. (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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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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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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Caneva, S.L. (author), Gehring, P. (author), Suárez, Víctor García (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)
. Consistent with the principles of subwavelength optics, the wave nature of...
journal article 2018
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Deshpande, S.R. (author), Spoelstra, W.K. (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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Restrepo Perez, L. (author), Joo, C. (author), Dekker, C. (author)
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example,...
review 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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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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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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Spoelstra, W.K. (author), Deshpande, S.R. (author), Dekker, C. (author)
Recently, the bottom-up assembly of a synthetic cell has emerged as a daring novel approach that can be expected to have major impact in generating fundamental insight in the organization and function of actual biological cells, as well as in stimulating a broad range of applications from drug delivery systems to chemical nanofactories. A...
review 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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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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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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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
Searched for: author:"Dekker, C."
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