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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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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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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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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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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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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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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)
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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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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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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Jansen, A.J. (author), Dekker, M.C. (author), van der Steen, Diederik (author)
Providing athletes with real-time feedback on their performance is becoming common in many sports, also in speed skating. This research-by-design project aims at finding a tool that allows the speed skater to get real-time feedback on his performance. Speed skaters often mention a so-called “good feeling” when skating behind a better skater. It...
conference paper 2018
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Eeftens, J.M. (author), Dekker, C. (author)
Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here, we review the...
review 2017
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Berghuis, B.A. (author), Raducanu, Vlad-Stefan (author), Elshenawy, Mohamed M. (author), Jergic, S (author), Depken, S.M. (author), Dixon, NE (author), Hamdan, Samir M. (author), Dekker, N.H. (author)
Synchronizing the convergence of the two-oppositely moving DNA replication machineries at specific termination sites is a tightly coordinated process in bacteria. In Escherichia coli, a “replication fork trap” – found within a chromosomal region where forks are allowed to enter but not leave – is set by the protein–DNA roadblock Tus–Ter. The...
journal article 2017
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Terakawa, Tsuyoshi (author), Bisht, Shveta (author), Eeftens, J.M. (author), Dekker, C. (author), Haering, Christian H. (author), Greene, Eric C. (author)
Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. We used single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of adenosine triphosphate hydrolysis–dependent translocation along double-stranded DNA....
journal article 2017
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Restrepo Perez, L. (author), John, Shalini (author), Aksimentiev, Aleksei (author), Joo, C. (author), Dekker, C. (author)
Using nanopores for single-molecule sequencing of proteins – similar to nanopore-based sequencing of DNA – faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule...
journal article 2017
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Kabiri, Y. (author), Ananth, A.N. (author), van der Torre, J. (author), Katan, A.J. (author), Hong, Jin Yong (author), Malladi, S.R.K. (author), Kong, Jing (author), Zandbergen, H.W. (author), Dekker, C. (author)
While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported...
journal article 2017
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