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CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion

Davidson, Iain F. (author), Barth, R. (author), Zaczek, Maciej (author), van der Torre, J. (author), Tang, Wen (author), Nagasaka, Kota (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Wutz, Gordana (author), Dekker, C. (author), Peters, Jan Michael (author)

In eukaryotes, genomic DNA is extruded into loops by cohesin¹. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)^2,3 that have important roles in gene regulation and recombination during development and disease^1,4–7. How CTCF...

journal article 2023

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Single-Molecule Structure and Topology of Kinetoplast DNA Networks

He, P. (author), Katan, A.J. (author), Tubiana, Luca (author), Dekker, C. (author), Michieletto, Davide (author)

Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked DNA minicircles found in certain parasites called trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here, we...

journal article 2023

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Correction: Aeropropulsive Performance Modelling of Over-The-Wing Propulsion at Incidence

Dekker, H.N.J. (author), Tuinstra, Marthijn (author), Baars, W.J. (author), Scarano, F. (author), Ragni, D. (author)

conference paper 2023

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Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells

Yang, Sora (author), Klughammer, N. (author), Barth, A. (author), Tanenbaum, M. (author), Dekker, C. (author)

Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic...

journal article 2023

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Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

Kolbeck, Pauline J. (author), Tišma, M. (author), Analikwu, B.T. (author), Vanderlinden, Willem (author), Dekker, C. (author), Lipfert, Jan (author)

DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and...

journal article 2023

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Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation

Ramirez Montero, D.F. (author), Sanchez González, H. (author), van Veen, E.N.W. (author), van Laar, T. (author), Solano Hermosilla, B.P. (author), Diffley, John F.X. (author), Dekker, N.H. (author)

The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that...

journal article 2023

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Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Roslon, I.E. (author), Japaridze, A. (author), Rodenhuis, Stef (author), Hamoen, Lieke (author), Ghatkesar, M.K. (author), Steeneken, P.G. (author), Dekker, C. (author), Alijani, F. (author)

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The...

journal article 2023

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De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features

Ramirez Montero, D.F. (author), Liu, Z. (author), Dekker, N.H. (author)

DNA constructs for single-molecule experiments often require specific sequences and/or extrahelical/noncanonical structures to study DNA-processing mechanisms. The precise introduction of such structures requires extensive control of the sequence of the initial DNA substrate. A commonly used substrate in the synthesis of DNA constructs is...

journal article 2023

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Identifying energy model fingerprints in mitigation scenarios

Dekker, Mark M. (author), Daioglou, Vassilis (author), Pietzcker, Robert (author), Rodrigues, Renato (author), de Boer, Harmen Sytze (author), Dalla Longa, Francesco (author), Drouet, Laurent (author), Emmerling, Johannes (author), Fattahi, Amir (author), Fotiou, Theofano (author), Fragkos, Panagiotis (author), Fricko, Oliver (author), Gusheva, E. (author), Harmsen, Mathijs (author), Huppmann, Daniel (author), Kannavou, Maria (author), Krey, Volker (author), Lombardi, F. (author), Luderer, Gunnar (author), Pfenninger, Stefan (author), Tsiropoulos, Ioannis (author), Zakeri, Behnam (author), van der Zwaan, Bob (author), Usher, Will (author), van Vuuren, Detlef (author)

Energy models are used to study emissions mitigation pathways, such as those compatible with the Paris Agreement goals. These models vary in structure, objectives, parameterization and level of detail, yielding differences in the computed energy and climate policy scenarios. To study model differences, diagnostic indicators are common practice...

journal article 2023

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Electrostatic control of the proximity effect in the bulk of semiconductor-superconductor hybrids

van Loo, N. (author), Mazur, G.P. (author), Dvir, T. (author), Wang, Guanzhong (author), Dekker, R.C. (author), Lemang, M.F. (author), Sfiligoj, C. (author), Bordin, A. (author), van Driel, D. (author), Kouwenhoven, Leo P. (author)

The proximity effect in semiconductor-superconductor nanowires is expected to generate an induced gap in the semiconductor. The magnitude of this induced gap, together with the semiconductor properties like spin-orbit coupling and g-factor, depends on the coupling between the materials. It is predicted that this coupling can be adjusted...

journal article 2023

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Detection of phosphorylation post-translational modifications along single peptides with nanopores

Nova, I.C. (author), Ritmejeris, J. (author), Brinkerhoff, H.D. (author), Koenig, T.J.R. (author), Gundlach, Jens H. (author), Dekker, C. (author)

Current methods to detect post-translational modifications of proteins, such as phosphate groups, cannot measure single molecules or differentiate between closely spaced phosphorylation sites. We detect post-translational modifications at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants by...

journal article 2023

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Three-dimensional localization microscopy with increased axial precision through TIRF angle modulation

Fan, D. (author), Cnossen, J.P. (author), Hung, S. (author), Kromm, D. (author), Dekker, N.H. (author), Verbiest, G.J. (author), Smith, C.S. (author)

To better understand the interactions between biological molecules, a high optical resolution in all three dimensions is crucial. The intrinsically lower axial resolution of microscopes however, is a limiting factor in fluorescence imaging, correspondingly in fluorescence based single molecule localization microscopy (SMLM). Here, we present...

journal article 2023

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Looping the Genome with SMC Complexes

Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)

SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...

review 2023

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Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical Nanopores

Klughammer, N. (author), Barth, A. (author), Dekker, Maurice (author), Fragasso, A. (author), Onck, Patrick R. (author)

The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single...

journal article 2023

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Dynamin A as a one-component division machinery for synthetic cells

De Franceschi, N. (author), Barth, R. (author), Meindlhumer, S. (author), Fragasso, A. (author), Dekker, C. (author)

Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division...

journal article 2023

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Unsteady flow behaviour of multi-rotors in ground proximity

Dekker, H.N.J. (author), Baars, W.J. (author), Scarano, F. (author), Tuinstra, Marthijn (author), Ragni, D. (author)

The unsteady flow behaviour of two side-by-side rotors in ground proximity is experimentally investigated. The rotors induce a velocity distribution interacting with the ground causing the radial expansion of the rotor wakes. In between the rotors, an interaction of the two wakes takes place, resulting in an upward flow similar to a fountain....

journal article 2023

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DAIS: The Delft Database of EEG Recordings of Dutch Articulated and Imagined Speech

Dekker, Bo (author), Schouten, A.C. (author), Scharenborg, O.E. (author)

Silent speech interfaces could enable people who lost the ability to use their voice or gestures to communicate with the external world, e.g., through decoding the person’s brain signals when imagining speech. Only a few and small databases exist that allow for the development and training of brain computer interfaces (BCIs) that can decode...

conference paper 2023

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Partial and complete replanning of an intermodal logistic system under disruptions

Akyüz, M. Hakan (author), Dekker, Rommert (author), Sharif Azadeh, S. (author)

The exclusive and excessive use of long-distance road transportation is not suitable way to reduce the negative environmental impacts of logistics systems. Intermodal transport, combining road with other transport modes, has the potential to reduce both operating costs and carbon footprints. One of the reasons for the low share of intermodal...

journal article 2023

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Directing Min protein patterns with advective bulk flow

Meindlhumer, S. (author), Brauns, Fridtjof (author), Finžgar, Jernej Rudi (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)

The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD...

journal article 2023

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A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint

Sanchez González, H. (author), Liu, Z. (author), van Veen, E.N.W. (author), van Laar, T. (author), Diffley, John F.X. (author), Dekker, N.H. (author)

Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin...

journal article 2023