Searched for: author:"Dekker, C."
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Last, M.G.F. (author), Deshpande, S.R. (author), Dekker, C. (author)
Membraneless organelles formed by liquid-liquid phase separation are dynamic structures that are employed by cells to spatiotemporally regulate their interior. Indeed, complex coacervation-based phase separation is involved in a multitude of biological tasks ranging from photosynthesis to cell division to chromatin organization, and more....
journal article 2020
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Smith, Kathleen Beth (author), Wehrli, Monika (author), Japaridze, A. (author), Assenza, Salvatore (author), Dekker, C. (author), Mezzenga, Raffaele (author)
The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by...
journal article 2020
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Fragasso, A. (author), Schmid, S. (author), Dekker, C. (author)
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of...
review 2020
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Japaridze, A. (author), Gogou, Christos (author), Kerssemakers, J.W.J. (author), Nguyen, Huyen My (author), Dekker, C. (author)
The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move...
journal article 2020
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Kim, E. (author), Kerssemakers, J.W.J. (author), Shaltiel, Indra A. (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA<sup>1</sup>. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to...
journal article 2020
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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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Wu, Fabai (author), Japaridze, A. (author), Zheng, X.Z. (author), Wiktor, J.M. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower...
journal article 2019
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Restrepo Perez, L. (author), Huang, Gang (author), Bohländer, Peggy R. (author), Worp, N.M. (author), Eelkema, R. (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author)
While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in...
journal article 2019
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Schaich, Michael (author), Cama, Jehangir (author), Al Nahas, Kareem (author), Sobota, Diana (author), Sleath, Hannah (author), Jahnke, Kevin (author), Deshpande, S.R. (author), Dekker, C. (author), Keyser, Ulrich F. (author)
The low membrane permeability of candidate drug molecules is a major challenge in drug development, and insufficient permeability is one reason for the failure of antibiotic treatment against bacteria. Quantifying drug transport across specific pathways in living systems is challenging because one typically lacks knowledge of the exact...
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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Verschueren, Daniel (author), Shi, X. (author), Dekker, C. (author)
Single-molecule sensing technologies aim to detect and characterize single biomolecules, but generally need labeling while the measurement times and throughput are severely restricted by a lack of positional control over the molecule. Here, a plasmonic nanopore biosensor is reported where single molecules can be electrophoretically delivered...
journal article 2019
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Fanalista, F. (author), Birnie, A.T.F. (author), Maan, R. (author), Burla, Federica (author), Charles, Kevin (author), Pawlik, Grzegorz (author), Deshpande, Siddharth (author), Koenderink, Gijsje H. (author), Dogterom, A.M. (author), Dekker, C. (author)
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is...
journal article 2019
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Zhao, Shidi (author), Restrepo-Pérez, Laura (author), Soskine, Misha (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author), Aksimentiev, Aleksei (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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Elbatsh, Ahmed M.O. (author), Kim, E. (author), Eeftens, Jorine M. (author), Raaijmakers, Jonne A. (author), van der Weide, Robin H. (author), García-Nieto, Alberto (author), Bravo, Sol (author), Ganji, Mahipal (author), Dekker, C. (author)
Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster...
journal article 2019
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Al Nahas, K. (author), Cama, J. (author), Schaich, M. (author), Hammond, K. (author), Deshpande, S. (author), Dekker, C. (author), Ryadnov, M. G. (author), Keyser, U. F. (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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Hol, Felix J.H. (author), Whitesides, George M. (author), Dekker, C. (author)
Habitat spatial structure has a profound influence on bacterial life, yet there currently are no low-cost equipment-free laboratory techniques to reproduce the intricate structure of natural bacterial habitats. Here, we demonstrate the use of paper scaffolds to create landscapes spatially structured at the scales relevant to bacterial ecology...
journal article 2019
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Restrepo Perez, L. (author), Wong, C.H. (author), Maglia, Giovanni (author), Dekker, C. (author), Joo, C. (author)
Post-translational modifications (PTMs) of proteins play key roles in cellular processes. Hence, PTM identification is crucial for elucidating the mechanism of complex cellular processes and disease. Here we present a method for PTM detection at the single-molecule level using FraC biological nanopores. We focus on two major PTMs,...
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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Fragasso, A. (author), Pud, S. (author), Dekker, C. (author)
The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f noise in such nanopores, that, unlike previous reports, accounts for contributions from both the pore-cylinder, pore-surface, and access regions. To...
journal article 2019
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Deshpande, S.R. (author), Wunnava Venkata, S.S. (author), Hueting, D.A. (author), Dekker, C. (author)
Recent years have seen a tremendous interest in the bottom-up reconstitution of minimal biomolecular systems, with the ultimate aim of creating an autonomous synthetic cell. One of the universal features of living systems is cell growth, where the cell membrane expands through the incorporation of newly synthesized lipid molecules. Here, the...
journal article 2019
Searched for: author:"Dekker, C."
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