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A nanophysics approach to synthetic cell division

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Publications

Mapping out Min protein patterns in fully confined fluidic chambers

Author(s): Yaron Caspi, Cees Dekker
Published in: eLife, Issue 5, 2016, ISSN 2050-084X
DOI: 10.7554/eLife.19271

Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points

Author(s): Yael Nechemia-Arbely, Daniele Fachinetti, Karen H. Miga, Nikolina Sekulic, Gautam V. Soni, Dong Hyun Kim, Adeline K. Wong, Ah Young Lee, Kristen Nguyen, Cees Dekker, Bing Ren, Ben E. Black, Don W. Cleveland
Published in: The Journal of Cell Biology, Issue 216/3, 2017, Page(s) 607-621, ISSN 0021-9525
DOI: 10.1083/jcb.201608083

Bacterial Predator-prey dynamics in microscale patchy landscapes

Author(s): F.J.H. Hol, O. Rotem, E. Jurkevitch, C. Dekker, D.A. Koster
Published in: Proceedings of the Royal Society B, Issue 283, 2016, Page(s) 20152154, ISSN 0962-8452
DOI: 10.1098/rspb.2015.2154

Multistability and dynamic transitions of intracellular Min protein patterns

Author(s): Reiter, Matthias; Halatek, Jacob; Frey, Erwin; Wu, Fabai; Dekker, Cees; Kingma, Enzo
Published in: Molecular Systems Biology, Issue 1, 2016, ISSN 1744-4292
DOI: 10.15252/msb.20156724

Intercalation-based single-molecule fluorescence assay to study DNA supercoil dynamics

Author(s): M. Ganji, S. H. Kim, J. van der Torre, E. Abbondanzieri, C. Dekker
Published in: Nano Letters, Issue 16, 2016, Page(s) 4699, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.6b02213

Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic

Author(s): Allard J. Katan; Markus Hassler; Essam M. Dief; Jorine M. Eeftens; Liza de Wilde; Marc Kschonsak; Cees Dekker; Christian H. Haering
Published in: Cell Reports, Issue 1, 2016, ISSN 2211-1247
DOI: 10.1016/j.celrep.2016.01.063

Nanofabricated structures and microfluidic devices for bacteria: from techniques to biology

Author(s): F. Wu, C. Dekker
Published in: Chemical Society Reviews, Issue 45, 2016, Page(s) 268-280, ISSN 0306-0012
DOI: 10.1039/c5cs00514k

Direct observation of DNA knots using a solid-state nanopore

Author(s): Calin Plesa, Daniel Verschueren, Sergii Pud, Jaco van der Torre, Justus W. Ruitenberg, Menno J. Witteveen, Magnus P. Jonsson, Alexander Y. Grosberg, Yitzhak Rabin, Cees Dekker
Published in: Nature Nanotechnology, Issue 11, 2016, Page(s) 1093-1097, ISSN 1748-3387
DOI: 10.1038/nnano.2016.153

CRISPR-mediated control of the bacterial initiation of replication

Author(s): Jakub Wiktor, Christian Lesterlin, David J. Sherratt, Cees Dekker
Published in: Nucleic Acids Research, Issue 44/8, 2016, Page(s) 3801-3810, ISSN 0305-1048
DOI: 10.1093/nar/gkw214

Graphene nanodevices for DNA sequencing

Author(s): Stephanie J. Heerema, Cees Dekker
Published in: Nature Nanotechnology, Issue 11/2, 2016, Page(s) 127-136, ISSN 1748-3387
DOI: 10.1038/nnano.2015.307

Mechanical Trapping of DNA in a Double-Nanopore System

Author(s): Sergii Pud, Shu-Han Chao, Maxim Belkin, Daniel Verschueren, Teun Huijben, Casper van Engelenburg, Cees Dekker, and Aleksei Aksimentiev
Published in: Nano Letters, Issue 16, 2016, Page(s) 8021-8028, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.6b04642

The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes

Author(s): R. Vlijm, S. H. Kim, P. L. De Zwart, Y. Dalal, C. Dekker
Published in: Nanoscale, Issue 9/5, 2017, Page(s) 1862-1870, ISSN 2040-3364
DOI: 10.1039/C6NR06245H

Comparing the Assembly and Handedness Dynamics of (H3.3-H4)2 Tetrasomes to Canonical Tetrasomes

Author(s): Orkide Ordu; Alexandra Lusser; Dekker, Nynke H.; Mina Lee; Rifka Vlijm; Cees Dekker; Anastasiya Boltengagen
Published in: PLoS ONE, Vol 10, Iss 10, p e0141267 (2015), Issue 1, 2015, ISSN 1932-6203
DOI: 10.1371/journal.pone.0141267

Self-aligned plasmonic nanopores by optically controlled dielectric breakdown

Author(s): S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M.P. Jonsson,C. Dekker
Published in: Nano Letters, Issue 15, 2015, Page(s) 7112-7, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.5b03239

Octanol-assisted liposome assembly on chip

Author(s): Siddharth Deshpande, Yaron Caspi, Anna E. C. Meijering, Cees Dekker
Published in: Nature Communications, Issue 7, 2016, Page(s) 10447, ISSN 2041-1723
DOI: 10.1038/ncomms10447

CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly

Author(s): Dalal, Yamini; Dekker, Cees; Vlijm, Rifka; Kim, Sung Hyun; van der Torre, Jaco
Published in: PLoS ONE, Issue 1, 2016, ISSN 1932-6203
DOI: 10.1371/journal.pone.0165078

Tailoring the appearance: what will synthetic cells look like?

Author(s): Willem Kasper Spoelstra, Siddharth Deshpande, Cees Dekker
Published in: Current Opinion in Biotechnology, Issue 51, 2018, Page(s) 47-56, ISSN 0958-1669
DOI: 10.1016/j.copbio.2017.11.005

Through-membrane electron-beam lithography for ultrathin membrane applications

Author(s): M. Neklyudova, A. K. Erdamar, L. Vicarelli, S. J. Heerema, T. Rehfeldt, G. Pandraud, Z. Kolahdouz, C. Dekker, H. W. Zandbergen
Published in: Applied Physics Letters, Issue 111/6, 2017, Page(s) 063105, ISSN 0003-6951
DOI: 10.1063/1.4986991

Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics

Author(s): Adithya N Ananth, Ankur Mishra, Steffen Frey, Arvind Dwarkasing, Roderick Versloot, Erik van der Giessen, Dirk Görlich, Patrick Onck, Cees Dekker
Published in: eLife, Issue 7, 2018, ISSN 2050-084X
DOI: 10.7554/eLife.31510

On-chip density-based purification of liposomes

Author(s): Siddharth Deshpande, Anthony Birnie, Cees Dekker
Published in: Biomicrofluidics, Issue 11/3, 2017, Page(s) 034106, ISSN 1932-1058
DOI: 10.1063/1.4983174

SDS-assisted protein transport through solid-state nanopores

Author(s): Laura Restrepo-Pérez, Shalini John, Aleksei Aksimentiev, Chirlmin Joo, Cees Dekker
Published in: Nanoscale, Issue 9/32, 2017, Page(s) 11685-11693, ISSN 2040-3364
DOI: 10.1039/c7nr02450a

Bacteria‐in‐paper, a versatile platform to study bacterial ecology

Author(s): Felix J. H. Hol, George M. Whitesides, Cees Dekker
Published in: Ecology Letters, 2019, ISSN 1461-023X
DOI: 10.1111/ele.13274

Distinct Roles for Condensin’s Two ATPase Sites in Chromosome Condensation

Author(s): Ahmed M.O. Elbatsh, Eugene Kim, Jorine M. Eeftens, Jonne A. Raaijmakers, Robin H. van der Weide, Alberto García-Nieto, Sol Bravo, Mahipal Ganji, Jelmi uit de Bos, Hans Teunissen, René H. Medema, Elzo de Wit, Christian H. Haering, Cees Dekker, Benjamin D. Rowland
Published in: Molecular Cell, Issue 76/5, 2019, Page(s) 724-737.e5, ISSN 1097-2765
DOI: 10.1016/j.molcel.2019.09.020

Real-time imaging of DNA loop extrusion by condensin

Author(s): Mahipal Ganji, Indra A. Shaltiel, Shveta Bisht, Eugene Kim, Ana Kalichava, Christian H. Haering, Cees Dekker
Published in: Science, Issue 360/6384, 2018, Page(s) 102-105, ISSN 0036-8075
DOI: 10.1126/science.aar7831

Membrane Tension–Mediated Growth of Liposomes


Published in: ISSN 1613-6810
DOI: 10.1002/smll.201902898

An Integrated Microfluidic Platform for Quantifying Drug Permeation across Biomimetic Vesicle Membranes

Author(s): Michael Schaich, Jehangir Cama, Kareem Al Nahas, Diana Sobota, Hannah Sleath, Kevin Jahnke, Siddharth Deshpande, Cees Dekker, Ulrich F. Keyser
Published in: Molecular Pharmaceutics, Issue 16/6, 2019, Page(s) 2494-2501, ISSN 1543-8384
DOI: 10.1021/acs.molpharmaceut.9b00086

Shape and Size Control of Artificial Cells for Bottom-Up Biology

Author(s): Federico Fanalista, Anthony Birnie, Renu Maan, Federica Burla, Kevin Charles, Grzegorz Pawlik, Siddharth Deshpande, Gijsje H. Koenderink, Marileen Dogterom, Cees Dekker
Published in: ACS Nano, Issue 13/5, 2019, Page(s) 5439-5450, ISSN 1936-0851
DOI: 10.1021/acsnano.9b00220

Visualization of unstained DNA nanostructures with advanced in-focus phase contrast TEM techniques

Author(s): Yoones Kabiri, Raimond B. G. Ravelli, Tibor Lehnert, Haoyuan Qi, Allard J. Katan, Natascha Roest, Ute Kaiser, Cees Dekker, Peter J. Peters, Henny Zandbergen
Published in: Scientific Reports, Issue 9/1, 2019, ISSN 2045-2322
DOI: 10.1038/s41598-019-43687-5

On-chip microfluidic production of cell-sized liposomes

Author(s): Siddharth Deshpande, Cees Dekker
Published in: Nature Protocols, Issue 13/5, 2018, Page(s) 856-874, ISSN 1754-2189
DOI: 10.1038/nprot.2017.160

Reversible Immobilization of Proteins in Sensors and Solid-State Nanopores


Published in: ISSN 1613-6810
DOI: 10.1002/smll.201703357

Movement dynamics of divisome proteins and PBP2x:FtsW in cells of Streptococcus pneumoniae

Author(s): Amilcar J. Perez, Yann Cesbron, Sidney L. Shaw, Jesus Bazan Villicana, Ho-Ching T. Tsui, Michael J. Boersma, Ziyun A. Ye, Yanina Tovpeko, Cees Dekker, Seamus Holden, Malcolm E. Winkler
Published in: Proceedings of the National Academy of Sciences, Issue 116/8, 2019, Page(s) 3211-3220, ISSN 0027-8424
DOI: 10.1073/pnas.1816018116

Direct imaging of the circular chromosome in a live bacterium

Author(s): Fabai Wu, Aleksandre Japaridze, Xuan Zheng, Jakub Wiktor, Jacob W. J. Kerssemakers, Cees Dekker
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-10221-0

The condensin complex is a mechanochemical motor that translocates along DNA

Author(s): Tsuyoshi Terakawa, Shveta Bisht, Jorine M. Eeftens, Cees Dekker, Christian H. Haering, Eric C. Greene
Published in: Science, Issue 358/6363, 2017, Page(s) 672-676, ISSN 0036-8075
DOI: 10.1126/science.aan6516

Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores

Author(s): Wayne Yang, Laura Restrepo-Pérez, Michel Bengtson, Stephanie J. Heerema, Anthony Birnie, Jaco van der Torre, Cees Dekker
Published in: Nano Letters, Issue 18/10, 2018, Page(s) 6469-6474, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.8b02968

Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate

Author(s): Shidi Zhao, Laura Restrepo-Pérez, Misha Soskine, Giovanni Maglia, Chirlmin Joo, Cees Dekker, Aleksei Aksimentiev
Published in: ACS Nano, 2019, ISSN 1936-0851
DOI: 10.1021/acsnano.8b09266

Synthetic life on a chip

Author(s): Siddharth Deshpande, Cees Dekker
Published in: Emerging Topics in Life Sciences, Issue 3/5, 2019, Page(s) 559-566, ISSN 2397-8554
DOI: 10.1042/etls20190097

Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division

Author(s): Alexandre W. Bisson-Filho, Yen-Pang Hsu, Georgia R. Squyres, Erkin Kuru, Fabai Wu, Calum Jukes, Yingjie Sun, Cees Dekker, Seamus Holden, Michael S. VanNieuwenhze, Yves V. Brun, Ethan C. Garner
Published in: Science, Issue 355/6326, 2017, Page(s) 739-743, ISSN 0036-8075
DOI: 10.1126/science.aak9973

Spatiotemporal control of coacervate formation within liposomes

Author(s): Siddharth Deshpande, Frank Brandenburg, Anson Lau, Mart G. F. Last, Willem Kasper Spoelstra, Louis Reese, Sreekar Wunnava, Marileen Dogterom, Cees Dekker
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-09855-x

Label-Free Detection of Post-translational Modifications with a Nanopore

Author(s): Laura Restrepo-Pérez, Chun Heung Wong, Giovanni Maglia, Cees Dekker, Chirlmin Joo
Published in: Nano Letters, Issue 19/11, 2019, Page(s) 7957-7964, ISSN 1530-6984
DOI: 10.1021/acs.nanolett.9b03134

Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques


Published in: ISSN 1613-6810
DOI: 10.1002/smll.201700876

Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery

Author(s): Yaron Caspi, Cees Dekker
Published in: Frontiers in Microbiology, Issue 9, 2018, ISSN 1664-302X
DOI: 10.3389/fmicb.2018.00174

DNA sequence encodes the position of DNA supercoils

Author(s): Sung Hyun Kim, Mahipal Ganji, Eugene Kim, Jaco van der Torre, Elio Abbondanzieri, Cees Dekker
Published in: eLife, Issue 7, 2018, ISSN 2050-084X
DOI: 10.7554/elife.36557

FtsZ-Induced Shape Transformation of Coacervates

Author(s): Federico Fanalista, Siddharth Deshpande, Anson Lau, Grzegorz Pawlik, Cees Dekker
Published in: Advanced Biosystems, Issue 2/9, 2018, Page(s) 1800136, ISSN 2366-7478
DOI: 10.1002/adbi.201800136

Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

Author(s): Laura Restrepo-Pérez, Gang Huang, Peggy R. Bohländer, Nathalie Worp, Rienk Eelkema, Giovanni Maglia, Chirlmin Joo, Cees Dekker
Published in: ACS Nano, Issue 13/12, 2019, Page(s) 13668-13676, ISSN 1936-0851
DOI: 10.1021/acsnano.9b05156

Mechanical Division of Cell-Sized Liposomes

Author(s): Siddharth Deshpande, Willem Kasper Spoelstra, Marleen van Doorn, Jacob Kerssemakers, Cees Dekker
Published in: ACS Nano, Issue 12/3, 2018, Page(s) 2560-2568, ISSN 1936-0851
DOI: 10.1021/acsnano.7b08411

A microfluidic platform for the characterisation of membrane active antimicrobials

Author(s): K. Al Nahas, J. Cama, M. Schaich, K. Hammond, S. Deshpande, C. Dekker, M. G. Ryadnov, U. F. Keyser
Published in: Lab on a Chip, Issue 19/5, 2019, Page(s) 837-844, ISSN 1473-0197
DOI: 10.1039/c8lc00932e

Paving the way to single-molecule protein sequencing

Author(s): Laura Restrepo-Pérez, Chirlmin Joo, Cees Dekker
Published in: Nature Nanotechnology, Issue 13/9, 2018, Page(s) 786-796, ISSN 1748-3387
DOI: 10.1038/s41565-018-0236-6

Intercalating Electron Dyes for TEM Visualization of DNA at the Single‐Molecule Level


Published in: ISSN 1439-4227
DOI: 10.1002/cbic.201800638

Real‐time detection of condensin‐driven DNA compaction reveals a multistep binding mechanism

Author(s): Jorine M Eeftens, Shveta Bisht, Jacob Kerssemakers, Marc Kschonsak, Christian H Haering, Cees Dekker
Published in: The EMBO Journal, Issue 36/23, 2017, Page(s) 3448-3457, ISSN 0261-4189
DOI: 10.15252/embj.201797596

Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores


Published in: ISSN 2366-9608
DOI: 10.1002/smtd.201800465

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

Author(s): Philip Ketterer, Adithya N. Ananth, Diederik S. Laman Trip, Ankur Mishra, Eva Bertosin, Mahipal Ganji, Jaco van der Torre, Patrick Onck, Hendrik Dietz, Cees Dekker
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-03313-w

Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Author(s): Fabai Wu, Pinaki Swain, Louis Kuijpers, Xuan Zheng, Kevin Felter, Margot Guurink, Jacopo Solari, Suckjoon Jun, Thomas S. Shimizu, Debasish Chaudhuri, Bela Mulder, Cees Dekker
Published in: Current Biology, Issue 29/13, 2019, Page(s) 2131-2144.e4, ISSN 0960-9822
DOI: 10.1016/j.cub.2019.05.015