Bottom up biophysics approach to resolve the looping structure of chromosomes

Project Information

LoopingDNA

Grant agreement ID: 883684

DOI 10.3030/883684

EC signature date 12 May 2020

Start date 1 July 2020

End date 30 June 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 500 000,00

EU contribution € 2 500 000,00

Coordinated by

TECHNISCHE UNIVERSITEIT DELFT
Netherlands

Publications

Peer reviewed articles (34)

Bulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro

Author(s): F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, E. Frey, C. Dekker
Published in: Nature Comm. 12, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23412-5

Palladium Zero-Mode Waveguides for Optical Single Molecule Detection with Nanopores

Author(s): Klughammer, Nils; Dekker, Cees
Published in: Nanotechnology 32, Issue 2, 2021, ISSN 0957-4484
Publisher: Institute of Physics Publishing
DOI: 10.48550/arxiv.2010.00276

High-resolution imaging of bacterial spatial organization with Vertical Cell Imaging by Nanostructured Immobilisation

Author(s): K.D. Whitley, S. Middlemiss, C. Jukes, C. Dekker, S. Holden
Published in: Nature Protocols 17, 2022, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-021-00668-1

Studying Phase Separation in Confinement

Author(s): S. Deshpande, C. Dekker
Published in: Curr. Opin. Colloid Interface Sci. 52, 2021, ISSN 1359-0294
Publisher: Pergamon Press
DOI: 10.1016/j.cocis.2021.101419

Quantitative analysis of surface wave patterns of Min proteins

Author(s): S. Meindlhumer, J. Kerssemakers, C. Dekker
Published in: Frontiers in Physics, 2022, ISSN 2296-424X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphy.2022.930811

Reconstitution of Ultrawide DNA Origami Pores in Liposomes for Transmembrane Transport of Macromolecules.

Author(s): Alessio Fragasso; Nicola De Franceschi; P. Stoemmer; E. O. Van der Sluis; Hendrik Dietz; Cees Dekker
Published in: ACS Nano (online), 15(8), Issue 5, 2021, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.1c01669

Bridging scales in a multiscale pattern-forming system

Author(s): L. Würthner, F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, C. Dekker, E. Frey
Published in: PNAS 119, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2206888119

SMC complexes can traverse physical roadblocks bigger than their ring size

Author(s): B. Pradhan, R. Barth, E. Kim, I.F. Davidson, B. Bauer, T. van Laar, W. Yang, J.-K. Ryu, J. van der Torre, J.-M. Peters, C. Dekker
Published in: Cell Reports 41, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111491

DNA sequence-directed cooperation between nucleoid-associated proteins

Author(s): A. Japaridze, W. Yang, C. Dekker, W. Nasser, G. Muskhelishvili
Published in: iScience 24, 2021, ISSN 1095-9203
Publisher: American Association for the Advancement of Science
DOI: 10.1016/j.isci.2021.102408

Comparing current noise in biological and solid-state nanopores

Author(s): A. Fragasso, S. Schmid, C. Dekker
Published in: ACS Nano 14, 2020, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.9b09353

Nanopores – a Versatile Tool to Study Protein Dynamics

Author(s): S. Schmid, C. Dekker
Published in: Essays in Biochemistry EBC20200020, 2020, ISSN 0006-2960
Publisher: American Chemical Society
DOI: 10.1042/ebc20200020

FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in bacterial cell division

Author(s): K.D. Whitley, C. Jukes, N. Tregidgo, E. Karinou, P. Almada, R. Henriques, C. Dekker, S. Holden
Published in: Nature Comm. 12, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22526-0

Condensin-driven loop extrusion on supercoiled DNA

Author(s): E. Kim, A. Martin Gonzalez, B. Pradhan, J. van der Torre, C. Dekker
Published in: Nature Struct. Molec. Biol. 29, 2022, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-022-00802-x

Multiple re-reading of single proteins at single-amino-acid resolution using nanopores

Author(s): H. Brinkerhoff, A.S.W. Kang, J. Liu, A. Aksimentiev, C. Dekker
Published in: Science 374, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abl4381

Transport receptor occupancy in Nuclear Pore Complex mimics

Author(s): A. Fragasso, H.W. de Vries, J. Andersson, E.O. van der Sluis, E. van der Giessen, P.R. Onck, C. Dekker
Published in: Nano Research, 2022, ISSN 1998-0124
Publisher: Tsinghua Univ Press
DOI: 10.1007/s12274-022-4647-1

CENP-B-mediated DNA loops regulate activity and stability of human centromeres

Author(s): F. Chardon, A. Japaridze, H. Witt, L. Velikovsky, C. Chakraborty, T. Wihelm, M. Dumont, W. Yang, C. Kikuti, S. Gangnard, G. Wuite, C. Dekker, D. Fachinetti
Published in: Molec. Cell 82, 2022, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2022.02.032

Towards a synthetic cell cycle

Author(s): L. Olivi, M. Berger, R.N.P. Creyghton, N. De Franceschi, C. Dekker, B.M. Mulder, N.J. Claassens, P.R. ten Wolde, J. van der Oost
Published in: Nature Comm.12, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24772-8

Probing nanomotion of single bacteria with graphene drums

Author(s): Irek Rosłoń; Peter Steeneken; Aleksandre Japaridze; Cees Dekker; Farbod Alijani
Published in: Nature Nanotechnology 17, Issue 9, 2022, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1101/2021.09.21.461186

pH-controlled coacervate-membrane interactions within liposomes

Author(s): M.G.F. Last, S. Deshpande, C.Dekker
Published in: ACS Nano 14, 2020, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.9b10167

ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment

Author(s): M. Tišma, M. Panoukidou, H. Antar, Y.-M. Soh, R. Barth, B. Pradhan, J. van der Torre, D. Michieletto, S. Gruber, C. Dekker
Published in: Science Advances 8, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abn3299

Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations

Author(s): S. Schmid, P. Stömmer, H. Dietz, C. Dekker
Published in: Nature Nanotechn. 16, 2021, ISSN 1748-3387
Publisher: Nature Publishing Group
DOI: 10.1038/s41565-021-00958-5

Mechanisms for Chromosome Segregation in Bacteria

Author(s): C. Gogou, A. Japaridze, C. Dekker
Published in: Frontiers Microbiol. 12, 2021, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2021.685687

A designer FG-Nup that reconstitutes the selective transport barrier of the Nuclear Pore Complex

Author(s): A. Fragasso, H.W. de Vries, E.O. van der Sluis, E. van der Giessen, P.R. Onck, C. Dekker
Published in: Nature Comm. 12, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22293-y

Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore

Author(s): X. Shi, A.-K. Pumm, J. Isensee, W. Zhao, D. Verschueren, A. Martin-Gonzalez, R. Golestanian, H. Dietz, C. Dekker
Published in: Nature Physics, 2022, ISSN 1745-2473
Publisher: Nature Publishing Group
DOI: 10.1038/s41567-022-01683-z

DNA-loop extruding condensin complexes can traverse one another

Author(s): E. Kim, J. Kerssemakers, I.A. Shaltiel, C.H. Haering, C. Dekker
Published in: Nature 579, 2020, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2067-5

CRISPR-dCas9 based DNA detection scheme for diagnostics in resource limited settings

Author(s): M. Bengtson, M. Bharadwaj, O. Franch, J. van der Torre, V. Meerdink, H. Schallig, C. Dekker
Published in: Nanoscale 14, 2022, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1nr06557b

Simultaneous orientation and 3D localization microscopy with a Vortex point spread function

Author(s): C.N. Hulleman, R.Ø. Thorsen, E. Kim, C. Dekker, S. Stallinga, B. Rieger
Published in: Nature Comm. 12, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26228-5

Bridging-induced phase separation induced by cohesin SMC protein complexes

Author(s): J.‐K. Ryu, C. Bouchoux, H.W. Liu, E. Kim, M. Minamino, R. de Groot, A.J. Katan, A. Bonato, D. Marenduzzo, D. Michieletto, F. Uhlmann, C. Dekker
Published in: Science Advances 7, 2021, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abe5905

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

Author(s): J.-K. Ryu, S.-H. Rah, R. Janissen, J.W.J. Kerssemakers, C. Dekker
Published in: Nucl. Acid Res. 50, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1268

Genome-in-a-Box: Building a Chromosome from the Bottom Up.

Author(s): Anthony Birnie; Cees Dekker
Published in: VOLUME=15;ISSUE=1;ISSN=1936-0851;TITLE=ACS Nano (online), Issue 3, 2020, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.0c07397

Direct observation of independently moving replisomes in Escherichia coli

Author(s): A. Japaridze, C. Gogou, J. W. J. Kerssemakers, H. M. Nguyen, C. Dekker
Published in: Nature Comm. 11, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/733956

The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC

Author(s): A. Blanch Jover, N. De Franceschi, D. Fenel, W. Weissenhorn, C. Dekker
Published in: FEBS Lett. 596, 2022, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.14324

Optimized cDICE for efficient reconstitution of biological systems in giant unilamellar vesicles

Author(s): L. Van de Cauter, F. Fanalista, L. van Buren, N. De Franceschi, E. Godino, S. Bouw, C. Danelon, C. Dekker, G.H. Koenderink, K.A. Ganzinger
Published in: ACS Synth. Biol. 10, 2021, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.1c00068

The condensin holocomplex cycles dynamically between open and collapsed states

Author(s): J.-K Ryu, A.J. Katan, E.O. van der Sluis, T. Wisse, R. de Groot, C. Haering, C. Dekker
Published in: Nature Struct. Molec. Biol. 27, 2020, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-020-0508-3

Monographic books (1)

Single-molecule ionic and optical sensing with nanoapertures

Author(s): W. Yang, C. Dekker
Published in: Book chapter in ' Single Molecule Nanosensors and Nanosystems' (Eds. W. Bowen, R. Gordon, F. Vollmer; Springer book series Nanostructure Science and Technology), 2021, Page(s) 367-387
Publisher: Springer
DOI: 10.1007/978-3-030-90339-8_12