Bottom up biophysics approach to resolve the looping structure of chromosomes

Project Information

LoopingDNA

Grant agreement ID: 883684

DOI

10.3030/883684

Project closed

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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (54)

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

Author(s): Pauline J Kolbeck, Miloš Tišma, Brian T Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 59-72, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad1055

Cohesin supercoils DNA during loop extrusion

Author(s): Iain F. Davidson, Roman Barth, Kota Nagasaka, Wen Tang, Gordana Wutz, Sabrina Horn, Richard Janissen, Roman R. Stocsits, Emilia Chlosta, Benedikt W. Bauer, Cees Dekker, Jan-Michael Peters
Published in: Cell Reports, Issue 44, 2025, Page(s) 115856, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2025.115856

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

SMC motor proteins extrude DNA asymmetrically and can switch directions

Author(s): Roman Barth, Iain F. Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker
Published in: Cell, Issue 188, 2025, Page(s) 749-763.e21, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2024.12.020

The archaeal Cdv cell division system

Author(s): Alberto Blanch Jover, Cees Dekker
Published in: Trends in Microbiology, Issue 31, 2023, Page(s) 601-615, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2022.12.006

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

Two CTCF motifs impede cohesin-mediated DNA loop extrusion

Author(s): Roman Barth, Richard Janissen, Laura Muras, Jaco van der Torre, Gabriele Litos, Eli van der Sluis, Ashmiani van der Graaf, Iain F. Davidson, Jan-Michael Peters, Cees Dekker
Published in: Molecular Cell, Issue under review, 2025, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1101/2025.01.26.634934

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

Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells

Author(s): Miloš Tišma, Florian Patrick Bock, Jacob Kerssemakers, Hammam Antar, Aleksandre Japaridze, Stephan Gruber, Cees Dekker
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-47094-x

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

Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation

Author(s): Miloš Tišma, Richard Janissen, Hammam Antar, Alejandro Martin-Gonzalez, Roman Barth, Twan Beekman, Jaco van der Torre, Davide Michieletto, Stephan Gruber, Cees Dekker
Published in: Nucleic Acids Research, Issue 51, 2023, Page(s) 11856-11875, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad868

MukBEF-dependent chromosomal organization in widened Escherichia coli

Author(s): Aleksandre Japaridze, Raman van Wee, Christos Gogou, Jacob W. J. Kerssemakers, Daan F. van den Berg, Cees Dekker
Published in: Frontiers in Microbiology, Issue 14, 2023, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2023.1107093

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

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

Author(s): Iain F. Davidson, Roman Barth, Maciej Zaczek, Jaco van der Torre, Wen Tang, Kota Nagasaka, Richard Janissen, Jacob Kerssemakers, Gordana Wutz, Cees Dekker, Jan-Michael Peters
Published in: Nature, Issue 616, 2023, Page(s) 822-827, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-05961-5

A microfluidic platform for extraction and analysis of bacterial genomic DNA

Author(s): Alex Joesaar, Martin Holub, Leander Lutze, Marco Emanuele, Jacob Kerssemakers, Martin Pabst, Cees Dekker
Published in: Lab on a Chip, Issue 25, 2025, Page(s) 1767-1775, ISSN 1473-0197
Publisher: Royal Society of Chemistry
DOI: 10.1039/d4lc00839a

All eukaryotic SMC proteins induce a twist of −0.6 at each DNA loop extrusion step

Author(s): Richard Janissen, Roman Barth, Iain F. Davidson, Jan-Michael Peters, Cees Dekker
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.adt1832

DNA supercoiling enhances DNA condensation by ParB proteins

Author(s): Alejandro Martin-Gonzalez, Miloš Tišma, Brian T Analikwu, Anders Barth, Richard Janissen, Hammam Antar, Gianluca Kemps, Stephan Gruber, Cees Dekker
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 13255-13268, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae936

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

Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments

Author(s): Martin Holub, Anthony Birnie, Aleksandre Japaridze, Jaco van der Torre, Maxime den Ridder, Carol de Ram, Martin Pabst, Cees Dekker
Published in: Cell Reports Methods, Issue 2, 2023, Page(s) 100366, ISSN 2667-2375
Publisher: Elsevier BV
DOI: 10.1016/j.crmeth.2022.100366

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

Looping the Genome with SMC Complexes

Author(s): Eugene Kim, Roman Barth, Cees Dekker
Published in: Annual Review of Biochemistry, Issue 92, 2023, Page(s) 15-41, ISSN 0066-4154
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-biochem-032620-110506

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

Single-molecule visualization of twin-supercoiled domains generated during transcription

Author(s): Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 1677-1687, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad1181

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

How do molecular motors fold the genome?

Author(s): Cees Dekker, Christian H. Haering, Jan-Michael Peters, Benjamin D. Rowland
Published in: Science, Issue 382, 2024, Page(s) 646-648, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.adi8308

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

Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies

Author(s): Miloš Tišma, Jovana Kaljević, Stephan Gruber, Tung B K Le, Cees Dekker
Published in: FEMS Microbiology Reviews, Issue 48, 2024, ISSN 1574-6976
Publisher: Oxford University Press (OUP)
DOI: 10.1093/femsre/fuad067

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

Author(s): Pinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker, Davide Michieletto
Published in: Physical Review X, Issue 13, 2023, ISSN 2160-3308
Publisher: American Physical Society
DOI: 10.1103/physrevx.13.021010

Telomeres stall DNA loop extrusion by condensin

Author(s): Brian T. Analikwu, Alice Deshayes, Jaco van der Torre, Thomas M. Guérin, Allard J. Katan, Claire Béneut, Roman Barth, Jamie Phipps, Vittore Scolari, Xavier Veaute, Didier Busso, Karine Dubrana, Stefano Mattarocci, Cees Dekker, Stéphane Marcand
Published in: Cell Reports, Issue 44, 2025, Page(s) 115900, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2025.115900

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

Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments

Author(s): Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan-Michael Peters, Cees Dekker
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-35359-2

Monographic books (2)

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), Issue 6, 2022, Page(s) pp 367–387
Publisher: Springer

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