Bottom up biophysics approach to resolve the looping structure of chromosomes

Información del proyecto

LoopingDNA

Identificador del acuerdo de subvención: 883684

DOI

10.3030/883684

Proyecto cerrado

Fecha de la firma de la CE 12 Mayo 2020

Fecha de inicio 1 Julio 2020

Fecha de finalización 30 Junio 2025

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 2 500 000,00

Aportación de la UE

€ 2 500 000,00

Coordinado por

TECHNISCHE UNIVERSITEIT DELFT
Netherlands

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (54)

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

Autores: Pauline J Kolbeck, Miloš Tišma, Brian T Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) 59-72, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkad1055

Cohesin supercoils DNA during loop extrusion

Autores: 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
Publicado en: Cell Reports, Edición 44, 2025, Página(s) 115856, ISSN 2211-1247
Editor: 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

Autores: F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, E. Frey, C. Dekker
Publicado en: Nature Comm. 12, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-23412-5

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

Autores: Klughammer, Nils; Dekker, Cees
Publicado en: Nanotechnology 32, Edición 2, 2021, ISSN 0957-4484
Editor: Institute of Physics Publishing
DOI: 10.48550/arxiv.2010.00276

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

Autores: K.D. Whitley, S. Middlemiss, C. Jukes, C. Dekker, S. Holden
Publicado en: Nature Protocols 17, 2022, ISSN 1754-2189
Editor: Nature Publishing Group
DOI: 10.1038/s41596-021-00668-1

Studying Phase Separation in Confinement

Autores: S. Deshpande, C. Dekker
Publicado en: Curr. Opin. Colloid Interface Sci. 52, 2021, ISSN 1359-0294
Editor: Pergamon Press
DOI: 10.1016/j.cocis.2021.101419

Quantitative analysis of surface wave patterns of Min proteins

Autores: S. Meindlhumer, J. Kerssemakers, C. Dekker
Publicado en: Frontiers in Physics, 2022, ISSN 2296-424X
Editor: Frontiers Media S.A.
DOI: 10.3389/fphy.2022.930811

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

Autores: Alessio Fragasso; Nicola De Franceschi; P. Stoemmer; E. O. Van der Sluis; Hendrik Dietz; Cees Dekker
Publicado en: ACS Nano (online), 15(8), Edición 5, 2021, ISSN 1936-0851
Editor: American Chemical Society
DOI: 10.1021/acsnano.1c01669

SMC motor proteins extrude DNA asymmetrically and can switch directions

Autores: Roman Barth, Iain F. Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker
Publicado en: Cell, Edición 188, 2025, Página(s) 749-763.e21, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.cell.2024.12.020

The archaeal Cdv cell division system

Autores: Alberto Blanch Jover, Cees Dekker
Publicado en: Trends in Microbiology, Edición 31, 2023, Página(s) 601-615, ISSN 0966-842X
Editor: Elsevier BV
DOI: 10.1016/j.tim.2022.12.006

Bridging scales in a multiscale pattern-forming system

Autores: L. Würthner, F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, C. Dekker, E. Frey
Publicado en: PNAS 119, 2022, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2206888119

SMC complexes can traverse physical roadblocks bigger than their ring size

Autores: 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
Publicado en: Cell Reports 41, 2022, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2022.111491

DNA sequence-directed cooperation between nucleoid-associated proteins

Autores: A. Japaridze, W. Yang, C. Dekker, W. Nasser, G. Muskhelishvili
Publicado en: iScience 24, 2021, ISSN 1095-9203
Editor: American Association for the Advancement of Science
DOI: 10.1016/j.isci.2021.102408

Comparing current noise in biological and solid-state nanopores

Autores: A. Fragasso, S. Schmid, C. Dekker
Publicado en: ACS Nano 14, 2020, ISSN 1936-0851
Editor: American Chemical Society
DOI: 10.1021/acsnano.9b09353

Nanopores – a Versatile Tool to Study Protein Dynamics

Autores: S. Schmid, C. Dekker
Publicado en: Essays in Biochemistry EBC20200020, 2020, ISSN 0006-2960
Editor: American Chemical Society
DOI: 10.1042/ebc20200020

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

Autores: K.D. Whitley, C. Jukes, N. Tregidgo, E. Karinou, P. Almada, R. Henriques, C. Dekker, S. Holden
Publicado en: Nature Comm. 12, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-22526-0

Two CTCF motifs impede cohesin-mediated DNA loop extrusion

Autores: 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
Publicado en: Molecular Cell, Edición under review, 2025, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1101/2025.01.26.634934

Condensin-driven loop extrusion on supercoiled DNA

Autores: E. Kim, A. Martin Gonzalez, B. Pradhan, J. van der Torre, C. Dekker
Publicado en: Nature Struct. Molec. Biol. 29, 2022, ISSN 1545-9993
Editor: Nature Publishing Group
DOI: 10.1038/s41594-022-00802-x

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

Autores: H. Brinkerhoff, A.S.W. Kang, J. Liu, A. Aksimentiev, C. Dekker
Publicado en: Science 374, 2021, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abl4381

Transport receptor occupancy in Nuclear Pore Complex mimics

Autores: A. Fragasso, H.W. de Vries, J. Andersson, E.O. van der Sluis, E. van der Giessen, P.R. Onck, C. Dekker
Publicado en: Nano Research, 2022, ISSN 1998-0124
Editor: Tsinghua Univ Press
DOI: 10.1007/s12274-022-4647-1

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

Autores: Miloš Tišma, Florian Patrick Bock, Jacob Kerssemakers, Hammam Antar, Aleksandre Japaridze, Stephan Gruber, Cees Dekker
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-024-47094-x

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

Autores: 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
Publicado en: Molec. Cell 82, 2022, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2022.02.032

Towards a synthetic cell cycle

Autores: 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
Publicado en: Nature Comm.12, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-24772-8

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

Autores: Miloš Tišma, Richard Janissen, Hammam Antar, Alejandro Martin-Gonzalez, Roman Barth, Twan Beekman, Jaco van der Torre, Davide Michieletto, Stephan Gruber, Cees Dekker
Publicado en: Nucleic Acids Research, Edición 51, 2023, Página(s) 11856-11875, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkad868

MukBEF-dependent chromosomal organization in widened Escherichia coli

Autores: Aleksandre Japaridze, Raman van Wee, Christos Gogou, Jacob W. J. Kerssemakers, Daan F. van den Berg, Cees Dekker
Publicado en: Frontiers in Microbiology, Edición 14, 2023, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2023.1107093

Probing nanomotion of single bacteria with graphene drums

Autores: Irek Rosłoń; Peter Steeneken; Aleksandre Japaridze; Cees Dekker; Farbod Alijani
Publicado en: Nature Nanotechnology 17, Edición 9, 2022, ISSN 1748-3387
Editor: Nature Publishing Group
DOI: 10.1101/2021.09.21.461186

pH-controlled coacervate-membrane interactions within liposomes

Autores: M.G.F. Last, S. Deshpande, C.Dekker
Publicado en: ACS Nano 14, 2020, ISSN 1936-0851
Editor: American Chemical Society
DOI: 10.1021/acsnano.9b10167

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

Autores: M. Tišma, M. Panoukidou, H. Antar, Y.-M. Soh, R. Barth, B. Pradhan, J. van der Torre, D. Michieletto, S. Gruber, C. Dekker
Publicado en: Science Advances 8, 2022, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abn3299

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

Autores: 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
Publicado en: Nature, Edición 616, 2023, Página(s) 822-827, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-023-05961-5

A microfluidic platform for extraction and analysis of bacterial genomic DNA

Autores: Alex Joesaar, Martin Holub, Leander Lutze, Marco Emanuele, Jacob Kerssemakers, Martin Pabst, Cees Dekker
Publicado en: Lab on a Chip, Edición 25, 2025, Página(s) 1767-1775, ISSN 1473-0197
Editor: Royal Society of Chemistry
DOI: 10.1039/d4lc00839a

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

Autores: Richard Janissen, Roman Barth, Iain F. Davidson, Jan-Michael Peters, Cees Dekker
Publicado en: Science Advances, Edición 10, 2024, ISSN 2375-2548
Editor: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.adt1832

DNA supercoiling enhances DNA condensation by ParB proteins

Autores: Alejandro Martin-Gonzalez, Miloš Tišma, Brian T Analikwu, Anders Barth, Richard Janissen, Hammam Antar, Gianluca Kemps, Stephan Gruber, Cees Dekker
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) 13255-13268, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae936

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

Autores: S. Schmid, P. Stömmer, H. Dietz, C. Dekker
Publicado en: Nature Nanotechn. 16, 2021, ISSN 1748-3387
Editor: Nature Publishing Group
DOI: 10.1038/s41565-021-00958-5

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

Autores: Martin Holub, Anthony Birnie, Aleksandre Japaridze, Jaco van der Torre, Maxime den Ridder, Carol de Ram, Martin Pabst, Cees Dekker
Publicado en: Cell Reports Methods, Edición 2, 2023, Página(s) 100366, ISSN 2667-2375
Editor: Elsevier BV
DOI: 10.1016/j.crmeth.2022.100366

Mechanisms for Chromosome Segregation in Bacteria

Autores: C. Gogou, A. Japaridze, C. Dekker
Publicado en: Frontiers Microbiol. 12, 2021, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2021.685687

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

Autores: A. Fragasso, H.W. de Vries, E.O. van der Sluis, E. van der Giessen, P.R. Onck, C. Dekker
Publicado en: Nature Comm. 12, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-22293-y

Looping the Genome with SMC Complexes

Autores: Eugene Kim, Roman Barth, Cees Dekker
Publicado en: Annual Review of Biochemistry, Edición 92, 2023, Página(s) 15-41, ISSN 0066-4154
Editor: Annual Reviews, Inc.
DOI: 10.1146/annurev-biochem-032620-110506

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

Autores: X. Shi, A.-K. Pumm, J. Isensee, W. Zhao, D. Verschueren, A. Martin-Gonzalez, R. Golestanian, H. Dietz, C. Dekker
Publicado en: Nature Physics, 2022, ISSN 1745-2473
Editor: Nature Publishing Group
DOI: 10.1038/s41567-022-01683-z

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

Autores: Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) 1677-1687, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkad1181

DNA-loop extruding condensin complexes can traverse one another

Autores: E. Kim, J. Kerssemakers, I.A. Shaltiel, C.H. Haering, C. Dekker
Publicado en: Nature 579, 2020, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-020-2067-5

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

Autores: M. Bengtson, M. Bharadwaj, O. Franch, J. van der Torre, V. Meerdink, H. Schallig, C. Dekker
Publicado en: Nanoscale 14, 2022, ISSN 2040-3364
Editor: Royal Society of Chemistry
DOI: 10.1039/d1nr06557b

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

Autores: C.N. Hulleman, R.Ø. Thorsen, E. Kim, C. Dekker, S. Stallinga, B. Rieger
Publicado en: Nature Comm. 12, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-26228-5

Bridging-induced phase separation induced by cohesin SMC protein complexes

Autores: 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
Publicado en: Science Advances 7, 2021, ISSN 2375-2548
Editor: 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

Autores: J.-K. Ryu, S.-H. Rah, R. Janissen, J.W.J. Kerssemakers, C. Dekker
Publicado en: Nucl. Acid Res. 50, 2022, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkab1268

How do molecular motors fold the genome?

Autores: Cees Dekker, Christian H. Haering, Jan-Michael Peters, Benjamin D. Rowland
Publicado en: Science, Edición 382, 2024, Página(s) 646-648, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.adi8308

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

Autores: Anthony Birnie; Cees Dekker
Publicado en: VOLUME=15;ISSUE=1;ISSN=1936-0851;TITLE=ACS Nano (online), Edición 3, 2020, ISSN 1936-0851
Editor: American Chemical Society
DOI: 10.1021/acsnano.0c07397

Direct observation of independently moving replisomes in Escherichia coli

Autores: A. Japaridze, C. Gogou, J. W. J. Kerssemakers, H. M. Nguyen, C. Dekker
Publicado en: Nature Comm. 11, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/733956

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

Autores: Miloš Tišma, Jovana Kaljević, Stephan Gruber, Tung B K Le, Cees Dekker
Publicado en: FEMS Microbiology Reviews, Edición 48, 2024, ISSN 1574-6976
Editor: Oxford University Press (OUP)
DOI: 10.1093/femsre/fuad067

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

Autores: Pinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker, Davide Michieletto
Publicado en: Physical Review X, Edición 13, 2023, ISSN 2160-3308
Editor: American Physical Society
DOI: 10.1103/physrevx.13.021010

Telomeres stall DNA loop extrusion by condensin

Autores: 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
Publicado en: Cell Reports, Edición 44, 2025, Página(s) 115900, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2025.115900

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

Autores: A. Blanch Jover, N. De Franceschi, D. Fenel, W. Weissenhorn, C. Dekker
Publicado en: FEBS Lett. 596, 2022, ISSN 0014-5793
Editor: Elsevier BV
DOI: 10.1002/1873-3468.14324

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

Autores: 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
Publicado en: ACS Synth. Biol. 10, 2021, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.1c00068

The condensin holocomplex cycles dynamically between open and collapsed states

Autores: J.-K Ryu, A.J. Katan, E.O. van der Sluis, T. Wisse, R. de Groot, C. Haering, C. Dekker
Publicado en: Nature Struct. Molec. Biol. 27, 2020, ISSN 1545-9993
Editor: 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

Autores: Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan-Michael Peters, Cees Dekker
Publicado en: Scientific Reports, Edición 13, 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-35359-2

Monographic books (2)

Single-molecule ionic and optical sensing with nanoapertures

Autores: W. Yang, C. Dekker
Publicado en: Book chapter in ' Single Molecule Nanosensors and Nanosystems' (Eds. W. Bowen, R. Gordon, F. Vollmer; Springer book series Nanostructure Science and Technology), Edición 6, 2022, Página(s) pp 367–387
Editor: Springer

Single-molecule ionic and optical sensing with nanoapertures

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