Bottom up biophysics approach to resolve the looping structure of chromosomes

Informazioni relative al progetto

LoopingDNA

ID dell’accordo di sovvenzione: 883684

DOI

10.3030/883684

Progetto chiuso

Data della firma CE 12 Maggio 2020

Data di avvio 1 Luglio 2020

Data di completamento 30 Giugno 2025

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 2 500 000,00

Contributo UE

€ 2 500 000,00

Coordinato da

TECHNISCHE UNIVERSITEIT DELFT
Netherlands

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (54)

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

Autori: Pauline J Kolbeck, Miloš Tišma, Brian T Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, Pagina/e 59-72, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad1055

Cohesin supercoils DNA during loop extrusion

Autori: 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
Pubblicato in: Cell Reports, Numero 44, 2025, Pagina/e 115856, ISSN 2211-1247
Editore: 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

Autori: F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, E. Frey, C. Dekker
Pubblicato in: Nature Comm. 12, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-23412-5

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

Autori: Klughammer, Nils; Dekker, Cees
Pubblicato in: Nanotechnology 32, Numero 2, 2021, ISSN 0957-4484
Editore: Institute of Physics Publishing
DOI: 10.48550/arxiv.2010.00276

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

Autori: K.D. Whitley, S. Middlemiss, C. Jukes, C. Dekker, S. Holden
Pubblicato in: Nature Protocols 17, 2022, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-021-00668-1

Studying Phase Separation in Confinement

Autori: S. Deshpande, C. Dekker
Pubblicato in: Curr. Opin. Colloid Interface Sci. 52, 2021, ISSN 1359-0294
Editore: Pergamon Press
DOI: 10.1016/j.cocis.2021.101419

Quantitative analysis of surface wave patterns of Min proteins

Autori: S. Meindlhumer, J. Kerssemakers, C. Dekker
Pubblicato in: Frontiers in Physics, 2022, ISSN 2296-424X
Editore: Frontiers Media S.A.
DOI: 10.3389/fphy.2022.930811

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

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

SMC motor proteins extrude DNA asymmetrically and can switch directions

Autori: Roman Barth, Iain F. Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker
Pubblicato in: Cell, Numero 188, 2025, Pagina/e 749-763.e21, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2024.12.020

The archaeal Cdv cell division system

Autori: Alberto Blanch Jover, Cees Dekker
Pubblicato in: Trends in Microbiology, Numero 31, 2023, Pagina/e 601-615, ISSN 0966-842X
Editore: Elsevier BV
DOI: 10.1016/j.tim.2022.12.006

Bridging scales in a multiscale pattern-forming system

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

SMC complexes can traverse physical roadblocks bigger than their ring size

Autori: 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
Pubblicato in: Cell Reports 41, 2022, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2022.111491

DNA sequence-directed cooperation between nucleoid-associated proteins

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

Comparing current noise in biological and solid-state nanopores

Autori: A. Fragasso, S. Schmid, C. Dekker
Pubblicato in: ACS Nano 14, 2020, ISSN 1936-0851
Editore: American Chemical Society
DOI: 10.1021/acsnano.9b09353

Nanopores – a Versatile Tool to Study Protein Dynamics

Autori: S. Schmid, C. Dekker
Pubblicato in: Essays in Biochemistry EBC20200020, 2020, ISSN 0006-2960
Editore: American Chemical Society
DOI: 10.1042/ebc20200020

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

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

Two CTCF motifs impede cohesin-mediated DNA loop extrusion

Autori: 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
Pubblicato in: Molecular Cell, Numero under review, 2025, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1101/2025.01.26.634934

Condensin-driven loop extrusion on supercoiled DNA

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

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

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

Transport receptor occupancy in Nuclear Pore Complex mimics

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

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

Autori: Miloš Tišma, Florian Patrick Bock, Jacob Kerssemakers, Hammam Antar, Aleksandre Japaridze, Stephan Gruber, Cees Dekker
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-47094-x

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

Autori: 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
Pubblicato in: Molec. Cell 82, 2022, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2022.02.032

Towards a synthetic cell cycle

Autori: 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
Pubblicato in: Nature Comm.12, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-24772-8

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

Autori: Miloš Tišma, Richard Janissen, Hammam Antar, Alejandro Martin-Gonzalez, Roman Barth, Twan Beekman, Jaco van der Torre, Davide Michieletto, Stephan Gruber, Cees Dekker
Pubblicato in: Nucleic Acids Research, Numero 51, 2023, Pagina/e 11856-11875, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad868

MukBEF-dependent chromosomal organization in widened Escherichia coli

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

Probing nanomotion of single bacteria with graphene drums

Autori: Irek Rosłoń; Peter Steeneken; Aleksandre Japaridze; Cees Dekker; Farbod Alijani
Pubblicato in: Nature Nanotechnology 17, Numero 9, 2022, ISSN 1748-3387
Editore: Nature Publishing Group
DOI: 10.1101/2021.09.21.461186

pH-controlled coacervate-membrane interactions within liposomes

Autori: M.G.F. Last, S. Deshpande, C.Dekker
Pubblicato in: ACS Nano 14, 2020, ISSN 1936-0851
Editore: American Chemical Society
DOI: 10.1021/acsnano.9b10167

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

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

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

Autori: 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
Pubblicato in: Nature, Numero 616, 2023, Pagina/e 822-827, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-023-05961-5

A microfluidic platform for extraction and analysis of bacterial genomic DNA

Autori: Alex Joesaar, Martin Holub, Leander Lutze, Marco Emanuele, Jacob Kerssemakers, Martin Pabst, Cees Dekker
Pubblicato in: Lab on a Chip, Numero 25, 2025, Pagina/e 1767-1775, ISSN 1473-0197
Editore: Royal Society of Chemistry
DOI: 10.1039/d4lc00839a

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

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

DNA supercoiling enhances DNA condensation by ParB proteins

Autori: Alejandro Martin-Gonzalez, Miloš Tišma, Brian T Analikwu, Anders Barth, Richard Janissen, Hammam Antar, Gianluca Kemps, Stephan Gruber, Cees Dekker
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, Pagina/e 13255-13268, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkae936

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

Autori: S. Schmid, P. Stömmer, H. Dietz, C. Dekker
Pubblicato in: Nature Nanotechn. 16, 2021, ISSN 1748-3387
Editore: Nature Publishing Group
DOI: 10.1038/s41565-021-00958-5

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

Autori: Martin Holub, Anthony Birnie, Aleksandre Japaridze, Jaco van der Torre, Maxime den Ridder, Carol de Ram, Martin Pabst, Cees Dekker
Pubblicato in: Cell Reports Methods, Numero 2, 2023, Pagina/e 100366, ISSN 2667-2375
Editore: Elsevier BV
DOI: 10.1016/j.crmeth.2022.100366

Mechanisms for Chromosome Segregation in Bacteria

Autori: C. Gogou, A. Japaridze, C. Dekker
Pubblicato in: Frontiers Microbiol. 12, 2021, ISSN 1664-302X
Editore: Frontiers Media
DOI: 10.3389/fmicb.2021.685687

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

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

Looping the Genome with SMC Complexes

Autori: Eugene Kim, Roman Barth, Cees Dekker
Pubblicato in: Annual Review of Biochemistry, Numero 92, 2023, Pagina/e 15-41, ISSN 0066-4154
Editore: Annual Reviews, Inc.
DOI: 10.1146/annurev-biochem-032620-110506

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

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

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

Autori: Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, Pagina/e 1677-1687, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad1181

DNA-loop extruding condensin complexes can traverse one another

Autori: E. Kim, J. Kerssemakers, I.A. Shaltiel, C.H. Haering, C. Dekker
Pubblicato in: Nature 579, 2020, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-020-2067-5

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

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

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

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

Bridging-induced phase separation induced by cohesin SMC protein complexes

Autori: 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
Pubblicato in: Science Advances 7, 2021, ISSN 2375-2548
Editore: 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

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

How do molecular motors fold the genome?

Autori: Cees Dekker, Christian H. Haering, Jan-Michael Peters, Benjamin D. Rowland
Pubblicato in: Science, Numero 382, 2024, Pagina/e 646-648, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.adi8308

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

Autori: Anthony Birnie; Cees Dekker
Pubblicato in: VOLUME=15;ISSUE=1;ISSN=1936-0851;TITLE=ACS Nano (online), Numero 3, 2020, ISSN 1936-0851
Editore: American Chemical Society
DOI: 10.1021/acsnano.0c07397

Direct observation of independently moving replisomes in Escherichia coli

Autori: A. Japaridze, C. Gogou, J. W. J. Kerssemakers, H. M. Nguyen, C. Dekker
Pubblicato in: Nature Comm. 11, 2020, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1101/733956

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

Autori: Miloš Tišma, Jovana Kaljević, Stephan Gruber, Tung B K Le, Cees Dekker
Pubblicato in: FEMS Microbiology Reviews, Numero 48, 2024, ISSN 1574-6976
Editore: Oxford University Press (OUP)
DOI: 10.1093/femsre/fuad067

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

Autori: Pinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker, Davide Michieletto
Pubblicato in: Physical Review X, Numero 13, 2023, ISSN 2160-3308
Editore: American Physical Society
DOI: 10.1103/physrevx.13.021010

Telomeres stall DNA loop extrusion by condensin

Autori: 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
Pubblicato in: Cell Reports, Numero 44, 2025, Pagina/e 115900, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2025.115900

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

Autori: A. Blanch Jover, N. De Franceschi, D. Fenel, W. Weissenhorn, C. Dekker
Pubblicato in: FEBS Lett. 596, 2022, ISSN 0014-5793
Editore: Elsevier BV
DOI: 10.1002/1873-3468.14324

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

Autori: 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
Pubblicato in: ACS Synth. Biol. 10, 2021, ISSN 2161-5063
Editore: American Chemical Society
DOI: 10.1021/acssynbio.1c00068

The condensin holocomplex cycles dynamically between open and collapsed states

Autori: J.-K Ryu, A.J. Katan, E.O. van der Sluis, T. Wisse, R. de Groot, C. Haering, C. Dekker
Pubblicato in: Nature Struct. Molec. Biol. 27, 2020, ISSN 1545-9993
Editore: 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

Autori: Roman Barth, Biswajit Pradhan, Eugene Kim, Iain F. Davidson, Jaco van der Torre, Jan-Michael Peters, Cees Dekker
Pubblicato in: Scientific Reports, Numero 13, 2023, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-023-35359-2

Monographic books (2)

Single-molecule ionic and optical sensing with nanoapertures

Autori: W. Yang, C. Dekker
Pubblicato in: Book chapter in ' Single Molecule Nanosensors and Nanosystems' (Eds. W. Bowen, R. Gordon, F. Vollmer; Springer book series Nanostructure Science and Technology), Numero 6, 2022, Pagina/e pp 367–387
Editore: Springer

Single-molecule ionic and optical sensing with nanoapertures

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