Topologically Active Polymers

Project Information

TAP

Grant agreement ID: 947918

DOI

10.3030/947918

Project closed

EC signature date 20 October 2020

Start date 1 January 2021

End date 31 December 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 950,00

EU contribution

€ 1 499 950,00

Coordinated by

THE UNIVERSITY OF EDINBURGH
United Kingdom

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 .

Deliverables

Open Research Data Pilot (1)

Open Research Data Pilot

Publications

Peer reviewed articles (32)

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

Runaway transition in irreversible polymer condensation with cyclization

Author(s): Maria Panoukidou, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado, Martin Lenz, Davide Michieletto
Published in: Physical Review Research, Issue 6, 2024, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/physrevresearch.6.023189

Topology in soft and biological matter

Author(s): Luca Tubiana, Gareth P. Alexander, Agnese Barbensi, Dorothy Buck, Julyan H.E. Cartwright, Mateusz Chwastyk, Marek Cieplak, Ivan Coluzza, Simon Čopar, David J. Craik, Marco Di Stefano, Ralf Everaers, Patrícia F.N. Faísca, Franco Ferrari, Achille Giacometti, Dimos Goundaroulis, Ellinor Haglund, Ya-Ming Hou, Nevena Ilieva, Sophie E. Jackson, Aleksandre Japaridze, Noam Kaplan, Alexander R. Klotz, H
Published in: Physics Reports, Issue 1075, 2024, Page(s) 1-137, ISSN 0370-1573
Publisher: Elsevier BV
DOI: 10.1016/j.physrep.2024.04.002

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids

Author(s): G. Forte, D. Michieletto, D. Marenduzzo, E. Orlandini
Published in: Journal of The Royal Society Interface, Issue 18, 2021, Page(s) 20210229, ISSN 1742-5662
Publisher: The Royal Society
DOI: 10.1098/rsif.2021.0229

Topological digestion drives time-varying rheology of entangled DNA fluids

Author(s): Michieletto D,Neill P, Weir S, Evans D, Crist N, Martinez V, Robertson-Anderson R
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31828-w

Geometric learning of knot topology

Author(s): Joseph Lahoud Sleiman; Filippo Conforto; Yair Augusto Gutierrez Fosado; Davide Michieletto
Published in: Crossref, Issue 5, 2024, ISSN 1744-6848
Publisher: RSC
DOI: 10.1039/d3sm01199b

An Inter-strand Loop Extrusion Model

Author(s): Andrea Bonato; Davide Michieletto
Published in: Biophysical Journal, Issue 1, 2021, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.48550/arxiv.2111.00332

Fluidification of entanglements by a DNA bending protein

Author(s): Yair A. G. Fosado; Jamieson Howard; Simon Weir; Agnes Noy; Mark C. Leake; Davide Michieletto
Published in: Physical Review Letters, Issue 130, 2023, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.48550/arxiv.2205.03510

Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates

Author(s): Davide Michieletto; Mattia Marenda
Published in: JACS Au, Issue 2, 2022, ISSN 2691-3704
Publisher: ACS
DOI: 10.1021/jacsau.2c00055

Topological gelation of reconnecting polymers

Author(s): Andrea Bonato; Davide Marenduzzo; Davide Michieletto; Enzo Orlandini
Published in: PNAS, Issue 119, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1101/2022.09.21.508941

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

Author(s): MILOŠ TIŠMA, MARIA PANOUKIDOU, HAMMAM ANTAR, YOUNG-MIN SOH, ROMAN BARTH, BISWAJIT PRADHAN, ANDERS BARTH, JACO VAN DER TORRE, DAVIDE MICHIELETTO, STEPHAN GRUBER, CEES DEKKER
Published in: Science Advances, Issue 8, 2022, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.abn3299

Kinetoplast DNA: a polymer physicist’s topological Olympic dream

Author(s): Davide Michieletto
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae1206

Parameter-free molecular super-structures quantification in single-molecule localization microscopy.

Author(s): Mattia Marenda; Elena Lazarova; Sebastian van de Linde; Nick Gilbert; Davide Michieletto
Published in: Journal of Cell Biology, Issue 1, 2021, ISSN 0021-9525
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202010003

Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search

Author(s): Andrea Bonato, Jae-Won Jang, Do-Gyun Kim, Kyoung-Wook Moon, Davide Michieletto, Je-Kyung Ryu
Published in: Nucleic Acids Research, Issue 53, 2025, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf725

Effects of monovalent and divalent cations on the rheology of entangled DNA

Author(s): Jennifer Harnett, Simon Weir, Davide Michieletto
Published in: Soft Matter, Issue 20, 2024, Page(s) 3980-3986, ISSN 1744-683X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sm00957b

Universal and Programmable Thinning and Thickening of Topologically-Active DNA Fluids

Author(s): Davide Michieletto; P. Neill; S. Weir; Vincent A. Martinez; David M. Evans; Crist N; Anderson R
Published in: Nature Communications, Issue 13, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.48550/arxiv.2106.08861

Link to Densify: Topological Transitions and Origin of Hysteresis During the Compression and Decompression of Amorphous Ices

Author(s): Yair Augusto Gutiérrez Fosado, Davide Michieletto, Fausto Martelli
Published in: Physical Review Letters, Issue 133, 2025, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.133.266102

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

Author(s): Je-Kyung Ryu; Sang-Hyun Rah; Richard Janissen; Jacob W. J. Kerssemakers; Andrea Bonato; Davide Michieletto; Cees Dekker
Published in: Ryu , J-K , Rah , S-H , Janissen , R , Kerssemakers , J W J , Bonato , A , Michieletto , D & Dekker , C 2022 , ' Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events ' , Nucleic Acids Research , vol. 50 , no. 2 , pp. 820-832 . https://doi.org/10.1093/nar/gkab1268, Issue 3, 2022, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1101/2020.11.04.368506

Single-Molecule Morphology of Topologically Digested Olympic Networks

Author(s): Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutierrez Fosado, Luca Tubiana, Willem Vanderlinden, Nicholas Jon Savill, Achim Schnaufer, Davide Michieletto
Published in: PRX Life, Issue 2, 2024, ISSN 2835-8279
Publisher: American Physical Society (APS)
DOI: 10.1103/prxlife.2.013009

Fluidification of entangled polymers by loop extrusion

Author(s): Filippo Conforto, Yair Gutierrez Fosado, Davide Michieletto
Published in: Physical Review Research, Issue 6, 2024, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/physrevresearch.6.033160

Nanostars planarity modulates the elasticity of DNA hydrogels

Author(s): Fosado, Yair Augusto Gutierrez
Published in: Soft Matter, Issue 6, 2023, ISSN 1744-6848
Publisher: RSC
DOI: 10.1039/d2sm00221c

Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation

Author(s): Davide Michieletto; Yair A G Fosado; Elias Melas; Marco Baiesi; Luca Tubiana; Enzo Orlandini
Published in: Nucleic Acids Research, Issue 50, 2022, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac260

Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction

Author(s): Jorine M. Eeftens, Manya Kapoor, Davide Michieletto, Clifford P. Brangwynne
Published in: Nature Communications, Issue 12, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26147-5

Geometric Predictors of Knotted and Linked Arcs

Author(s): Joseph L. Sleiman; Robin H. Burton; Michele Caraglio; Yair Augusto Gutierrez Fosado; Davide Michieletto
Published in: ACS Polymers Au, Issue 2, 2022, ISSN 2694-2453
Publisher: ACS
DOI: 10.1021/acspolymersau.2c00021

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

Author(s): Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley, Davide Marenduzzo
Published in: PNAS, Issue 118, 2021, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1905215118

Topological linking determines elasticity in limited valence networks

Author(s): Giorgia Palombo, Simon Weir, Davide Michieletto, Yair Augusto Gutiérrez Fosado
Published in: Nature Materials, Issue 24, 2025, Page(s) 454-461, ISSN 1476-1122
Publisher: Nature Publishing Group
DOI: 10.1038/s41563-024-02091-9

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

Author(s): Tišma, Miloš; Panoukidou, Maria; Antar, Hammam; Soh, Young-Min; Barth, Roman; Pradhan, Biswajit; Barth, Anders; van der Torre, Jaco; Michieletto, Davide; Gruber, Stephan; Dekker, Cees
Published in: Science advances, vol. 8, no. 26, pp. eabn3299, Issue 12, 2023, ISSN 2375-2548
Publisher: AAAS

Simplifying topological entanglements by entropic competition of slip-links

Author(s): Andrea Bonato; Davide Marenduzzo; Davide Michieletto
Published in: Physical Review Research, Issue 2, 2021, ISSN 2643-1564
Publisher: APS
DOI: 10.1103/physrevresearch.3.043070

Topological Tuning of DNA Mobility in Entangled Solutions of Supercoiled Plasmids

Author(s): Jan Smrek; Jonathan Garamella; Rae M. Robertson-Anderson; Davide Michieletto
Published in: Science Advances, Issue 2, 2021, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1101/2020.09.21.306092

Topology-Controlled Microphase Separation and Interconversion of Twist and Writhe Domains in Supercoiled Annealed Polyelectrolytes

Author(s): Roman Staňo, Christos N. Likos, Davide Michieletto, Jan Smrek
Published in: Physical Review Letters, Issue 135, 2025, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/7fh5-frst

Topologically-crosslinked hydrogels based on γ-cyclodextrins

Author(s): Ella Sapsford, Davide Michieletto
Published in: Communications Chemistry, Issue 8, 2025, ISSN 2399-3669
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s42004-025-01469-3

Loops are Geometric Catalysts for DNA Integration

Author(s): Cleis Battaglia, Davide Michieletto
Published in: Nucleic Acids Research, Issue 52, 2026, ISSN 1362-4962
Publisher: OUP
DOI: 10.1101/2023.06.21.545982