ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Figure 1Loading Img

Molecular Crowding Increases Knots Abundance in Linear Polymers

View Author Information
SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
*E-mail [email protected] (G.D.).
Cite this: Macromolecules 2015, 48, 17, 6337–6346
Publication Date (Web):August 17, 2015
Copyright © 2015 American Chemical Society

    Article Views





    Read OnlinePDF (3 MB)
    Supporting Info (1)»


    Abstract Image

    Stochastic simulations are used to study the effects of molecular crowding on the self-entanglement of linear polymers. We consider flexible chains of beads of up to 1000 monomers and examine how their knotting properties vary in the presence spherical crowders that are 4 times smaller than the chains themselves and which occupy 35% of the solution volume. We find that crowding boosts the incidence of physical knots by more than an order of magnitude for all considered chain lengths. Furthermore, most crowding-induced knots are found to be significantly longer than in the free case. We show that the observed properties follow from the screening of excluded volume interactions mediated by the crowders at length scales larger than their size.

    Supporting Information

    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.macromol.5b01323.

    • Additional details for the implicit crowders model; radial distribution functions in the zero-density limit and the depletion thickness; crowding-induced chain compactification, extrapolation for Nm → ∞; typical relaxation times for a chain of beads with/without crowders; selection of genuine physical knots; size of knotted and unknotted subchains; absolute incidence of knots: number of sampled configurations and knotted states (PDF)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system:

    Cited By

    This article is cited by 26 publications.

    1. Anna Braghetto, Sumanta Kundu, Marco Baiesi, Enzo Orlandini. Machine Learning Understands Knotted Polymers. Macromolecules 2023, 56 (7) , 2899-2909.
    2. Liang Dai, Beatrice W. Soh, Patrick S. Doyle. Effects of Side Chains on Polymer Knots. Macromolecules 2019, 52 (17) , 6792-6800.
    3. Liang Dai, Patrick S. Doyle. Universal Knot Spectra for Confined Polymers. Macromolecules 2018, 51 (16) , 6327-6333.
    4. Maximilian Liebetreu, Marisol Ripoll, Christos N. Likos. Trefoil Knot Hydrodynamic Delocalization on Sheared Ring Polymers. ACS Macro Letters 2018, 7 (4) , 447-452.
    5. Liang Dai and Patrick S. Doyle . Effects of Intrachain Interactions on the Knot Size of a Polymer. Macromolecules 2016, 49 (19) , 7581-7587.
    6. Guido Polles, Enzo Orlandini, and Cristian Micheletti . Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement. ACS Macro Letters 2016, 5 (8) , 931-935.
    7. Giuseppe D’Adamo , Andrea Pelissetto , Carlo Pierleoni . Phase Diagram and Structure of Mixtures of Large Colloids and Linear Polymers under Good-Solvent Conditions. Macromolecules 2016, 49 (14) , 5266-5280.
    8. Chao Yang, Xiaoya Song, Yuyu Feng, Guangju Zhao, Yanhui Liu. Stability of DNA and RNA hairpins: a comparative study based on ox-DNA. Journal of Physics: Condensed Matter 2023, 35 (26) , 265101.
    9. Ting Liang, Chao Yang, Xiaoya Song, Yuyu Feng, Yanhui Liu, Hu Chen. Quantification of macromolecule crowding at single-molecule level. Physical Review E 2023, 108 (1)
    10. Keerthi Radhakrishnan, Sunil P. Singh. Compression of a confined semiflexible polymer under direct and oscillating fields. Physical Review E 2023, 108 (1)
    11. Davide Michieletto, Yair A G Fosado, Elias Melas, Marco Baiesi, Luca Tubiana, Enzo Orlandini. Dynamic and facilitated binding of topoisomerase accelerates topological relaxation. Nucleic Acids Research 2022, 50 (8) , 4659-4668.
    12. Caiyun Xiong, Xiaolin Nie, Yixue Peng, Xun Zhou, Yangtao Fan, Hu Chen, Yanhui Liu. Influences of flexible defect on the interplay of supercoiling and knotting of circular DNA*. Communications in Theoretical Physics 2021, 73 (7) , 075602.
    13. Maciej Piejko, Szymon Niewieczerzal, Joanna I. Sulkowska. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Israel Journal of Chemistry 2020, 60 (7) , 713-724.
    14. Maxime Pouokam, Brian Cruz, Sean Burgess, Mark R. Segal, Mariel Vazquez, Javier Arsuaga. The Rabl configuration limits topological entanglement of chromosomes in budding yeast. Scientific Reports 2019, 9 (1)
    15. Anpu Chen, Nanrong Zhao. Comparative study of the crowding-induced collapse effect in hard-sphere, flexible polymer and rod-like polymer systems. Physical Chemistry Chemical Physics 2019, 21 (23) , 12335-12345.
    16. Enzo Orlandini, Davide Marenduzzo, Davide Michieletto. Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology. Proceedings of the National Academy of Sciences 2019, 116 (17) , 8149-8154.
    17. Erica Uehara, Lucia Coronel, Cristian Micheletti, Tetsuo Deguchi. Bimodality in the knotting probability of semiflexible rings suggested by mapping with self-avoiding polygons. Reactive and Functional Polymers 2019, 134 , 141-149.
    18. Susan Amin, Ahmed Khorshid, Lili Zeng, Philip Zimny, Walter Reisner. A nanofluidic knot factory based on compression of single DNA in nanochannels. Nature Communications 2018, 9 (1)
    19. Luca Tubiana, Guido Polles, Enzo Orlandini, Cristian Micheletti. KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers. The European Physical Journal E 2018, 41 (6)
    20. Yani Zhao, Pawel Dabrowski-Tumanski, Szymon Niewieczerzal, Joanna I. Sulkowska, . The exclusive effects of chaperonin on the behavior of proteins with 52 knot. PLOS Computational Biology 2018, 14 (3) , e1005970.
    21. Enzo Orlandini. Statics and dynamics of DNA knotting. Journal of Physics A: Mathematical and Theoretical 2018, 51 (5) , 053001.
    22. Liang Dai, Patrick Doyle. Trapping a Knot into Tight Conformations by Intra-Chain Repulsions. Polymers 2017, 9 (12) , 57.
    23. Andrés Bustamante, Juan Sotelo-Campos, Daniel G. Guerra, Martin Floor, Christian A. M. Wilson, Carlos Bustamante, Mauricio Báez. The energy cost of polypeptide knot formation and its folding consequences. Nature Communications 2017, 8 (1)
    24. Szymon Niewieczerzal, Joanna I. Sulkowska, . Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume. PLOS ONE 2017, 12 (5) , e0176744.
    25. Saeed Najafi, Luca Tubiana, Rudolf Podgornik, Raffaello Potestio. Chirality modifies the interaction between knots. EPL (Europhysics Letters) 2016, 114 (5) , 50007.
    26. Giuseppe D'Adamo, Giovanni Dietler, Cristian Micheletti. Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains. Soft Matter 2016, 12 (32) , 6708-6715.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect