IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1003456.html
   My bibliography  Save this article

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

Author

Listed:
  • Pascal Carrivain
  • Maria Barbi
  • Jean-Marc Victor

Abstract

We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.Author Summary: Video game techniques are designed to simulate rigid body dynamics of macroscopic bodies, e.g. characters or vehicles, in a realistic manner. However they are not able to deal with temperature effects, hence they are not able to deal with molecules. In order to extend these powerful techniques to molecular modeling, we implement here Langevin Dynamics in an open source library called Open Dynamics Engine. Moreover we add a “global thermostat” to this Langevin Dynamics, which accelerates the simulation sampling by two orders of magnitude. With these radically new simulation techniques, we prove that we can accurately reproduce single-molecule manipulation experiments in silico, in particular force-extension as well as rotation-extension curves of reference experimental studies. The method developed here represents an unparalleled tool for the study of more complex single molecule manipulation experiments, notably when DNA interacts with proteins. Furthermore the simulation technique that we propose here has all the functionalities required to tackle the nuclear organization of chromosomes at every length scale, from DNA to whole nuclei.

Suggested Citation

  • Pascal Carrivain & Maria Barbi & Jean-Marc Victor, 2014. "In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics," PLOS Computational Biology, Public Library of Science, vol. 10(2), pages 1-13, February.
  • Handle: RePEc:plo:pcbi00:1003456
    DOI: 10.1371/journal.pcbi.1003456
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003456
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003456&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1003456?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Terence R. Strick & Vincent Croquette & David Bensimon, 2000. "Single-molecule analysis of DNA uncoiling by a type II topoisomerase," Nature, Nature, vol. 404(6780), pages 901-904, April.
    2. Zev Bryant & Michael D. Stone & Jeff Gore & Steven B. Smith & Nicholas R. Cozzarelli & Carlos Bustamante, 2003. "Structural transitions and elasticity from torque measurements on DNA," Nature, Nature, vol. 424(6946), pages 338-341, July.
    3. Daniel A. Koster & Vincent Croquette & Cees Dekker & Stewart Shuman & Nynke H. Dekker, 2005. "Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB," Nature, Nature, vol. 434(7033), pages 671-674, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ian L Morgan & Omar A Saleh, 2021. "Tweezepy: A Python package for calibrating forces in single-molecule video-tracking experiments," PLOS ONE, Public Library of Science, vol. 16(12), pages 1-18, December.
    2. Korbinian Liebl & Martin Zacharias, 2020. "How global DNA unwinding causes non-uniform stress distribution and melting of DNA," PLOS ONE, Public Library of Science, vol. 15(5), pages 1-21, May.
    3. Jack W. Shepherd & Sebastien Guilbaud & Zhaokun Zhou & Jamieson A. L. Howard & Matthew Burman & Charley Schaefer & Adam Kerrigan & Clare Steele-King & Agnes Noy & Mark C. Leake, 2024. "Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Jaeyoon Lee & Meiling Wu & James T. Inman & Gundeep Singh & Seong ha Park & Joyce H. Lee & Robert M. Fulbright & Yifeng Hong & Joshua Jeong & James M. Berger & Michelle D. Wang, 2023. "Chromatinization modulates topoisomerase II processivity," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Oi Kwan Wong & Martin Guthold & Dorothy A Erie & Jeff Gelles, 2008. "Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments," PLOS Biology, Public Library of Science, vol. 6(9), pages 1-15, September.
    6. Fang-Chieh Chou & Jan Lipfert & Rhiju Das, 2014. "Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-19, August.
    7. Camille Brème & François Heslot, 2013. "Mapping of Single-Base Differences between Two DNA Strands in a Single Molecule Using Holliday Junction Nanomechanics," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-9, February.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1003456. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.