IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0232976.html
   My bibliography  Save this article

How global DNA unwinding causes non-uniform stress distribution and melting of DNA

Author

Listed:
  • Korbinian Liebl
  • Martin Zacharias

Abstract

DNA unwinding is an important process that controls binding of proteins, gene expression and melting of double-stranded DNA. In a series of all-atom MD simulations on two DNA molecules containing a transcription start TATA-box sequence we demonstrate that application of a global restraint on the DNA twisting dramatically changes the coupling between helical parameters and the distribution of deformation energy along the sequence. Whereas only short range nearest-neighbor coupling is observed in the relaxed case, long-range coupling is induced in the globally restrained case. With increased overall unwinding the elastic deformation energy is strongly non-uniformly distributed resulting ultimately in a local melting transition of only the TATA box segment during the simulations. The deformation energy tends to be stored more in cytidine/guanine rich regions associated with a change in conformational substate distribution. Upon TATA box melting the deformation energy is largely absorbed by the melting bubble with the rest of the sequences relaxing back to near B-form. The simulations allow us to characterize the structural changes and the propagation of the elastic energy but also to calculate the associated free energy change upon DNA unwinding up to DNA melting. Finally, we design an Ising model for predicting the local melting transition based on empirical parameters. The direct comparison with the atomistic MD simulations indicates a remarkably good agreement for the predicted necessary torsional stress to induce a melting transition, for the position and length of the melted region and for the calculated associated free energy change between both approaches.

Suggested Citation

  • 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.
  • Handle: RePEc:plo:pone00:0232976
    DOI: 10.1371/journal.pone.0232976
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232976
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0232976&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0232976?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. 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.
    2. Carlos Bustamante & Zev Bryant & Steven B. Smith, 2003. "Ten years of tension: single-molecule DNA mechanics," Nature, Nature, vol. 421(6921), pages 423-427, January.
    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. 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.
    2. Li Liu & Ying Fang & Qingsheng Huang & Jianhua Wu, 2011. "A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic α-Helical Peptide HP(2–20) and Its Four Analogues," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-8, January.
    3. 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.
    4. 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.
    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. Young-Joo Kim & Do-Nyun Kim, 2016. "Structural Basis for Elastic Mechanical Properties of the DNA Double Helix," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-11, April.
    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.
    8. Sangram Kadam & Kiran Kumari & Vinoth Manivannan & Shuvadip Dutta & Mithun K. Mitra & Ranjith Padinhateeri, 2023. "Predicting scale-dependent chromatin polymer properties from systematic coarse-graining," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

    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:pone00:0232976. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.