IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v518y2019icp80-88.html
   My bibliography  Save this article

Statistical mechanical modeling of a DNA nanobiostructure at the base-pair level

Author

Listed:
  • Shekaari, Ashkan
  • Jafari, Mahmoud

Abstract

We have modeled a double-stranded DNA nanostructure within the framework of statistical mechanics and ensemble theory as composed of a large number of base pairs with rotational degrees of freedom around the bases to generate helical or bent configurations. Different binding energies associated with the two kinds of the base pairs have been found only via statistical considerations and as an implication of the tendency of the system to minimize its free energy irrespective of the nature or the number of bonds making the base pairs. The temperature-dependent alternative for the relation of information capacity has been also derived in the canonical formalism as a more realistic expression compared to its microcanonical counterpart with a possible importance in DNA-based, information-bearing, nano-scale devices. Results demonstrate the degeneracy associated with the rotational degrees of freedom as a potential factor for further increasing the information capacity of such a nanobiostructure.

Suggested Citation

  • Shekaari, Ashkan & Jafari, Mahmoud, 2019. "Statistical mechanical modeling of a DNA nanobiostructure at the base-pair level," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 518(C), pages 80-88.
    • Handle: RePEc:eee:phsmap:v:518:y:2019:i:c:p:80-88
    DOI: 10.1016/j.physa.2018.11.054
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437118314912
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2018.11.054?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Florian Praetorius & Benjamin Kick & Karl L. Behler & Maximilian N. Honemann & Dirk Weuster-Botz & Hendrik Dietz, 2017. "Biotechnological mass production of DNA origami," Nature, Nature, vol. 552(7683), pages 84-87, December.
    2. Nick Goldman & Paul Bertone & Siyuan Chen & Christophe Dessimoz & Emily M. LeProust & Botond Sipos & Ewan Birney, 2013. "Towards practical, high-capacity, low-maintenance information storage in synthesized DNA," Nature, Nature, vol. 494(7435), pages 77-80, February.
    3. Kafri, Y. & Mukamel, D. & Peliti, L., 2002. "Denaturation and unzipping of DNA: statistical mechanics of interacting loops," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 306(C), pages 39-50.
    4. Ebbe S. Andersen & Mingdong Dong & Morten M. Nielsen & Kasper Jahn & Ramesh Subramani & Wael Mamdouh & Monika M. Golas & Bjoern Sander & Holger Stark & Cristiano L. P. Oliveira & Jan Skov Pedersen & V, 2009. "Self-assembly of a nanoscale DNA box with a controllable lid," Nature, Nature, vol. 459(7243), pages 73-76, May.
    5. Paul W. K. Rothemund, 2006. "Folding DNA to create nanoscale shapes and patterns," Nature, Nature, vol. 440(7082), pages 297-302, March.
    6. Shekaari, Ashkan & Jafari, Mahmoud, 2018. "Effect of pairwise additivity on finite-temperature behavior of classical ideal gas," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 497(C), pages 101-108.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Nikitiuk, Aleksandr S. & Bayandin, Yuriy V. & Naimark, Oleg B., 2022. "Statistical thermodynamics of DNA with open states," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 607(C).

    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. Chao Pan & S. Kasra Tabatabaei & S. M. Hossein Tabatabaei Yazdi & Alvaro G. Hernandez & Charles M. Schroeder & Olgica Milenkovic, 2022. "Rewritable two-dimensional DNA-based data storage with machine learning reconstruction," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Jingwei Hong & Abdur Rasool & Shuo Wang & Djemel Ziou & Qingshan Jiang, 2024. "VSD: A Novel Method for Video Segmentation and Storage in DNA Using RS Code," Mathematics, MDPI, vol. 12(8), pages 1-21, April.
    3. Abdur Rasool & Qiang Qu & Yang Wang & Qingshan Jiang, 2022. "Bio-Constrained Codes with Neural Network for Density-Based DNA Data Storage," Mathematics, MDPI, vol. 10(5), pages 1-21, March.
    4. Christopher N. Takahashi & David P. Ward & Carlo Cazzaniga & Christopher Frost & Paolo Rech & Kumkum Ganguly & Sean Blanchard & Steve Wender & Bichlien H. Nguyen & Jake A. Smith, 2024. "Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    5. Jeroen F. Dyck & Jonathan R. Burns & Kyle I. P. Huray & Albert Konijnenberg & Stefan Howorka & Frank Sobott, 2022. "Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    6. Tomoya Maruyama & Jing Gong & Masahiro Takinoue, 2024. "Temporally controlled multistep division of DNA droplets for dynamic artificial cells," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Cheng Kai Lim & Jing Wui Yeoh & Aurelius Andrew Kunartama & Wen Shan Yew & Chueh Loo Poh, 2023. "A biological camera that captures and stores images directly into DNA," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Swarup Dey & Adam Dorey & Leeza Abraham & Yongzheng Xing & Irene Zhang & Fei Zhang & Stefan Howorka & Hao Yan, 2022. "A reversibly gated protein-transporting membrane channel made of DNA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    9. Ruohong Shi & Kuan-Lin Chen & Joshua Fern & Siming Deng & Yixin Liu & Dominic Scalise & Qi Huang & Noah J. Cowan & David H. Gracias & Rebecca Schulman, 2024. "Programming gel automata shapes using DNA instructions," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Eva Bertosin & Christopher M. Maffeo & Thomas Drexler & Maximilian N. Honemann & Aleksei Aksimentiev & Hendrik Dietz, 2021. "A nanoscale reciprocating rotary mechanism with coordinated mobility control," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    11. Muhammad Yaseen & Muhammad Humayun & Abbas Khan & Muhammad Usman & Habib Ullah & Asif Ali Tahir & Habib Ullah, 2021. "Preparation, Functionalization, Modification, and Applications of Nanostructured Gold: A Critical Review," Energies, MDPI, vol. 14(5), pages 1-88, February.
    12. Yahong Chen & Chaoyong Yang & Zhi Zhu & Wei Sun, 2022. "Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    13. Mária Brunderová & Vojtěch Havlíček & Ján Matyašovský & Radek Pohl & Lenka Poštová Slavětínská & Matouš Krömer & Michal Hocek, 2024. "Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    14. Alexandru Amărioarei & Frankie Spencer & Gefry Barad & Ana-Maria Gheorghe & Corina Iţcuş & Iris Tuşa & Ana-Maria Prelipcean & Andrei Păun & Mihaela Păun & Alfonso Rodriguez-Paton & Romică Trandafir & , 2021. "DNA-Guided Assembly for Fibril Proteins," Mathematics, MDPI, vol. 9(4), pages 1-17, February.
    15. Punnag Padhy & Mohammad Asif Zaman & Michael Anthony Jensen & Yao-Te Cheng & Yogi Huang & Mo Wu & Ludwig Galambos & Ronald Wayne Davis & Lambertus Hesselink, 2024. "Dielectrophoretic bead-droplet reactor for solid-phase synthesis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Afsaneh Sadremomtaz & Robert F. Glass & Jorge Eduardo Guerrero & Dennis R. LaJeunesse & Eric A. Josephs & Reza Zadegan, 2023. "Digital data storage on DNA tape using CRISPR base editors," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    17. Jessica A. Kretzmann & Anna Liedl & Alba Monferrer & Volodymyr Mykhailiuk & Samuel Beerkens & Hendrik Dietz, 2023. "Gene-encoding DNA origami for mammalian cell expression," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    18. Katya Ahmad & Abid Javed & Conor Lanphere & Peter V. Coveney & Elena V. Orlova & Stefan Howorka, 2023. "Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    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:eee:phsmap:v:518:y:2019:i:c:p:80-88. 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: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    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.