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

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  • 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
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    References listed on IDEAS

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    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.
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    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).

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