Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars

Naskar, S and Bhatia, D and Lin, S-T and Maiti, PK (2023) Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars. In: Physical Chemistry Chemical Physics .

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Abstract

The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly. © 2023 The Royal Society of Chemistry

Item Type:	Journal Article
Publication:	Physical Chemistry Chemical Physics
Publisher:	Royal Society of Chemistry
Additional Information:	The copyright for this article belongs to Royal Society of Chemistry.
Keywords:	Bioinformatics; Coarse-grained modeling; Distribution functions; DNA; Dynamics; Entropy; Gels; Molecular dynamics; Phase transitions; Potential energy; Self assembly; Temperature, Gel phasis; Liquid Phase; Liquid phasis; Mechanistics; Molecular building blocks; Nanostar; Periodic arrays; Sequence specificity; Translational entropies; Unique sequence, Gelation
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	20 Mar 2023 09:24
Last Modified:	20 Mar 2023 09:24
URI:	https://eprints.iisc.ac.in/id/eprint/81021

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