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The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.

Lam-Kiu Fong, Ziwei Wang, George C Schatz

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    DNA hybridization on nanoparticle surfaces (spherical nucleic acids) is enthalpically enhanced due to structural confinement. Reduced confinement lowers this thermodynamic advantage, impacting SNA-based material design.

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    Area of Science:

    • Nanotechnology
    • Biophysics
    • Molecular Biology

    Background:

    • DNA hybridization is enhanced on nanoparticle surfaces compared to solution.
    • Spherical nucleic acids (SNAs) leverage DNA functionalization on nanoparticle cores.

    Purpose of the Study:

    • To elucidate the thermodynamic basis for enhanced DNA hybridization on nanoparticle surfaces.
    • To investigate the role of structural confinement in DNA hybridization thermodynamics.
    • To inform the design of DNA-nanoparticle hybrid materials.

    Main Methods:

    • Isothermal titration calorimetry (ITC) to measure hybridization thermodynamics.
    • Coarse-grained molecular dynamics (MD) simulations to model DNA behavior.
    • Systematic variation of DNA surface density and confinement.

    Main Results:

    • Hybridization enhancement on SNAs is enthalpically dominated (∼20 kcal/mol), not entropically.
    • Structural confinement of DNA on the nanoparticle surface stabilizes duplex formation.
    • Decreased confinement (lower density, greater distance) reduces the enthalpic advantage.

    Conclusions:

    • Structural confinement is the primary driver of enhanced DNA hybridization on nanoparticle surfaces.
    • The thermodynamic benefits of SNAs are tunable by controlling DNA surface density and confinement.
    • Findings guide the development of advanced DNA-based nanodiagnostics and therapeutics.