The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization

Abstract

DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ~20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.

Controlled Monofunctionalization of Molecular Spherical Nucleic Acids on a Buckminster Fullerene Core

“…This indicates electrostatic repulsion/steric crowding between the duplexes on fully loaded SNA ( S4 + 12 equiv of RNA). This observation is consistent with the previous findings in which a retarded loading of siRNAs onto SNAs has been observed. ,− However, it is notable that the fully loaded SNA ( S4 + 12 equiv of RNA) was virtually stable below the physiological temperature and the observed “’premature’” partial denaturation occurred at a higher temperature. Titration of S4 with the same complementary RNA verified the correct stoichiometry of the melting profiles (Figure B; note, the concentration of S4 was determined according to the Alexa content).…”

Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications

“…While several strategies have been developed to modify interaction interfaces after discovering of lead compounds/ligands to increase binding enthalpy change, there is yet no direct discovery strategy for identifying enthalpy-driven ligands. For example, the functional groups of a small-molecule drug or inhibitor can be optimized to increase the binding affinity and reduce off-target effects in complex systems. − Similarly, biomacromolecular ligands can be improved by chemical modification, site-specific protein engineering, or multivalent effects. − While proven to be feasible to obtain enthalpy-driven ligands, these reiterating design–derivatization–testing processes are time-consuming and inefficient. For example, in order to improve the clinical effect of HIV protease inhibitors, a decade of effort was taken to convert the initial entropy-driven inhibitor (Indinavir) into enthalpy-driven TMC-114. , A strategy capable of identifying enthalpy-driven ligands would open a new route for efficient discovery of robust recognition probes for a great variety of biomedical applications.…”

Self‐assembling cyclic peptide‐oligonucleotide conjugates: Synthetic strategies and the effect of cyclic topology on self‐assembly and base pairing

“…However, when self‐assembling peptides are conjugated, it would be possible for DNAs to be more double‐stranded due to thermodynamic advantages upon hybridization according to recent research. [ 33 ] It is revealed that DNAs decorated on large entities such as gold nanoparticles can form energetically more stable duplex than free DNAs, increasing enthalpic gain upon hybridization. Therefore, it seems that the same principle applied to the hybridization of DNAs on self‐assembled DNA‐peptide conjugates.…”