Thermodynamic modelling of DNA-Nanoparticle bonding and crystallization

Abstract

In this thesis, we discuss how structure prediction for DNA-NP solutions have been done previously, and expand upon the work done by using a model that includes three different energies present within bonds between DNA-NPs: duplex energy, elastic bending energy, and electrostatic potential energy. We first explain the various facets of the structure of these DNA-NPs, and how they play a role in determining the exact values for each of the three energies present in our model. In doing so, we develop quantitative expressions for the value of each of these energies, and determine the total bonding energy between DNA-NPs as a function of separation distance. We then use these plots to predict the lattice energies of various crystal structures the DNA-NPs may adopt, and predict which one(s) should be observed for different experimental parameters important to the model. Our results show that this model is capable of qualitatively explaining thermal expansion of DNA-NP lattices, a maximum separation distance less than twice the hydrodynamic radius of the DNA-NPs, a CsCl to AuCu transition within a DNA-NP solution by blending DNA strand coverages,and why CsCl is typically preferred over AuCu for purely-complementary DNA-NP systems.