Quantitative Study of the Association Thermodynamics and Kinetics of DNA-Coated Particles for Different Functionalization Schemes

Abstract

Surface functionalization with complementary single-stranded DNA sticky ends is increasingly used for guiding the self-assembly of nano- and micrometer-sized particles into larger scale ordered structures. Here we present measurements, formulas, and graphs that allow one to quantitatively predict the association behavior of DNA-coated particles from readily available Web-based data. From experiments it appears that the suspension behavior is very sensitive to the grafting details, such as the length and flexibility of the tether constructs and the particles' surface coverage. Thus, if one wants to control the interactions and assembly processes, insight is needed into the structural and dynamical features of the DNA coatings. We demonstrate how a straightforward measurement of the particles' association-dissociation kinetics during selected temperature cycles, combined with a simple quantitative model, can reveal the relevant properties. We used this method in a systematic study where we varied the temperature cycle, the bead concentration, the particles' surface coverage, and the DNA construct. Among other things, we find that the backbone that tethers the sticky ends to the surface can have a significant impact on the particles' dissociation properties, as it affects the total number of interparticle bonds and the configurational entropy cost associated with these bonds. We further find that, independent of the tether backbone, self-complementary "palindromic" sticky ends readily form intraparticle hairpins and loops, which greatly affect the particles' association behavior. Such secondary structure formation is increasingly important in faster temperature quenches, at lower particle concentration, and at lower surface coverage. The latter observations are especially useful for the design of so-called self-protected DNA-mediated interactions, which we pioneered recently and for which we expect to find an increasing use, as they enable more versatile assembly schemes.