Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling

Abstract

DNA bridging can be used to induce specific attractions between small particles, providing a highly versatile approach to creating unique particle-based materials having a variety of periodic structures. Surprisingly, given the fact that the thermodynamics of DNA strands in solution are completely understood, existing models for DNA-induced particle interactions are typically in error by more than an order of magnitude in strength and a factor of two in their temperature dependence. This discrepancy has stymied efforts to design the complex temperature, sequence and time-dependent interactions needed for the most interesting applications, such as materials having highly complex or multicomponent microstructures or the ability to reconfigure or self-replicate. Here we report high-spatial resolution measurements of DNA-induced interactions between pairs of polystyrene microspheres at binding strengths comparable to those used in self-assembly experiments, up to 6 k B T . We also describe a conceptually straightforward and numerically tractable model that quantitatively captures the separation dependence and temperature-dependent strength of these DNA-induced interactions, without empirical corrections. This model was equally successful when describing the more complex and practically relevant case of grafted DNA brushes with self-interactions that compete with interparticle bridge formation. Together, our findings motivate a nanomaterial design approach where unique functional structures can be found computationally and then reliably realized in experiment.colloidal iteractions | functional particles | nucleic acids | polymer entropy | optical tweezers A promising route to forming unique nanoparticle-based materials is directed self-assembly-where the interactions among multiple species of suspended particles are intentionally designed to favor the self-assembly of a specific cluster arrangement or nanostructure. DNA provides a natural tool (1-3) for directed particle assembly because DNA double helix formation is chemically specific-particles with short single-stranded DNAgrafted on their surfaces will be bridged together if and only if those strands have complementary base sequences, allowing the two strands to spontaneously hybridize to form double-stranded DNA. Moreover, the temperature-dependent stability of such DNA bridges allows the resulting attraction to be modulated (1, 2) from negligibly weak to effectively irreversible over a convenient range of temperatures. Several groups have recently used such interactions to drive the assembly of three-dimensional (3D), crystalline structures from nanoscopic (4-8) and microscopic (9, 10) particles. Ultimately, we envision a highly versatile nanomaterial design protocol in which a user-designed matrix of specific interactions among multiple particle species leads to sequential or even hierarchical assembly of complex particle structures, controlled by a user-designed thermal program. Unlike this vision of designable, sequential, and hierarchical assembly among a s...

Colloquium : Toward living matter with colloidal particles

“…Our simulation contains N colloidal spheres of diameter D, with an interaction range of 1.05D, a range corresponding roughly to that of 1-µm DNA-coated particles (Rogers and Crocker, 2011). For both the clusters of section II (with N < 10) and for larger, more complicated structures the theory quantitatively agrees with the simulations.…”

Polygamous particles

“…This configuration, where A-A and B-B bonds do not occur but A-B bonds do (14)(15)(16), has been exploited to form more complex crystals, such as BCC or CsCl structures (12,17). Over the past several years, there has been a great deal of progress in modeling the DNA-mediated interparticle interaction and making quantitative comparisons with experiments (16,(18)(19)(20)(21)(22)(23). Although nanoscale particles are typically coated with tens to hundreds of DNA molecules, and micrometer-scale colloids can be coated with 10 4 -10 5 DNA strands, there has been little work on coating particles with more than one type of DNA sequence on the same particle.…”

Stoichiometric control of DNA-grafted colloid self-assembly

“…Here, the linker and size ratios are defined as the ratio of the number of grafted DNA linkers and of the hydrodynamic radii of the complementary particles in the system, respectively. This result reinforces the commonly held view that the desired crystal will only form if the right stoichiometry is used.Similarly, several coarse-grained models also allow for the rapid determination of the crystal structure formed by binary mixtures of DNA-grafted colloids (23)(24)(25). The complementary contact model (CCM) is a canonical example of such a coarsegrained description (23).…”