DNACOLLOIDS · Self-assembly of DNA-coated colloidal particles

Self-assembly of DNA-coated colloidal particles

DNA has proven to be a versatile building material, e.g. nano- or micron-sized colloids can be dressed with polymers from which short single-stranded DNA sequences protrude. Such so-called 'sticky ends' can allow a colloid to bind to a colloid carrying the complementary sticky-end sequence, and thereby, colloids can form three-dimensional networks of auto-assembled particles. However, experimental exploration on self-assembling ordered structures is still in its infancy, with the main hurdle being the lack of understanding of the thermodynamics and kinetics of DNA-mediated self-assembly, which leads to limited control of the complexity of the structures that self-assemble. Theoretical work up to now was mainly based on assumption of pair interactions between DNA-coated colloids, which cannot capture the discrete nature of binding of single strands, while computational work was mainly based on ad-hoc coarse-grained models. While these efforts helped to gain qualitative insight into the behaviour of DNA coated colloids, quantitative models as well as adequate simulation techniques were lacking to date. In the current project, we developed accurate 'ab initio' models of DNA-coated colloids in a multi-stage coarse-graining procedure and at the experimentally relevant conditions in an effort to elucidate the necessary conditions to self-assemble complex structures. In a first step, we found a suitable coarse-graining for the DNA strands, modelling them as electrostatic freely jointed chains to capture the electrostatic repulsion of the phosphate-sugar backbone of DNA. While this is an appropriate description of the DNA used in the present systems, the model is too detailed to allow for large-scale computational exploration of the behaviour of DNA-coated colloids. We therefore further coarse-grained the system by identifying the important degrees of freedom: each reactive end is described as an entity, while the rest of the polymeric spacers and the colloid itself are combined to another entity. Further, we developed new Monte Carlo simulations containing an explicit binding move between sticky ends. With this accurate model ready at hand, we studied in detail the pair and three-body interactions between colloids. While the pair-interactions can be used as a further coarse-graining stage, we see from study of three-body influences that this is only an accurate model for large separations between DNA-coated colloids and at temperatures close to the melting temperature of the assemblies. We then implemented a detailed computational study of ordered structures of DNA coated colloids, based on an experimentally realised system. We considered several crystalline structures of different complexity via genetic algorithms and suitable MC simulations, which we developed from scratch. These methods (which are part of the main achievements of this project) provide powerful tools that can also be used beyond DNA-coated colloids for arbitrary colloidal soft matter systems, especially those where complex building blocks can explicitly bind to each other. This study provided a proof-of-principle of the strength of the present computational approach: our findings (as e.g. melting temperature of the crystals or equilibrium structure and lattice spacing) are compared to experimental results, showing agreement to within few percent. Therefore, our multi-stage coarse-graining approach allows to predict properties of arbitrary DNA-coated colloidal systems via direct mapping between the model and the experimental system under consideration, which we see as the major achievement of this project. In summary, the model developed in the current project allows for the computer-aided design of complex building blocks, helping to path the way to construction of complex self-assembled structures.

Data: CORDIS, © European Union