Engineering DNA-Mediated Colloidal Crystallization

Abstract

DNA is a powerful and versatile tool for nanoscale self-assembly. Several researchers have assembled nanoparticles and colloids into a variety of structures using the sequence-specific binding properties of DNA. Until recently, however, all of the reported structures were disordered, even in systems where ordered colloidal crystals might be expected. We detail the experimental approach and surface preparation that we used to form the first DNA-mediated colloidal crystals, using 1 mum diameter polystyrene particles. Control experiments based on the depletion interaction clearly indicate that two standard methods for grafting biomolecules to colloidal particles (biotin/avidin and water-soluble carbodiimide) do not lead to ordered structures, even when blockers are employed that yield nominally stable, reversibly aggregating dispersions. In contrast, a swelling/deswelling-based method with poly(ethylene glycol) spacers resulted in particles that readily formed ordered crystals. The sequence specificity of the interaction is demonstrated by the crystal excluding particles bearing a noninteracting sequence. The temperature dependence of gelation and crystallization agree well with a simple thermodynamic model and a more detailed model of the effective colloidal pair interaction potential. We hypothesize that the surfaces yielded by the first two chemistries somehow hinder the particle-particle rolling required for annealing ordered structures, while at the same time not inducing a significant mean-force interaction that would alter the self-assembly phase diagram. Finally, we observe that particle crystallization kinetics become faster as the grafted-DNA density is increased, consistent with the particle-particle binding process being reaction, rather than diffusion limited.

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

“…The material design space for this versatile technology-particles labeled with DNA-is vast: an engineered matrix of specific interactions between a library of different sized (and shaped) particle species whose core chemistry is effectively decoupled from the final structure and assembly processes. The material processing design space is equally vast: the ability to modulate the interactions using thermal schedules (5), added soluble strands (28), enzymes (29), photochemistry (30,31), and DNA actuators (6, 18) promise a wide variety of schemes for controlling nucleation (27), growth (10), structural transformations (6), and replication (30) to produce useful unique particle-based metamaterials in the form of clusters, bulk crystals, thin films, and heterojunctions. Navigating this complex space will rely on simulation now enabled by a framework for computing interparticle interaction matrices reliably, across a range of process conditions.…”

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

“…The sequence specificity, binding fidelity and mechanical rigidity of the DNA molecule have made it a promising building block for the construction of new materials [33][34][35] and devices [36]. DNA has also been conjugated to other particles to direct their assembly into higher-order superstructures [37,38], including encoding the delicate balance between attractive and repulsive interactions required to drive crystallisation in low density colloidal systems [39][40][41]. Hydrophobic modifications to DNA strands have recently been used to for the higher-order assembly of DNA-cages and the fabrication of DNA cages with hydrophobic cores that can host poorly water soluble guest compounds [42].…”

Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm

“…DNA-grafted colloids | inverse design | nanostructures | crystal lattice predictions | evolutionary algorithm A topic of much interest in the current literature is the selfassembly of colloid particles multiply grafted with ssDNA molecules (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). The typical experimental system consists of two types of colloids grafted with complementary ssDNA sequences.…”

“…However, there has been some progress in theory and simulation on understanding this assembly process (5,6,(11)(12)(13). The recent work of Starr and coworkers, for example, has emphasized the complicated phase and assembly behavior of these materials (11,12,14).…”