Manipulating DNA probe presentation via enzymatic cleavage of diluent strands

A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision

Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.

Altering colloidal surface functionalization using DNA encapsulated inside monodisperse gelatin microsphere templates

Soluble oligonucleotides are typically introduced to bulk solution to promote hybridization activity on DNA-functionalized surfaces. Here, an alternative approach is explored by encapsulating secondary target strands inside semipermeable colloidal satellite assemblies, then triggering their release at 37 °C for subsequent surface hybridization activity. To prepare DNA-loaded satellite assemblies, uniform gelatin microspheres are fabricated using microfluidics, loaded with 15 base-long secondary DNA targets, capped with a polyelectrolyte bilayer, and finally coated with a monolayer of polystyrene microspheres functionalized with duplexes comprised of immobilized probes and soluble, 13 base-long hybridization partner strands. Once warmed to 37 °C, secondary DNA targets are released from the gelatin template and then competitively displace the shorter, original hybridization partners on the polystyrene microspheres.

Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry

Imaging flow cytometry was used to analyze the self-assembly of DNA-conjugated polystyrene microspheres. This technique enables quantitative analysis of the assembly process and thereby enables detailed analysis of the effect of structural and process variables on the assembly yield. In a demonstration of the potential of this technique, the influence of DNA strand base pair (bp) length was examined, and it was found that 50 bp was sufficient to drive the assembly of microspheres efficiently, forming not only dimers but also chainlike structures. The effect of stoichiometry on the yield was also examined. The analysis demonstrated that self-assembly of 50 bp microspheres can be driven nearly to completion by stoichiometric excess in a manner similar to Le Chatelier's principle in common chemical equilibrium.

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

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.

DNA density-dependent assembly behavior of colloidal micelles

A key advantage of DNA-mediated colloidal assembly is the ability to tune the strength of adhesion between particles based on sequence characteristics. In the current study, we have investigated DNA-mediated assembly of polystyrene colloidal particles as a function of sequence length, sequence fidelity, and probe density for DNA sequences patterned from the Salmonella genome. The results of our work indicate that the density of DNA probe strands heavily influences the ability of immobilized sequences to hybridize between surfaces of bidisperse colloidal particles. Incubating suspensions at higher temperatures (to minimize secondary structures that might otherwise compromise duplex formation) was also found to have less effect than duplex density on DNA-mediated particle assembly. We believe these results may add to the understanding and design considerations of directed particle assembly using DNA hybridization, especially in the submicrometer and micrometer size regime.