How to build nanoblocks using DNA scaffolds

In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of microand nanoparticle clusters using DNA scaffolds. In this letter we consider a DNA scaffold method to self-assemble clusters of ”colored” particles. Stable clusters of identical microspheres have recently been produced by an entirely different method. Our DNA based approach self-assembles clusters with additional degrees of freedom associated with particle permutation. We demonstrate that in the non-equilibrium regime of irreversible binding the self-assembly process is experimentally feasible. These color degrees of freedom may allow for more diverse intercluster interactions essential for hierarchical self-assembly of larger structures. DNA has attracted significant attention for its potential applications in nanoscience ( [1], [2], [3], [4], [5], [6], [7], [8], [9], [10]). One recent non-DNA based advance is the self-assembly of stable clusters composed of identical microspheres [11]. In this letter we consider the self-assembly of microand nanoparticle clusters similar to those of [11], where DNA scaffolds govern the selfassembly process. The plan for the letter is the following. We first introduce the basic strategy of our self-assembly proposal. The goal is to maximize the yield for a particular type of cluster we call the star cluster. We analytically calculate the yield of the star cluster in the regime of irreversible binding. The analytical results are compared to the numerical results for the full aggregation equations. From an experimental perspective, the most important result is the determination of an optimal concentration ratio for experiments (see Eq. 8). To conclude we discuss the experimental feasibility of the self-assembly proposal. The basic idea behind the procedure is as follows (see Fig. 1). Particles are functionalized with single-stranded DNA (ssDNA) markers which determine the particle color. There may be many DNA attached to each particle, but on any given particle the marker sequence is identical. One then introduces DNA scaffolds to the system. The scaffold is a structure with f ssDNA markers, each marker complementary to one of the particle colors. Hybridization of the ssDNA markers on the particles to those on the scaffold results in the formation of colored particle clusters. Because there are many DNA attached to each particle, clusters can form which contain more than one scaffold. The essential goal of the procedure is to maximize the concentration of a particular type of cluster which we denote the star cluster. The star cluster contains one and only one scaffold to which f particles are attached, each particle having a distinct color. We should note that the role of the scaffold could also be played by a patchy particle ( [12], [13], [14]). For example, these patches are regions on the particle surface where one can graft ssDNA markers. In this case there may be several DNA connections between a patch and colored particle. Our conclusions will still be valid, provided the patch size is chosen so that a patch interacts with at most one particle. Previously we performed an equilibrium calculation to determine the yield of the star cluster [15]. The results of that study indicated that the concentration of scaffolds must be kept very small to prevent the aggregation of larger clusters. From an experimental perspective this result is somewhat disappointing, since the overall yield of the star cluster is proportional to the scaffold concentration. The situation is considerably improved in the regime of irreversible binding of particles to scaffolds. In what follows we present a calculation for the yield of the star cluster far from equilibrium.