2D and 3D DNA Lattices Via Staggered Assembly of the Double-Decker Tile

We report a two dimensional DNA lattice (named 2D staggered doubledecker lattice, abbreviated to 2D-SDD lattice) and a three dimensional DNA lattice (named 3D staggered doubledecker lattice, abbreviated to 3D-SDD lattice) self-assembled from the doubledecker tile. The doubledecker (DD) tile is a cross shaped DNA nanostructure that has previously been shown (Majumder et al., 2011) to assemble into large defect-free 2D lattices. It consists of two 4×4 cross tiles (Yan et al., 2003) sitting on top of each other, connected via a Holliday junction strand crossover between every pair of vertically adjacent double helices and every pair of horizontally adjacent double helices. There are 18 nucleotides between horizontal and vertical crossovers, approximating 1.75 full turns of the DNA double helix. We program the sticky end attachments so that neighboring tiles in the horizontal plane are vertically offset before attaching. This allows the DD tile to assemble in three mutually orthogonal directions, forming the 3D-SDD lattice (Fig. 1(d)). Each DD tile that attaches to the lattice grows the lattice by approximately 30nm in the horizontal plane and approximately 2nm vertically. This asymmetry in the dimensions of the DD tile implies that a perfect 3D-SDD lattice with equal number of tiles in all three orthogonal directions would be 15 times as wide as it is high. In practice, AFM images reveal that the 3D-SDD lattice spans several micrometers in the horizontal direction and upto 100nm vertically (1(e),(f)). Even accounting for the asymmetry in the DD tile dimensions, the 3D-SDD lattice prefers growth in the horizontal plane as opposed to vertical growth. The electrostatic repulsion between vertical layers of the lattice due to the negative charge on the DNA backbone might be a reason for this preference. We also report the assembly of a large two dimensional periodic square lattice (termed 2D-SDD lattice) via a staggered attachment of the DD tile (Figure 1(a)). The 2D-SDD lattice may be viewed as a single layer of the 3D-SDD lattice, achieved by using blunt strands (strands without sticky-ends) in one of the two layers of the DD tile. The layer that does not take part in the assembly exhibits glide-reflectional symmetry and alternately faces up and down as one moves over the lattice along the arms of the DD tile. This layer can be modified for attachment of proteins, gold nanoparticles etc. without affecting the structural integrity of the lattice. AFM images indicate that the 2D-SDD …