Design and Construction of Double-Decker Tile as a Route to Three-Dimensional Periodic Assembly of DNA

Abstract

DNA is a useful material for nanoscale construction. Due to highly specific Watson-Crick base pairing, the DNA sequences can be designed to form small tiles or origami. Adjacent helices in such nanostructures are connected via Holliday junction-like crossovers. DNA tiles can have sticky ends which can then be programmed to form large one-dimensional and two-dimensional periodic lattices. Recently, a three-dimensional DNA lattice has also been constructed. Here we report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it is proposed that the sticky ends of the double-decker tile can be programmed to form a three-dimensional periodic lattice with large cavities that could be used as a scaffold for precise positioning of molecules in space.

Patterning Porous Networks through Self‐Assembly of Programmed Biomacromolecules

“…[36] By exploitingt he same strategy,M ajumder et al designed and built "double-decker" tiles that afforded the self-assembly of 2D networks, extending over tens of micrometers in size ( Figure 8). [39] The double-decker tiles consist of two four-point stars lying one on top of the other,a nd linked by two crossovers in each arm, arranged perpendicular to the plane of the tile (Figure 8a). The sequence composition of each arm was the same, making the four arms of the doubledecker symmetric.…”

“…[76] with permission from Springer Nature, Copyright 2011. mica) for characterization. [31,32,39,40,42,45,49,59] Nevertheless,i n some cases it has been shown that, if the self-assembly of DNA is performedinthe presence of mica, it favors the adsorption of the arrays as it forms, avoiding destructive shear forces associated with the deposition process onto surfaces. Thee forces often lead to fragmentationo ft he fragile array.…”

Bio-surface engineering with DNA scaffolds for theranostic applications

“…For example, the double crossover (DX) motif was used to demonstrate the assembly of the first two dimensional crystalline DNA arrays ( Figure 1B) [2]. Other motifs used in the creation of 2D lattices are the triple-crossover (TX) motif [35], a cross-shaped double-decker tile [36], a tensegrity triangle with duplex [37] and double crossover edges [38], a three-point-star motif where each arm is a four-way junction [39], a four-point-star (cross) motif [40] and a sixpoint-star motif [41]. Recently, a motif based on paranemic crossover (PX) DNA was used to create 2D arrays [42,43].…”

Photonics and plasmonics go viral: self-assembly of hierarchical metamaterials

“…Technologies such as directed polymer assembly, DNA origami, and colloidal systems provide opportunities to organize composite materials in 3D space with high manufacturing precision. For example, DNA-based ‘programming’ exploits the sequence specificity of base pairing to position materials in 2D and 3D space (Doerr 2011; Endo and Sugiyama 2011; Han et al 2011; Lin et al 2006; Liu et al 2011; Majumder et al 2011; Park et al 2006; Rajendran et al 2012; Sacca and Niemeyer 2012; Shih and Lin 2010; Yun et al 2012). Examples of the intricate structures that can be formed with DNA origami can be found in Fig.…”