Three-Dimensional Structures Self-Assembled from DNA Bricks

Abstract

We describe a simple and robust method to construct complex three-dimensional (3D) structures using short synthetic DNA strands that we call “DNA bricks”. In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base-pair interaction between bricks defines a voxel with dimensions 2.5 nanometers by 2.5 nanometers by 2.7 nanometers, and a master brick collection defines a “molecular canvas” with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features as well as intricate interior cavities and tunnels.

DNA self-assembly scaled up

“…Collections of SSTs are used to form 2D sheets or 3D blocks that can be selectively 'sculpted' to create different patterns and shapes, simply by including or omitting specific SSTs 12 . But the sizes of the DNA structures produced in this way are generally comparable to the sizes of origami nanostructures; larger structures have been prepared only in low yields.…”

Beyond the smiley face: applications of structural DNA nanotechnology

“…Last, DNA bricks have been designed using 32-nucleotide (nt) synthetic DNA strands to create 3D structures [11]. A DNA brick comprised four 8-nt domains; two of these domains are ‘head’ domains while the other two are ‘tail’ domains (Figure 4).…”

“…Furthermore, the process was robust in sequence composition (as random sequences were used), strand synthesis (as the protocol did not require purified DNA), and stoichiometry (unlike previous efforts, no strict control was necessary). These assets will allow for new biotechnology such as programmable molecular probes, smart drug delivery particles, and photonics applications in the future [11].

10.1080/20022727.2018.1430976-F0004Figure 4.A DNA brick comprised four 8-nt domains; two of these domains are ‘head’ domains while the other two are ‘tail’ domains.

…”

Drug delivery systems based on nucleic acid nanostructures

“…As introduced above, the DNA origami technique deals with folding a ss long DNA strand into almost any 2D or 3D shape with the help of many different "staple" strands [8,76]. These strands bind to the long one at different positions to define the overall structure and they can be utilized to site specifically introduce additional functionalities by hybridization.…”