Complex shapes self-assembled from single-stranded DNA tiles

Abstract

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes1–25. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape9, 14–16,18–21,25. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA2–5,8,10–13,17,23 or RNA7,22 tiles into periodic3,4,7,22 and algorithmic5 two-dimensional lattices, extended ribbons10,12 and tubes4,12,13, three-dimensional crystals17, polyhedra11 and simple finite two-dimensional shapes7,8. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a ‘single-stranded tile’ (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly12. Although ribbons and tubes with controlled circumferences12 have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands—folded into a 3nm-by-7 nm tile and attached to four neighbouring tiles—acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.

Nucleic Acid Nanotechnology

“…Since its origination in the early 1980s, one of the most important developments in the area is undoubtedly Paul Rothemund's expansion of the scale of target objects through the use of DNA origami (Rothemund 2006). Peng Yin et al's follow-up of scaffold-free large-object construction nicely complements Rothemund's advance (Wei et al 2012). The other key breakthrough in nucleic acid nanotechnology was the development of isothermal strand displacement by Yurke et al (2000); as a consequence of this development, robust sequence-specific (i.e., programmable) devices have been developed (Yan et al 2002) and significantly more complex computations have been undertaken successfully (Qian and Winfree 2011).…”

A Stochastic Approach to Shortcut Bridging in Programmable Matter

“…In passive systems, computational units cannot control their movement and have (at most) very limited computational abilities, relying instead on their physical structure and interactions with the environment to achieve locomotion (e.g., [28,1,21]). A large body of research in molecular self-assembly falls under this category, which has mainly focused on shape formation (e.g., [13,8,27]). Rather than focusing on constructing a specific fixed target shape, our work examines building dynamic bridges whose exact shape is not predetermined.…”

Complex DNA Nanostructures from Oligonucleotide Ensembles

“…Similar limitations in yield have been observed in a related, independently developed strategy for creating DNA nanostructures. 23 In that approach, termed the "single-stranded tile" method, a stencil pattern is used to mask a preconfigured selfassembled DNA "canvas" comprised of a few hundred oligonucleotides. The mask defines the required subset of oligonucleotides to create a large number of different shapes from the same canvas.…”