self-assembly-complex-two-dimensional-shapes-from-single-stranded-dna

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Current methods in DNA nano-architecture have successfully engineered a variety of 2D and 3D structures using principles of self-assembly. In this ...

A new triple crossover triangle (TXT) motif was conceived on the basis of the DNA triple crossover (TX) motif. The new motif is rigid and triangular prism-shaped, out of which 1-D, 2-D, and 3-D DNA structures can be assembled. The 1-D TXT array was self-assembled and was observed by the TEM with negative staining by uranyl acetate. The architectural schemes for 2-D and 3-D structures are presented.

A new triple crossover triangle (TXT) motif for DNA self-assembly.

Capture and release of protein by a reversible DNA-induced sol-gel transition system.

A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 x 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions.

UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation.

We report the design and construction of a nanometer-sized tetrahedron from a single strand of DNA that is 286 nucleotides long. The formation of the tetrahedron was verified by restriction enzyme digestion, Ferguson analysis, and atomic force microscopy (AFM) imaging. We further demonstrate that synthesis of the tetrahedron can be easily scaled up through in vivo replication using standard molecular cloning techniques. We found that the in vivo replication efficiency of the tetrahedron is significantly higher in comparison to in vitro replication using rolling-circle amplification (RCA). Our results suggest that it is now possible to design and replicate increasingly complex, single-stranded DNA nanostructures in vivo.

A replicable tetrahedral nanostructure self-assembled from a single DNA strand.

An aptamer-based DNA strand, captured with a specific molecule from a multi-species system, was used to initiate crosslinking of the hydrogel. The hydrogel can then be dissolved with a displacement of the DNA strand and the captured molecule can be released. Recognition and separation at the molecular level is thus achieved.

Aptamer based reversible DNA induced hydrogel system for molecular recognition and separation.

Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. 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-assembly. Although ribbons and tubes with controlled circumferences 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 3 nm-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.

Complex shapes self-assembled from single-stranded DNA tiles.

We describe a method to form custom-shaped inorganic oxide nanostructures by using DNA nanostructure templates. We show that a DNA nanostructure can modulate the rate of chemical vapor deposition (CVD) of SiO2 and TiO2 with nanometer scale spatial resolution. The resulting oxide nanostructure inherits its shape from the DNA template. This method generates both positive-tone and negative-tone patterns on a wide range of substrates and is compatible with conventional silicon nanofabrication processes. Our result opens the door to use DNA nanostructure as a general purpose template for high resolution nanofabrication.

Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates.

Nucleic acids have emerged as effective materials for assembling complex nanoscale structures. To tailor the structures to function optimally for particular applications, a broad structural design space is desired. Despite the many discrete and extended structures demonstrated in the past few decades, the design space remains to be fully explored. In particular, the complex finite-sized structures produced to date have been typically based on a small number of structural motifs. Here, we perform a comprehensive study of the design space for complex DNA structures, using more than 30 distinct motifs derived from single-stranded tiles. These motifs self-assemble to form structures with diverse strand weaving patterns and specific geometric properties, such as curvature and twist. We performed a systematic study to control and characterize the curvature of the structures, and constructed a flat structure with a corrugated strand pattern. The work here reveals the broadness of the design space for complex DNA nanostructures.

Design space for complex DNA structures.

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold-mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural-reconfiguration method that utilizes the modularly interconnected architecture of single-stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two-dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three-dimensional DNA cuboid.

Article	Year
A new triple crossover triangle (TXT) motif for DNA self-assembly. Biomacromolecules\| PubMed ID: 16153089	2005
Capture and release of protein by a reversible DNA-induced sol-gel transition system. Angewandte Chemie (International ed. in English)\| PubMed ID: 18033711	2008
UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation. Nucleic acids research\| PubMed ID: 19228709	2009
A replicable tetrahedral nanostructure self-assembled from a single DNA strand. Journal of the American Chemical Society\| PubMed ID: 19737020	2009
Aptamer based reversible DNA induced hydrogel system for molecular recognition and separation. Chemical communications (Cambridge, England)\| PubMed ID: 20672164	2010
Complex shapes self-assembled from single-stranded DNA tiles. Nature\| PubMed ID: 22660323	2012
Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates. Journal of the American Chemical Society\| PubMed ID: 23574340	2013
Design space for complex DNA structures. Journal of the American Chemical Society\| PubMed ID: 24256506	2013
Complex reconfiguration of DNA nanostructures. Angewandte Chemie (International ed. in English)\| PubMed ID: 24899518	2014

Bryan Wei

Biography

JoVE Journal Publications

Other Publications