DNA Origami: Synthesis and Self‐Assembly
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- Abstract
- Table of Contents
- Materials
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- Literature Cited
Abstract
DNA origami is an emerging technology for designing defined two? and three?dimensional (2D and 3D) DNA nanostructures. Here, we report an introductory practical guide with step?by?step experimental details for the design and synthesis of origami structures, and their size expansion in 1D and 2D space by means of self?assembly. Curr. Protoc. Nucleic Acid Chem. 48:12.9.1?12.9.18. © 2012 by John Wiley & Sons, Inc.
Keywords: DNA origami; designed nanospace; self?assembly; DNA nanotechnology; atomic force microscopy
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Basic Protocol 1: Structural Design of DNA Origami and Additional Design Strategies for 1D and 2D Self‐Assembly
- Basic Protocol 2: Synthesis of DNA Origami
- Basic Protocol 3: 1D Self‐Assembly of Origami Structures
- Basic Protocol 4: 2D Self‐Assembly of Multiple Origami Structures
- Reagents and Solutions
- Commentary
- Literature Cited
- Figures
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Basic Protocol 1: Structural Design of DNA Origami and Additional Design Strategies for 1D and 2D Self‐Assembly
Materials
Basic Protocol 2: Synthesis of DNA Origami
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Figure 12.9.1 The schematic drawing of the structures prepared using the DNA origami method and their AFM images. The top row represents the folding paths of the scaffold. Only the raster fill patterns of the scaffold are shown and the staples are not included here. The middle row represents the diagrams after the addition of staples, showing the bend of helices at crossovers where helices touch and away from crossovers where helices bend apart. AFM images of the representative schemes are given in the bottom row. AFM images correspond to a size of 165 × 165 nm. View Image -
Figure 12.9.2 Design of a DNA origami structure. (A ) The schematic design of a shape (red) approximated by parallel double helices joined by periodic crossovers (blue). (B ) A scaffold strand (black) runs through every helix and forms more crossovers (red). (C ) As first designed, most staples bind two helices and are 16‐mers. Arrows point to nicks that can be sealed to create longer strands. The yellow diamond indicates a position at which staples may be cut and resealed to bridge the seam. (D ) A finished design after merges and rearrangements of the staples along the seam. Most staples are 32‐mers spanning three helices. View Image -
Figure 12.9.3 The design of a DNA origami “jigsaw piece” structure and its self‐assembly. (A ) Structure of the designed DNA jigsaw piece with a tenon and mortise. (B ) Scheme of the self‐assembly of the DNA jigsaw piece monomer. (C ) The detailed connection around the tenon and mortise between neighboring DNA jigsaw piece monomers. Black and colored DNA sequences denote the M13 and the staple strands, respectively. Blue and green arrow staples represent the left‐ and right‐side edges of the DNA jigsaw piece monomer, respectively. Red arrows represent the connecting staples that bridge the neighboring tiles. View Image -
Figure 12.9.4 (A ) A model structure of the designed DNA JP having a mortise and a tenon (JP‐5). (B ) Scheme of the JP‐5 represented as a matrix of blocks. One block represents four 32‐mer duplexes. (C ) Scheme of the nine monomer JPs showing the position of the tenon, the mortise, and the hairpin markers along with their AFM images. Pink blocks at the bottom of each JP represent the loops. Circles denote the set of four individual hairpin markers. AFM images correspond to a size of 200 × 200 nm. View Image -
Figure 12.9.5 AFM images of the rectangular DNA origami JP (left) and frame structure (right) lyophilized and redissolved in Milli‐Q water. The image sizes are given in each image. View Image -
Figure 12.9.6 DNA JP monomers and self‐assembled structures. (A ) Schematic drawings of the monomers A‐D. Each JP differs by their relative positions of the tenon and mortise. Pink blocks represent hairpin DNA markers for the identification of the tenon and mortise in the AFM image. (B ) AFM images of the DNA jigsaw piece monomers A, B, C, and D after fast annealing from 85° to 25°C at a rate of −2°C/min. (C ) Oligomerization of the single DNA jigsaw piece monomer by self‐assembly from 50° to 15°C at a rate of –0.05°C/min. View Image -
Figure 12.9.7 Self‐assembly of five different DNA JP monomers. (A ) Scheme of the five different monomers and their self‐assembly. (B ) AFM images of the DNA jigsaw piece monomers after fast annealing. (C ) AFM image of the self‐assembled pentamer after slow annealing. View Image -
Figure 12.9.8 (A ) Schemes and AFM images of the trimers assembled along the helical side. (B ) Schematic drawing of the desired final structure of the self‐assembly. (C ) AFM image of the self‐assembled structure prepared from the pre‐assembled trimers. The bright spots in the image represent the loops at the bottom of each monomer. Light spots represent the hairpin markers, which are adjacent to the tenons and the mortises. The image sizes are shown below each image. View Image
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