DNA Origami: Synthesis and Self‐Assembly

Arivazhagan Rajendran1, Masayuki Endo2, Hiroshi Sugiyama2

1 CREST, Japan Science and Technology Corporation (JST), Tokyo, Japan, 2 Institute for Integrated Cell‐Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 12.9
DOI:  10.1002/0471142700.nc1209s48
Online Posting Date:  March, 2012
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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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Table 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

  • Required set of staple strands based on the origami design (see protocol 1)
  • M13mp18 single‐stranded DNA (New England Biolabs, cat. no, N4040S)
  • 10× origami buffer (see recipe)
  • Deionized water by a Milli‐Q system (≥ 18.0 MΩ cm specific resistance; Millipore)
  • Sephacryl S‐300 (High resolution; GE Healthcare, cat. no., 17‐0599‐01)
  • Sephacryl S‐300 solution (see recipe)
  • PCR tubes
  • Thermal cycler
  • Automatic shaker
  • Micro Bio‐Spin chromatography columns (Bio‐Rad, cat. no. 732‐6204)
  • 1.5‐mL microcentrifuge tubes
  • Vortex mixer
  • Microcentrifuge
  • Mica plate (e.g., 1.5‐mm plate; Nano Live Vision, RIBM)
  • AFM instrument
  • –80°C freezer
  • Lyophilizer
NOTE: The use of a particular brand chemical, reagent, or material throughout this protocol is purely the authors' choice. In fact, any brand can be used with the same or similar grade.

Basic Protocol 2: Synthesis of DNA Origami

  • AFM instrument
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Literature Cited

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