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Summary

Abstract

Introduction

Protocol

Representative Results

Discussion

Acknowledgements

Materials

References

Bioengineering

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published: August 15th, 2018

DOI:

10.3791/58364

1Department of Electrical and Computer Engineering, Seoul National University, 2Interdisciplinary Program for Bioengineering, Seoul National University, 3Institute of Entrepreneurial Bio Convergence, Seoul National University, 4Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital
* These authors contributed equally

We describe the detailed protocol for design, simulation, wet-lab experiments, and analysis for a reconfigurable DNA accordion rack of 6 by 6 meshes.

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration.

In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.

Mechanical systems based on DNA nanostructures or DNA nanomachines1,2,3,4,5 are unique because they produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, according to various biomolecular stimuli2,3,6. By attaching functional materials on these structures and controlling their positions, these structures can be applied to various areas. For example, DNA nanomachines have b....

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1. Design of the 6 by 6 DNA Accordion Rack with caDNAno14

  1. Download and install caDNAno 2.0 software14 to design a DNA accordion rack (caDNAno 2.5 is also available on https://github.com/cadnano/cadnano2.5). Open caDNAno14 and click the Square Tool to add a new part with a square lattice.
  2. Number each beam of the accordion rack and draw on the left lattice panel of the caDNAno14 (

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The designed 6 by 6 DNA accordion rack is simulated from the oxDNA16,17 and the results are shown in Figure 6. From the simulation result, it was confirmed that the intended structure is formed without distortion of the structure.

The TEM images in Figure 7 are images of configured structures with a lock length .......

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This protocol introduces the entire process from design, simulation, synthesis, and analysis of the basic 2D DNA accordion rack. The modified design and simulation rules have been described because the design rule differs from that of standard DNA origami, in that the DNA accordion rack has additional nucleotides at the crossovers for flexibility14,15. From this, we expect that the protocol can accelerate various researches using DNA accordion racks. In addition,.......

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This research was partially supported by the Global Research Development Center Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Science and ICT (MSIT) (2015K1A4A3047345) and Nano·Material Technology Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT) (2012M3A7A9671610). The Institute of Engineering Research at Seoul National University provided research facilities for this work. Authors acknowledge gratitude towards Tae-Young Yoon (Biological Sciences, Seoul National University) regarding the fluorescence spectroscopy for the FRET analysis.

....

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Name Company Catalog Number Comments
M13mp18 Single-stranded DNA NEB N4040s
1M MgCl2 Solution Biosesang M2001
Tris-EDTA buffer Biosesang T2142
Nuclease-Free Water Qiagen 129114
5M Sodium Chloride solution Biosesang s2007
PEG 8000 Sigma Aldrich 1546605
10N NaOH Biosesang S2038
Uranyl formate Thomas Science C993L42
Thermal cycler C1000 Biorad
Nanodropic 2000 Thermo Fisher Scientific
TEM (LIBRA 120)   Carl Zeiss
Fluorometer Enspire 2300 Perkin-Elmer
Centrifuge Labogene LZ-1580

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