Design and Synthesis of a Reconfigurable DNA Accordion Rack

Summary

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

Abstract

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.

Introduction

Mechanical systems based on DNA nanostructures or DNA nanomachines^1,2,3,4,5 are unique because they produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, according to various biomolecular stimuli^2,3,6. 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....

Protocol

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 (Figure 2).
3. Click the pencil tool and draw each beam on the right edit panel on the caDNAno¹⁴. Br....

Results

The designed 6 by 6 DNA accordion rack is simulated from the oxDNA^16,17 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 .......

Discussion

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 flexibility^14,15. From this, we expect that the protocol can accelerate various researches using DNA accordion racks. In addition,.......

Materials

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