5I36 image
Deposition Date 2016-02-09
Release Date 2017-01-18
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5I36
Keywords:
DNA
Title:
Crystal structure of color device state A
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
5.12 Å
R-Value Free:
0.16
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 1
5I36 validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
Chain IDs:A
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (26-MER)
Chain IDs:B
Chain Length:26
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
Chain IDs:C
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3')
Chain IDs:D
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3')
Chain IDs:E
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*AP*GP*AP*TP*AP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*TP*AP*CP*G)-3')
Chain IDs:F
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
Chain IDs:G
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
A device that operates within a self-assembled 3D DNA crystal.
Nat Chem 9 824 827 (2017)
PMID: 28754940 DOI: 10.1038/nchem.2745

Abstact

Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

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Primary Citation of related structures
5I36