5I36

Crystal structure of color device state A

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2016-02-09 Released: 2017-01-18 
  • Deposition Author(s): Hao, Y., Kristiansen, M., Sha, R., Birktoft, J., Mao, C., Seeman, N.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Army Research Office, Office of Naval Research, Department of Energy (DOE, United States), Gordon and Betty Moore Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.12 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

A device that operates within a self-assembled 3D DNA crystal.

Hao, Y., Kristiansen, M., Sha, R., Birktoft, J.J., Hernandez, C., Mao, C., Seeman, N.C.

(2017) Nat Chem 9: 824-827

  • DOI: https://doi.org/10.1038/nchem.2745
  • Primary Citation of Related Structures:  
    5I36, 5I6Q, 5I6T

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    Department of Chemistry, New York University, New York 10003, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
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')21synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (26-MER)26synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')14synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3')14synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3')14synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
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')21synthetic construct
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  • Reference Sequence

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Entity ID: 7
MoleculeChains LengthOrganismImage
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')21synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.12 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.53α = 98.19
b = 69.131β = 97.34
c = 70.106γ = 99.74
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-29554
National Science Foundation (NSF, United States)United StatesCMMI-1120890
National Science Foundation (NSF, United States)United StatesEFRI-1332411
National Science Foundation (NSF, United States)United StatesCCF-1117210
National Science Foundation (NSF, United States)United StatesCCF-1526650
Army Research OfficeUnited StatesMURI W911NF-11-1-0024
Office of Naval ResearchUnited StatesMURI N000140911118
Department of Energy (DOE, United States)United StatesDE-SC0007991
Gordon and Betty Moore FoundationUnited StatesGBMF3849

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description