8G4G

Crystal Engineering with One 8-mer DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Divergence and Convergence: Complexity Emerges in Crystal Engineering from an 8-mer DNA.

Zhao, J.Zhang, C.Lu, B.Sha, R.Noinaj, N.Mao, C.

(2023) J Am Chem Soc 145: 10475-10479

  • DOI: https://doi.org/10.1021/jacs.3c01941
  • Primary Citation of Related Structures:  
    8G4G

  • PubMed Abstract: 

    Biology provides plenty of examples on achieving complicated structures out of minimal numbers of building blocks. In contrast, structural complexity of designed molecular systems is achieved by increasing the numbers of component molecules. In this study, the component DNA strand assembles into a highly complex crystal structure via an unusual path of divergence and convergence. This assembly path suggests a route to minimalists for increasing structural complexity. The original purpose of this study is to engineer DNA crystals with high resolution, which is the primary motivation and a key objective for structural DNA nanotechnology. Despite great efforts in the last 40 years, engineered DNA crystals have not yet consistently reached resolution better than 2.5 Å, limiting their potential uses. Our research has shown that small, symmetrical building blocks generally lead to high resolution crystals. Herein, by following this principle, we report an engineered DNA crystal with unprecedented high resolution (2.17 Å) assembled from one single DNA component: an 8-base-long DNA strand. This system has three unique characteristics: (1) It has a very complex architecture, (2) the same DNA strand forms two different structural motifs, both of which are incorporated into the final crystal, and (3) the component DNA molecule is only an 8-base-long DNA strand, which is, arguably, the smallest DNA motif for DNA nanostructures to date. This high resolution opens the possibility of using these DNA crystals to precisely organize guest molecules at the Å level, which could stimulate a range of new investigations.


  • Organizational Affiliation

    Institute of Clinical Pharmacology, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Anhui Medical University, Hefei 230032, China.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*G)-3')A [auth E],
B [auth A]
3synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*CP*GP*GP*CP*CP*G)-3')C [auth B]8synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*CP*GP*G)-3')D [auth C],
E [auth D]
5synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.639α = 90
b = 69.639β = 90
c = 72.756γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCMMI-2025187
National Science Foundation (NSF, United States)United StatesCCF-2107393
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127884
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127896

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references