8EPD

Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions.

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

(2023) J Am Chem Soc 145: 4853-4859

  • DOI: https://doi.org/10.1021/jacs.3c00081
  • Primary Citation of Related Structures:  
    8EP8, 8EPB, 8EPD, 8EPE, 8EPF, 8EPG, 8EPI, 8F40, 8F42

  • PubMed Abstract: 

    Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA-molecule interactions because such information is critically needed for understanding the underlying rules of DNA-molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule-DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide-DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.


  • Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*TP*TP*CP*C)-3')A [auth C]6synthetic construct
Sequence Annotations
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  • Reference Sequence

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

Find similar nucleic acids by:  Sequence   |   3D Structure  

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.166α = 90
b = 34.166β = 90
c = 104.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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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 States1R01GM127884
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM127896

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description