5XK0

Structure of 8-mer DNA2

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

  • Deposited: 2017-05-04 Released: 2017-12-06 
  • Deposition Author(s): Liu, H.H., Gan, J.H.
  • Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs

Liu, H.H.Shen, F.S.Haruehanroengra, P.Yao, Q.Q.Cheng, Y.S.Chen, Y.Q.Yang, C.Zhang, J.Wu, B.X.Luo, Q.Cui, R.X.Li, J.X.Ma, J.B.Sheng, J.Gan, J.H.

(2017) Angew Chem Int Ed Engl 56: 9430-9434

  • DOI: https://doi.org/10.1002/anie.201704891
  • Primary Citation of Related Structures:  
    5XJZ, 5XK0, 5XK1

  • PubMed Abstract: 

    Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag I is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-Ag I -C pairs and the first reported G-Ag I -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag I -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence-dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between Ag I and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200433, China.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')8synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.012α = 90
b = 42.012β = 90
c = 25.016γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370728

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description