4RIP

BromoUracil substituted structure of intercalation-locked DNA tetraplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An intercalation-locked parallel-stranded DNA tetraplex.

Tripathi, S.Zhang, D.Paukstelis, P.J.

(2015) Nucleic Acids Res 43: 1937-1944

  • DOI: 10.1093/nar/gkv033
  • Primary Citation of Related Structures:  
    4RIM, 4RIP

  • PubMed Abstract: 
  • DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT) ...

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. (1)H-(1)H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, Center for Biomolecular Structure & Organization, Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA paukstel@umd.edu.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*(BRU)P*CP*GP*GP*AP*(BRU)P*GP*AP*T)-3')A11synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.10 Å
    • R-Value Free: 0.238 
    • R-Value Work: 0.232 
    • R-Value Observed: 0.233 
    • Space Group: P 62 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 26.4α = 90
    b = 26.4β = 90
    c = 166.452γ = 120
    Software Package:
    Software NamePurpose
    CBF1.3data collection
    SHELXSphasing
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-02-11
      Type: Initial release
    • Version 1.1: 2015-02-25
      Changes: Derived calculations
    • Version 1.2: 2015-03-04
      Changes: Database references