1D31

THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Three-dimensional structures of bulge-containing DNA fragments.

Joshua-Tor, L.Frolow, F.Appella, E.Hope, H.Rabinovich, D.Sussman, J.L.

(1992) J Mol Biol 225: 397-431

  • DOI: 10.1016/0022-2836(92)90929-e
  • Primary Citation of Related Structures:  
    1D31

  • PubMed Abstract: 
  • The three-dimensional structure of a DNA tridecamer d(CGCAGAATTCGCG)2 containing bulged adenine bases was determined by single crystal X-ray diffraction methods, at 120 K, to 2.6 A resolution. The structure is a B-DNA type double helix with a single duplex in the asymmetric unit ...

    The three-dimensional structure of a DNA tridecamer d(CGCAGAATTCGCG)2 containing bulged adenine bases was determined by single crystal X-ray diffraction methods, at 120 K, to 2.6 A resolution. The structure is a B-DNA type double helix with a single duplex in the asymmetric unit. One of the bulged adenine bases loops out from the double helix, while the other stacks in to it. This is in contrast to our preliminary finding, which indicated that both adenine bases were looped out. This revised model was confirmed by the use of a covalently bound heavy-atom derivative. The conformation of the looped-out bulge hardly disrupts base stacking interactions of the bases flanking it. This is achieved by the backbone making a "loop-the-loop" curve with the extra adenine flipping over with respect to the other nucleotides in the strand. The looped-out base intercalates into the stacked-in bulge site of a symmetrically related duplex. The looped-out and stacked-in bases form an A.A reversed Hoogsteen base-pair that stacks between the surrounding base-pairs, thus stabilizing both bulges. The double helix is frayed at one end with the two "melted" bases participating in intermolecular interactions. A related structure, of the same tridecamer, after soaking the crystals with proflavin, was determined to 3.2 A resolution. The main features of this B-DNA duplex are basically similar to the native tridecamer but differ in detail especially in the conformation of the bulged-out base. Accommodation of a large perturbation such as that described here with minimal disruption of the double helix shows both the flexibility and resiliency of the DNA molecule.


    Related Citations: 
    • The Three-Dimensional Structure of a DNA Duplex Containing Looped-out Bases
      Joshua-Tor, L., Rabinovich, D., Hope, H., Frolow, F., Appella, E., Sussman, J.L.
      (1988) Nature 334: 82
    • Crystallization of a DNA Tridecamer d(CGCAGAATTCGCG)
      Saper, M.A., Eldar, H., Mizuuchi, K., Nickol, J., Appella, E., Sussman, J.L.
      (1986) J Mol Biol 188: 111

    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B13N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Observed: 0.186 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.48α = 90
    b = 42.84β = 99.36
    c = 25.16γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement
    X-PLORrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1992-04-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance