1D99

STRUCTURAL FEATURES AND HYDRATION OF A DODECAMER DUPLEX CONTAINING TWO C.A MISPAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history


Literature

Structural features and hydration of a dodecamer duplex containing two C.A mispairs.

Hunter, W.N.Brown, T.Kennard, O.

(1987) Nucleic Acids Res 15: 6589-6605

  • DOI: 10.1093/nar/15.16.6589
  • Primary Citation of Related Structures:  
    1D99

  • PubMed Abstract: 
  • X-ray diffraction techniques have been used to characterise the crystal and molecular structure of the deoxyoligomer d(C-G-C-A-A-A-T-T-C-G-C-G) at 2.5A resolution. The final R factor is 0.19 with the location of 78 solvent molecules. The oligomer crystallises in a B-DNA type conformation with two strands coiled about each other to produce a duplex ...

    X-ray diffraction techniques have been used to characterise the crystal and molecular structure of the deoxyoligomer d(C-G-C-A-A-A-T-T-C-G-C-G) at 2.5A resolution. The final R factor is 0.19 with the location of 78 solvent molecules. The oligomer crystallises in a B-DNA type conformation with two strands coiled about each other to produce a duplex. This double helix consists of four A.T and six G.C Watson-Crick base pairs and two C.A mispairs. The mismatched base pairs adopt a "wobble" type structure with the cytosine displaced laterally into the major groove, the adenine into the minor groove. We have proposed that the two close contacts observed in the C.A pairing represent two hydrogen bonds one of which results from protonation of adenine. The mispairs are accommodated in the double helix with small adjustments in the conformation of the sugar-phosphate backbone. Details of the backbone conformation, base stacking interactions, thermal parameters and the hydration are now presented and compared with those of the native oligomer d(C-G-C-G-A-A-T-T-C-G-C-G) and with variations of this sequence containing G.T and G.A mispairs.


    Related Citations: 
    • Structure of an Adenine. Cytosine Base Pair in DNA and Its Implications for Mismatch Repair
      Hunter, W.N., Brown, T., Anand, N.N., Kennard, O.
      (1986) Nature 320: 552

    Organizational Affiliation

    Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität , Universitätsstr. 1, 40225 Düsseldorf, Germany.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B12N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Observed: 0.190 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 25.37α = 90
    b = 41.44β = 90
    c = 65.2γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1993-07-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance