1COC

SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA.

McAteer, K.Jing, Y.Kao, J.Taylor, J.S.Kennedy, M.A.

(1998) J Mol Biol 282: 1013-1032

  • DOI: 10.1006/jmbi.1998.2062
  • Primary Citation of Related Structures:  
    1TTD, 1COC

  • PubMed Abstract: 
  • The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments ...

    The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed.


    Organizational Affiliation

    Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*AP*CP*GP*AP*AP*TP*TP*AP*AP*G)-3')A12N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
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      DNA (5'-D(*CP*TP*TP*AP*AP*TP*TP*CP*GP*TP*GP*C)-3')B12N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Submitted: 
      • OLDERADO: 1COC Olderado

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1999-06-09
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance