1B6Y

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics.

Korobka, A.Cullinan, D.Cosman, M.Grollman, A.P.Patel, D.J.Eisenberg, M.de los Santos, C.

(1996) Biochemistry 35: 13310-13318

  • DOI: 10.1021/bi9605696
  • Primary Citation of Related Structures:  
    1B6Y

  • PubMed Abstract: 
  • The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics ...

    The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics. The spectroscopic data establish a right-handed duplex, with sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the exception of epsilon C.dA, Watson-Crick hydrogen bond alignment for all base pairs. Molecular dynamics simulations, restrained by the full relaxation matrix approach, produced a three-dimensional model with an NMR R-factor of 7%. The duplex structure shows no significant perturbation of the sugar-phosphate backbone, which remains in B-form. The exocyclic adduct and its partner dA are incorporated into the helix without producing a noticeable kink. The epsilon C.dA alignment adopts a staggered conformation with each residue displaced toward the 5'-terminus and intercalated between bases on the opposite strand, without increase of inter-phosphate distances. The partial intercalation of the epsilon C (anti).dA(anti) alignment allows stacking between the aromatic rings of epsilon C and dA and with base pairs adjacent to the lesion, suggesting an important role played by hydrophobic forces in the stabilization of the solution structure.


    Organizational Affiliation

    Department of Pharmacological Sciences, State University of New York at Stony Brook 11794-8651, USA.



Macromolecules
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3'A11N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3'B11N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 
      • Conformers Submitted: 
      • OLDERADO: 1B6Y Olderado

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1999-01-27
        Type: Initial release
      • Version 1.1: 2008-03-24
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2012-01-18
        Changes: Atomic model