1AXO

STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: ALL CONFORMERS WERE INCLUDED 

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This is version 1.2 of the entry. See complete history


Literature

Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction.

Feng, B.Gorin, A.Hingerty, B.E.Geacintov, N.E.Broyde, S.Patel, D.J.

(1997) Biochemistry 36: 13769-13779

  • DOI: 10.1021/bi970069s
  • Primary Citation of Related Structures:  
    1AXO

  • PubMed Abstract: 
  • This study reports on the solution conformation of the covalent (+)-trans-anti-[BP]dG adduct (derived from the binding of the highly mutagenic and tumorigenic (+)-anti-benzo[a]pyrene diol epoxide to the N2 of deoxyguanosine) positioned opposite dC at a junctional site in the d(A1-A2-C3-[BP]G4-C5- T6-A7-C8-C9-A10-T11-C12-C13) ...

    This study reports on the solution conformation of the covalent (+)-trans-anti-[BP]dG adduct (derived from the binding of the highly mutagenic and tumorigenic (+)-anti-benzo[a]pyrene diol epoxide to the N2 of deoxyguanosine) positioned opposite dC at a junctional site in the d(A1-A2-C3-[BP]G4-C5- T6-A7-C8-C9-A10-T11-C12-C13).d(G14-G15-A16-T17-+ ++G18-G19-T20-A21-G22-C23) 13/10-mer DNA sequence. The 13-mer represents the template strand containing the junction [BP]dG4 lesion while the complementary 10-mer models a primer strand which extends upto and is complementary to the modified dG4 residue. The solution conformation has been determined by initially incorporating intramolecular and intermolecular proton-proton distances defined by lower and upper bounds deduced from NOESY spectra as restraints in molecular mechanics computations in torsion angle space and subsequently through restrained molecular dynamics calculations based on a NOE distance and intensity refinement protocol. The duplex segment retains a minimally perturbed B-DNA conformation with all base pairs, including the junctional [BP]dG4.dC23 pair, in Watson-Crick hydrogen-bonded alignments. The pyrenyl ring is not stacked over the adjacent dC5.dG22 base pair but is positioned on the minor groove-side of the [BP]dG moiety and directed toward the 5'-end of the template strand. The pyrenyl ring stacks over the base of the non-adjacent dA2 residue in one direction and the sugar ring of dC23 in the other direction. The solution structure of the (+)-trans-anti-[BP]dG adduct opposite dC in the 13/10-mer in which the modified deoxyguanosine adopts an anti glycosidic torsion angle (this study) is in striking contrast to the structure of the same (+)-trans-anti-[BP]dG moiety in a 13/9-mer of the same sequence but without the dC23 residue positioned opposite the adduct site [Cosman, M., et al. (1995) Biochemistry 34, 15334-15350]. For the latter case, the aromatic portion of the BP residue stacks over the adjacent dC5.dG22 base pair, the modified deoxyguanosine adopts a syn glycosidic torsion angle and is displaced toward the major groove direction. Insights into the factors that affect the sequence and context dependent conformations of stereoisomeric [BP]dG lesions have emerged following comparison of these two structures with the minor groove conformations of the same (+)-trans-anti-[BP]dG lesion in the fully complementary 11-mer duplex [Cosman, M., et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1914-1918] and in the base displaced-intercalative conformation of the 11/10-mer deletion duplex containing a -1 deletion site opposite the lesion [Cosman, M., et al. (1994) Biochemistry 33, 11507-11517]. The contributing factors where applicable include Watson-Crick base pairing at the site of the lesion, positioning of the carcinogen within the floor of the minor groove, and the tendency of the bulky hydrophobic aromatic BP residue to assume stacked or intercalative conformations.


    Organizational Affiliation

    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, p5w York 10021, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA DUPLEX D(AAC-[BP]G-CTACCATCC)D(GGATGGTAGC)A13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA DUPLEX D(AAC-[BP]G-CTACCATCC)D(GGATGGTAGC)B10N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BAP (Subject of Investigation/LOI)
      Query on BAP

      Download Ideal Coordinates CCD File 
      C [auth A]1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
      C20 H16 O3
      GFANZDFKCCJYRF-NSISKUIASA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 
      • Conformers Submitted: 
      • Selection Criteria: ALL CONFORMERS WERE INCLUDED 
      • OLDERADO: 1AXO Olderado

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1998-07-01
        Type: Initial release
      • Version 1.1: 2008-03-24
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance