1AX7

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED AT A TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES


Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history


Literature

Solution structure of the aminofluorene-stacked conformer of the syn [AF]-C8-dG adduct positioned at a template-primer junction.

Mao, B.Gu, Z.Gorin, A.Hingerty, B.E.Broyde, S.Patel, D.J.

(1997) Biochemistry 36: 14491-14501

  • DOI: 10.1021/bi972206r
  • Primary Citation of Related Structures:  
    1AX7

  • PubMed Abstract: 
  • A solution structural study has been undertaken on the aminofluorene-C8-dG ([AF]dG) adduct located at a single strand-double strand d(A1-A2-C3-[AF]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13).d (G14-G15-A16-T17-G18-G19-T20-A 21-G22) 13/9-mer junction (designated [AF]dG 13/9-mer) using proton-proton distance and intensity restraints derived from NMR data in combination with a computational protocol, which includes intensity refinement ...

    A solution structural study has been undertaken on the aminofluorene-C8-dG ([AF]dG) adduct located at a single strand-double strand d(A1-A2-C3-[AF]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13).d (G14-G15-A16-T17-G18-G19-T20-A 21-G22) 13/9-mer junction (designated [AF]dG 13/9-mer) using proton-proton distance and intensity restraints derived from NMR data in combination with a computational protocol, which includes intensity refinement. This single strand-double strand junction models one arm of a replication fork composed of a 13-mer template strand, which contains the [AF]dG modification site, and a 9-mer primer strand, which has been elongated up to, but not including, the modified guanine. The NMR data establish that the duplex segment retains a minimally perturbed B-DNA conformation including Watson-Crick hydrogen-bonding at the junctional dC5.dG22 base pair. The NMR spectra are consistent with the guanine ring of the [AF]dG4 adduct adopting a syn glycosidic torsion angle and being displaced into the major groove with the adjacent dC3 residue displaced into the minor groove. Such a base displacement of the modified guanine is accompanied by stacking of one face of the fluorene ring of [AF]dG4 with the dC5.dG22 base pair, while the other face of the flourene ring is stacked with the purine ring of the nonadjacent dA2 residue in the intensity-refined solution structures of the [AF]dG 13/9-mer. A comparison of structural features of the C8-[AF]dG adduct (this study) with those of the (+)-trans-anti-N2-[BP]dG adduct [Cosman et al. (1995) Biochemistry 34, 15334-15350] in the same 13/9-mer junctional sequence context has identified common features associated with the alignment of the modified guanine adducts at the template-primer junction. Thus, despite differences in the covalent linkage site for the C8-[AF]dG and (+)-trans-anti-N2-[BP]dG adducts, one face of the aromatic ring of the carcinogen stacks over the junctional base pair and in so doing displaces the modified guanine in a syn alignment into the major groove. These results lend credence to earlier proposals that such an adduct alignment may represent a common mutagenic conformer at a template-primer junction associated with a replication fork.


    Organizational Affiliation

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



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA DUPLEX D(AAC-[AF]G-CTACCATCC)D(GGATGGTAG)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-[AF]G-CTACCATCC)D(GGATGGTAG)B9N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      AF (Subject of Investigation/LOI)
      Query on AF

      Download Ideal Coordinates CCD File 
      C [auth A]2-AMINOFLUORENE
      C13 H11 N
      CFRFHWQYWJMEJN-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 
      • Conformers Submitted: 
      • Selection Criteria: ALL CONFORMERS PRESENTED 
      • OLDERADO: 1AX7 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