1CR3

SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex.

Suri, A.K.Mao, B.Amin, S.Geacintov, N.E.Patel, D.J.

(1999) J.Mol.Biol. 292: 289-307

  • DOI: 10.1006/jmbi.1999.2974

  • PubMed Abstract: 
  • The solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S, 12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE, to the exocyclic N(6)am ...

    The solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S, 12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE, to the exocyclic N(6)amino group of the adenine residue dA6, (designated (+)- trans-anti -(B[g]C)dA6), positioned opposite a thymine residue dT17 in the DNA sequence context d(C1-T2-C3-T4-C5-(B[g]C)A6-C7-T8-T9-C10-C11). d(G12-G13-A14-A15-G16-T17-G18-A19-G20++ +-A21-G22) (designated (B[g]C)dA. dT 11-mer duplex), has been studied using structural information derived from NMR data in combination with molecular dynamics (MD) calculations. The solution structure of the (+)- trans-anti -(B[g]C)dA.dT 11-mer duplex has been determined using an MD protocol where both interproton distance and dihedral angle restraints deduced from NOESY and COSY spectra are used during the refinement process, followed by additional relaxation matrix refinement to the observed NOESY intensities to account for spin diffusion effects. The results established that the covalently attached benzo[g]chrysene ring intercalates into the DNA helix directed towards the 5'-side of the modified strand and stacks predominantly with dT17 when intercalated between dC5.dG18 and (B[g]C)dA6.dT17 base-pairs. All base-pairs, including the modified (B[g]C)dA6.dT17 base-pair, are aligned through Watson-Crick pairing as in normal B -DNA. In addition, the potential strain associated with the highly sterically hindered fjord region of the aromatic portion of the benzo[g]chrysenyl ring is relieved through the adoption of a non-planar, propeller-like geometry within the chrysenyl ring system. This conformation shares common structural features with the related (+)- trans-anti -(B[c]Ph)dA adduct in the identical base sequence context, derived from the fjord region (+)-(1S,2R,3R,4S)-3, 4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene stereoisomer, in which intercalation is also observed towards the 5'-side of the modified dA6.dT17 base-pair.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*CP*TP*CP*AP*CP*TP*TP*CP*C)-3')A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*AP*AP*GP*TP*GP*AP*GP*AP*G)-3')B11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BC
Query on BC

Download SDF File 
Download CCD File 
A
BENZO[G]CHRYSENE
C22 H18 O3
GSKJTEFMUWIEJJ-BVSLBCMMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 
  • Selection Criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance