1AG3

DUPLEX OLIGODEOXYNUCLEOTIDE CONTAINING PROPANODEOXYGUANOSINE OPPOSITE A TWO-BASE DELETION, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: CROMA BEST FIT 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a duplex oligodeoxynucleotide containing propanodeoxyguanosine opposite a two-base deletion in the (CpG)3 frame shift hotspot of Salmonella typhimurium hisD3052 determined by 1H NMR and restrained molecular dynamics.

Weisenseel, J.P.Moe, J.G.Reddy, G.R.Marnett, L.J.Stone, M.P.

(1995) Biochemistry 34: 50-64


  • PubMed Abstract: 
  • Structural refinement from solution 1H NMR data was performed on the 5'-d[ATCGC(PdG)-CGGCATG]-3'.5'-d[CATGCCGCGAT]-3' duplex, in which the adducted oligodeoxynucleotide containing the exocyclic lesion 1,N2-propano-2'-deoxyguanosine (PdG) was annealed ...

    Structural refinement from solution 1H NMR data was performed on the 5'-d[ATCGC(PdG)-CGGCATG]-3'.5'-d[CATGCCGCGAT]-3' duplex, in which the adducted oligodeoxynucleotide containing the exocyclic lesion 1,N2-propano-2'-deoxyguanosine (PdG) was annealed with the complementary strand which contained a CpG deletion. The resulting duplex required PdG and one adjacent cytosine to be unpaired. A total of 352 distances were utilized to restrain molecular dynamics calculations, of which 264 were NOE-derived. These distances were calculated using complete relaxation matrix methods from hybrid matrices, which were comprised of the experimentally determined distances and additional distances derived from either A-form or B-form DNA. A simulated annealing protocol combined with the distance restraints was able to refine a single structure with an average rms deviation of < 1.35 A. The accuracy of the refined structure was assessed using full relaxation matrix calculations, which gave good agreement with measured NOE intensities. PdG was found to be stacked into the helix below base pair C3.G18, whereas C5 was found to be unpaired and extruded toward the major groove and parallel to base pair G6.C17. This created a localized bend in the DNA helix of approximately 20-35 degrees at the junction between PdG and C5. The bending corroborated previous assays performed on this modified sequence [Moe, J. G., Reddy, G. R., Marnett, L. J., & Stone, M. P. (1994) Chem. Res. Toxicol. 7, 319-328].


    Related Citations: 
    • 1H NMR Characterization of a Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite a Two-Base Deletion in the (Cpg)3 Frameshift Hotspot of Salmonella Typhimurium Hisd3052
      Moe, J.G.,Reddy, G.R.,Marnett, L.J.,Stone, M.P.
      (1994) Chem.Res.Toxicol. 7: 319


    Organizational Affiliation

    Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*GP*CP*PP*CP*GP*GP*CP*AP*TP*G)-3')A13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*GP*CP*CP*GP*CP*GP*AP*T)-3')B11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
P
Query on P
A
DNA LINKINGC13 H18 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: CROMA BEST FIT 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance