1EXL

STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 30 
  • Selection Criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of an 11-mer DNA duplex containing the carbocyclic nucleotide analog: 2'-deoxyaristeromycin

Smirnov, S.Johnson, F.Marumoto, R.de los Santos, C.

(2000) J.Biomol.Struct.Dyn. 17: 981-991

  • DOI: 10.1080/07391102.2000.10506586

  • PubMed Abstract: 
  • 2'-deoxyaristeromycin (dAr) is a nucleoside analogue that is resistant to the action of DNA glycosylases. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of an 11-mer DNA cont ...

    2'-deoxyaristeromycin (dAr) is a nucleoside analogue that is resistant to the action of DNA glycosylases. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of an 11-mer DNA containing a single dAr.T base pair at its center. Analysis of the spectra revealed the existence of a right-handed duplex in solution, stabilized by Watson-Crick hydrogen bonding and base-stacking interactions. The carbocyclic sugar adopted a C1'-exo conformation and sugars of the 3'-flanking base pair had puckers in the O4'-endo range. The dAr.T base pair was mildly propeller twisted, and the dAr analogue showed a positive roll with the 3'-flanking base. Our findings indicate that the observed resistance of dAr-containing oligodeoxynucleotides to the catalytic action of DNA glycosylases relates to its electronic properties rather than structure, and validate the use of dAr and related carbocyclic nucleoside analogues for biological and structure/function relationship studies.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*TP*GP*(2AR)P*GP*TP*CP*AP*C)-3')A11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*GP*AP*CP*TP*CP*AP*CP*TP*G)-3')B11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2AR
Query on 2AR
A
DNA LINKINGC11 H16 N5 O5 PDA
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 30 
  • Selection Criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-28
    Type: Advisory