1QL5

DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Solution Structure of a DNA Decamer Duplex Containing the 3' T.T Base Pair of the Cis-Syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the Cis-Syn Dimer.

Lee, J.-H.Choi, Y.-J.Choi, B.-S.

(2000) Nucleic Acids Res. 28: 1794


  • PubMed Abstract: 
  • The cis - syn dimer is the major DNA photoproduct produced by UV irradiation. In order to determine the origin of the mutagenic property of the cis - syn dimer, we used NMR restraints and molecular dynamics to determine the solution structure of a DN ...

    The cis - syn dimer is the major DNA photoproduct produced by UV irradiation. In order to determine the origin of the mutagenic property of the cis - syn dimer, we used NMR restraints and molecular dynamics to determine the solution structure of a DNA decamer duplex containing a wobble pair between the 3'-T of the cis - syn dimer and the opposite T residue (CS/TA duplex). The solution structure of the CS/TA duplex revealed that the 3'-T x T base pair of the cis - syn dimer had base pair geometry that was significantly different from the canonical Watson-Crick base pair and caused destabilization and conformational distortion of its 3'-region. However, a 3'-T x A base pair at the cis - syn dimer within this related DNA decamer maintains the normal Watson-Crick base pair geometry and causes little distortion in the conformation of its 3'-side. Our results show that in spite of its stable hydrogen bonding, the insertion of a T residue opposite the 3'-T of the cis - syn dimer is inhibited by structural distortion caused by the 3'-T x T base pair. This may explain why the frequency of the 3'-T-->A transversion, which is the major mutation produced by the cis - syn dimer, is only 4%.


    Organizational Affiliation

    Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology, 373-1 Kusong-dong, Yusong-gu, Taejon 305-701, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3')A10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3')B10N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PBT
Query on PBT
A
DNA LINKINGC10 H17 N2 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-10
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references, Derived calculations, Version format compliance