2LSF

Structure and Stability of Duplex DNA Containing (5'S) 5',8-Cyclo-2'-Deoxyadenosine: An Oxidative Lesion Repair by NER


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Stability of Duplex DNA Containing (5'S)-5',8-Cyclo-2'-deoxyadenosine: An Oxidatively Generated Lesion Repaired by NER.

Zaliznyak, T.Lukin, M.de Los Santos, C.

(2012) Chem.Res.Toxicol. 25: 2103-2111

  • DOI: 10.1021/tx300193k

  • PubMed Abstract: 
  • Cellular respiration and ionizing radiation generate 5',8-cyclo-2'-deoxyribonucleosides, a special type of DNA damage that involves two modifications in the same nucleotide. These lesions evade the action of base excision glycosylases, and their remo ...

    Cellular respiration and ionizing radiation generate 5',8-cyclo-2'-deoxyribonucleosides, a special type of DNA damage that involves two modifications in the same nucleotide. These lesions evade the action of base excision glycosylases, and their removal is a function of the nucleotide excision repair pathway. Diastereomeric 5',8-cyclo-2'-deoxyadenosine blocks mammalian DNA replication, diminishes the levels of DNA transcription, and induces transcriptional mutagenesis. Using solution state NMR spectroscopy and restrained molecular dynamics simulations, we have determined the structure of an undecameric DNA duplex having a centrally located (5'S)-5',8-cyclo-2'-deoxyadenosine residue paired to T. The damaged duplex structure is a right-handed helix having Watson-Crick base-pair alignments throughout, and 2-deoxyribose puckers within the B-form conformation. Only small structural perturbations are observed at the lesion-containing and 5'-flanking base pair. The 2-deoxyribose of the damaged nucleotide adopts the O4'-exo conformation, and the S-cdA·T base pair is propeller twisted. The 5'-lesion-flanking base is tilted forming a significantly buckled base pair with its partner guanine. Analysis of UV-melting curves indicates mild thermal and thermodynamic destabilization on the damaged duplex. The S-cdA·T duplex structure shows many similarities to and some intriguing differences from the recently reported structure of an S-cdG·dC duplex³¹ that suggest different lesion site dynamics.


    Organizational Affiliation

    Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8651, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*CP*(02I)P*CP*AP*TP*GP*C)-3')B11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')D11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
02I
Query on 02I
B
DNA LINKINGC10 H12 N5 O6 P

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-10-03
    Type: Database references
  • Version 1.2: 2012-10-31
    Type: Database references