2LWN

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 19 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion

Lukin, M.Zaliznyak, T.Attaluri, S.Johnson, F.de Los Santos, C.

(2012) Chem.Res.Toxicol. 25: 2423-2431

  • DOI: 10.1021/tx300290b
  • Primary Citation of Related Structures:  2LWM, 2LWO

  • PubMed Abstract: 
  • The addition of hydroxyl radicals to the C8 position of guanine can lead to the formation of a 2,6-diamino-4-hydroxy-5-formamido-2'-deoxypyrimidine (Fapy-dG) lesion, whose endogenous levels in cellular DNA rival those of 8-oxo-7,8-dihydroxy-2'-deoxyg ...

    The addition of hydroxyl radicals to the C8 position of guanine can lead to the formation of a 2,6-diamino-4-hydroxy-5-formamido-2'-deoxypyrimidine (Fapy-dG) lesion, whose endogenous levels in cellular DNA rival those of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine. Despite its prevalence, the structure of duplex DNA containing Fapy-dG is unknown. We have prepared an undecameric duplex containing a centrally located β-cFapy-dG residue paired to dC and determined its solution structure by high-resolution NMR spectroscopy and restrained molecular dynamic simulations. The damaged duplex adopts a right-handed helical structure with all residues in an anti conformation, forming Watson-Crick base pair alignments, and 2-deoxyribose conformations in the C2'-endo/C1'-exo range. The formamido group of Fapy rotates out of the pyrimidine plane and is present in the Z and E configurations that equilibrate with an approximate 2:1 population ratio. The two isomeric duplexes show similar lesion-induced deviations from a canonical B-from DNA conformation that are minor and limited to the central three-base-pair segment of the duplex, affecting the stacking interactions with the 5-lesion-neighboring residue. We discuss the implications of our observations for translesion synthesis during DNA replication and the recognition of Fapy-dG by DNA glycosylases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*C*(LWM)P*CP*AP*TP*GP*C)-3')B11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3')D11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LWM
Query on LWM
B
DNA linkingC11 H18 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 19 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release