4R8J

d(TCGGCGCCGA) with lambda-[Ru(TAP)2(dppz)]2+ soaked in D2O


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy.

Hall, J.P.Poynton, F.E.Keane, P.M.Gurung, S.P.Brazier, J.A.Cardin, D.J.Winter, G.Gunnlaugsson, T.Sazanovich, I.V.Towrie, M.Cardin, C.J.Kelly, J.M.Quinn, S.J.

(2015) Nat Chem 7: 961-967

  • DOI: https://doi.org/10.1038/nchem.2369
  • Primary Citation of Related Structures:  
    4R8J

  • PubMed Abstract: 

    To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.


  • Organizational Affiliation

    Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*(THM)P*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')10synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.37α = 90
b = 42.37β = 90
c = 39.42γ = 90
Software Package:
Software NamePurpose
GDAdata collection
SHELXCDphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXEmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations