5ET2

Lambda-Ru(TAP)2(dppz)]2+ bound to d(TTGGCGCCAA)

  • Classification: DNA
  • Organism(s): synthetic construct

  • Deposited: 2015-11-17 Released: 2016-11-23 
  • Deposition Author(s): Hall, J.P., Cardin, C.J.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inosine Can Increase DNA's Susceptibility to Photo-oxidation by a Ru(II) Complex due to Structural Change in the Minor Groove.

Keane, P.M.Hall, J.P.Poynton, F.E.Poulsen, B.C.Gurung, S.P.Clark, I.P.Sazanovich, I.V.Towrie, M.Gunnlaugsson, T.Quinn, S.J.Cardin, C.J.Kelly, J.M.

(2017) Chemistry 23: 10344-10351

  • DOI: 10.1002/chem.201701447
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP)2 (dppz)]2+ (Λ-1) (dppz=dipyrid ...

    Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP)2 (dppz)]2+ (Λ-1) (dppz=dipyridophenazine) complex bound to either d{T1 C2 G3 G4 C5 G6 C7 C8 G9 A10 }2 (G9) or d{TCGGCGCCIA}2 (I9), the X-ray crystal structures show the dppz intercalated at the terminal T1 C2 ;G9 A10 step or T1 C2 ;I9 A10 step. Thus substitution of the G9 nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron-transfer, as determined by pico- and nanosecond time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH2 group. Similar behaviour and the same binding site in the crystal are found for d{TTGGCGCCAA}2 (A9). In solution, we propose that intercalation occurs at the C2 G3 ;C8 I9 or T2 G3 ;C8 A9 steps, respectively, with G3 the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH2 group) can facilitate binding of RuII dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer.


    Related Citations: 
    • Unexpected enhancement of sensitised photo-oxidation by a Ru(II) complex on replacement of guanine with inosine in DNA
      Keane, P.M.,Hall, J.P.,Poynton, F.E.,Gurung, S.P.,Clark, I.P.,Sazanovich, I.V.,Towrie, M.,Gunnlaugsson, T.,Brazier, J.A.,Quinn, S.J.,Cardin, C.J.,Kelly, J.M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*(THM)P*TP*GP*GP*CP*GP*CP*CP*AP*A)-3')A10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download SDF File 
Download CCD File 
A
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
RKL
Query on RKL

Download SDF File 
Download CCD File 
A
Ru(tap)2(dppz) complex
C38 H22 N12 Ru
PIKVAZQLFXBUSD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
THM
Query on THM
A
DNA OH 5 prime terminusC10 H14 N2 O5

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.380α = 90.00
b = 42.380β = 90.00
c = 39.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXphasing
xia2data reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K019279/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M004635/1

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence, Derived calculations