4LTI

Dehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 74% relative humidity (4/7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Controlled Dehydration of a Ruthenium Complex-DNA Crystal Induces Reversible DNA Kinking.

Hall, J.P.Sanchez-Weatherby, J.Alberti, C.Quimper, C.H.O'Sullivan, K.Brazier, J.A.Winter, G.Sorensen, T.Kelly, J.M.Cardin, D.J.Cardin, C.J.

(2014) J Am Chem Soc 136: 17505-17512

  • DOI: https://doi.org/10.1021/ja508745x
  • Primary Citation of Related Structures:  
    4LTF, 4LTG, 4LTH, 4LTI, 4LTJ, 4LTK, 4LTL

  • PubMed Abstract: 

    Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.


  • Organizational Affiliation

    Chemistry Department, University of Reading , Whiteknights, Reading, Berkshire RG6 6AD, United Kingdom.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA10N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.19α = 90
b = 44.19β = 90
c = 27.47γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2015-01-07
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description