1K2L

STRUCTURAL CHARACTERIZATION OF BISINTERCALATION IN HIGHER-ORDER DNA AT A JUNCTION-LIKE QUADRUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Characterisation of Bisintercalation in Higher-order DNA at a Junction-like Quadruplex

Teixeira, S.C.M.Thorpe, J.H.Todd, A.K.Powell, H.R.Adams, A.Wakelin, L.P.G.Denny, W.A.Cardin, C.J.

(2002) J.MOL.BIOL. 323: 167-171


  • PubMed Abstract: 
  • We report the single-crystal X-ray structure for the complex of the bisacridine bis-(9-aminooctyl(2-(dimethylaminoethyl)acridine-4-carboxamide)) with the oligonucleotide d(CGTACG)(2) to a resolution of 2.4A. Solution studies with closed circular DNA ...

    We report the single-crystal X-ray structure for the complex of the bisacridine bis-(9-aminooctyl(2-(dimethylaminoethyl)acridine-4-carboxamide)) with the oligonucleotide d(CGTACG)(2) to a resolution of 2.4A. Solution studies with closed circular DNA show this compound to be a bisintercalating threading agent, but so far we have no crystallographic or NMR structural data conforming to the model of contiguous intercalation within the same duplex. Here, with the hexameric duplex d(CGTACG), the DNA is observed to undergo a terminal cytosine base exchange to yield an unusual guanine quadruplex intercalation site through which the bisacridine threads its octamethylene linker to fuse two DNA duplexes. The 4-carboxamide side-chains form anchoring hydrogen-bonding interactions with guanine O6 atoms on each side of the quadruplex. This higher-order DNA structure provides insight into an unexpected property of bisintercalating threading agents, and suggests the idea of targeting such compounds specifically at four-way DNA junctions.


    Organizational Affiliation

    School of Chemistry, The University of Reading, Whiteknights, Berkshire, RG6 6AD, Reading, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*AP*CP*G)-3'A,B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
BDC
Query on BDC

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Download CCD File 
B
BIS-(9-OCTYLAMINO(2-DIMETHYLAMINOETHYL)ACRIDINE-4-CARBOXAMIDE
BIS-DACA
C44 H54 N8 O2
UUXARTGDSXDSRM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 29.507α = 90.00
b = 53.738β = 90.00
c = 40.061γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance