8BNA

BINDING OF HOECHST 33258 TO THE MINOR GROOVE OF B-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of Hoechst 33258 to the minor groove of B-DNA.

Pjura, P.E.Grzeskowiak, K.Dickerson, R.E.

(1987) J Mol Biol 197: 257-271

  • DOI: 10.1016/0022-2836(87)90123-9
  • Primary Citation of Related Structures:  
    8BNA

  • PubMed Abstract: 
  • An X-ray crystallographic structure analysis has been carried out on the complex between the antibiotic and DNA fluorochrome Hoechst 33258 and a synthetic B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G. The drug molecule, which can be schematized as: phenol-benzimidazole-benzimidazole-piperazine, sits within the minor groove in the A-T-T-C region of the DNA double helix, displacing the spine of hydration that is found in drug-free DNA ...

    An X-ray crystallographic structure analysis has been carried out on the complex between the antibiotic and DNA fluorochrome Hoechst 33258 and a synthetic B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G. The drug molecule, which can be schematized as: phenol-benzimidazole-benzimidazole-piperazine, sits within the minor groove in the A-T-T-C region of the DNA double helix, displacing the spine of hydration that is found in drug-free DNA. The NH groups of the benzimidazoles make bridging three-center hydrogen bonds between adenine N-3 and thymine O-2 atoms on the edges of base-pairs, in a manner both mimicking the spine of hydration and calling to mind the binding of the auti-tumor drug netropsin. Two conformers of Hoechst are seen in roughly equal populations, related by 180 degrees rotation about the central benzimidazole-benzimidazole bond: one form in which the piperazine ring extends out from the surface of the double helix, and another in which it is buried deep within the minor groove. Steric clash between the drug and DNA dictates that the phenol-benzimidazole-benzimidazole portion of Hoechst 33258 binds only to A.T regions of DNA, whereas the piperazine ring demands the wider groove characteristic of G.C regions. Hence, the piperazine ring suggests a possible G.C-reading element for synthetic DNA sequence-reading drug analogs.


    Related Citations: 
    • Isohelical Analysis of DNA Groove-Binding Drugs
      Goodsell, D., Dickerson, R.E.
      (1986) J Med Chem 29: 727
    • Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G
      Kopka, M.L., Yoon, C., Goodsell, D.S., Pjura, P., Dickerson, R.E.
      (1985) J Mol Biol 183: 553
    • Drugs and Minor Groove Binding in B-DNA Netropsin and Hoechst 33258
      Kopka, M.L., Pjura, P.E., Goodsell, D.S., Dickerson, R.E.
      () To be published --: --
    • The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin
      Kopka, M.L., Yoon, C., Goodsell, D.S., Pjura, P., Dickerson, R.E.
      (1985) Proc Natl Acad Sci U S A 82: 1376
    • Crystal Structure Analysis of a Complete Turn of B-DNA
      Wing, R., Drew, H.R., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E.
      (1980) Nature 287: 755

    Organizational Affiliation

    Molecular Biology Institute, University of California at Los Angeles 90024.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B12N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HT
Query on HT

Download Ideal Coordinates CCD File 
C [auth A]2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
C25 H24 N6 O
INAAIJLSXJJHOZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.04α = 90
b = 40.33β = 90
c = 65.85γ = 90
Software Package:
Software NamePurpose
JACK-LEVITTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1987-01-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-07-02
    Changes: Other