296D

SEQUENCE-DEPENDENT EFFECTS IN DRUG-DNA INTERACTION: THE CRYSTAL STRUCTURE OF HOECHST 33258 BOUND TO THE D(CGCAAATTTGCG)2 DUPLEX

• PDB DOI: https://doi.org/10.2210/pdb296D/pdb
• NAKB: 296D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-07-21 Released: 1996-12-04 
• Deposition Author(s): Spink, N., Brown, D.G., Skelly, J.V., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.185 

Literature

Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.

Spink, N., Brown, D.G., Skelly, J.V., Neidle, S.

(1994) Nucleic Acids Res 22: 1607-1612

• PubMed: 7515488 
• DOI: https://doi.org/10.1093/nar/22.9.1607
• Primary Citation of Related Structures:  
  296D


• PubMed Abstract: 
  

  The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width.

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Organizational Affiliation: 

CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.75 kDa 
• Atom Count: 583 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HT	C [auth B]	2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE C25 H24 N6 O INAAIJLSXJJHOZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.27	α = 90
b = 41.32	β = 90
c = 65.11	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement
XENGEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-04 
Deposition Author(s): Spink, N., Brown, D.G., Skelly, J.V., Neidle, S.

Revision History  

• Version 1.0: 1996-12-04
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations