PDBsum entry 109d

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PDB id:
Name: DNA
Title: Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(cgcgaattcgcg)2
Structure: DNA (5'-d( Cp Gp Cp Gp Ap Ap Tp Tp Cp Gp Cp G)- 3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
2.00Å     R-factor:   0.197    
Authors: A.Czarny,D.W.Boykin,A.A.Wood,C.M.Nunn,S.Neidle,M.Zhao, W.D.Wilson
Key ref: A.A.Wood et al. (1995). Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2. Nucleic Acids Res, 23, 3678-3684. PubMed id: 7478996
15-Feb-95     Release date:   08-May-95    


Nucleic Acids Res 23:3678-3684 (1995)
PubMed id: 7478996  
Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
A.A.Wood, C.M.Nunn, A.Czarny, D.W.Boykin, S.Neidle.
An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The structure has been solved by X-ray diffraction analysis and has been refined to an R-factor of 19.7% at a resolution of 2.0 A. The ligand is found to bind in the minor groove, at the central four AATT base pairs of the B-DNA double helix, with the involvement of a number of van der Waals contacts and hydrogen bonds. There are significant differences in minor groove width for the two compounds, along much of the AATT region. In particular this structure shows a narrower groove at the 3' end of the binding site consistent with the narrower cross-section of the imidazole group compared with the piperazine ring of Hoechst 33258 and therefore a smaller perturbation in groove width. The higher binding affinity to DNA shown by this analogue compared with Hoechst 33258 itself, has been rationalised in terms of these differences.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20694266 J.B.Mangrum, and N.P.Farrell (2010).
Excursions in polynuclear platinum DNA binding.
  Chem Commun (Camb), 46, 6640-6650.  
19899952 A.K.Jain, S.K.Gupta, and V.Tandon (2009).
Evaluation of electronic effect of phenyl ring substituents on the DNA minor groove binding properties of novel bis and terbenzimidazoles: synthesis and spectroscopic studies of ligand-DNA interaction.
  Oligonucleotides, 19, 329-340.  
19565329 D.Banerjee, A.Makhal, and S.K.Pal (2009).
Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes.
  J Fluoresc, 19, 1111-1118.  
15501936 W.Ge, B.Schneider, and W.K.Olson (2005).
Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids.
  Biophys J, 88, 1166-1190.  
12595560 C.Bailly, G.Chessari, C.Carrasco, A.Joubert, J.Mann, W.D.Wilson, and S.Neidle (2003).
Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition.
  Nucleic Acids Res, 31, 1514-1524.  
12694177 P.Borowski, J.Deinert, S.Schalinski, M.Bretner, K.Ginalski, T.Kulikowski, and D.Shugar (2003).
Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses.
  Eur J Biochem, 270, 1645-1653.  
11937631 C.Carrasco, M.Facompré, J.D.Chisholm, D.L.Van Vranken, W.D.Wilson, and C.Bailly (2002).
DNA sequence recognition by the indolocarbazole antitumor antibiotic AT2433-B1 and its diastereoisomer.
  Nucleic Acids Res, 30, 1774-1781.  
11876657 K.D.Leslie, and K.R.Fox (2002).
Interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments containing isolated ligand binding sites.
  Biochemistry, 41, 3484-3497.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
10580832 B.S.Reddy, S.M.Sondhi, and J.W.Lown (1999).
Synthetic DNA minor groove-binding drugs.
  Pharmacol Ther, 84, 1.  
10373586 J.Aymami, C.M.Nunn, and S.Neidle (1999).
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand.
  Nucleic Acids Res, 27, 2691-2698.
PDB codes: 458d 459d
9611230 A.Guerri, I.J.Simpson, and S.Neidle (1998).
Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.
  Nucleic Acids Res, 26, 2873-2878.
PDB code: 360d
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9162901 G.R.Clark, D.W.Boykin, A.Czarny, and S.Neidle (1997).
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.
  Nucleic Acids Res, 25, 1510-1515.
PDB code: 311d
9017011 G.R.Clark, C.J.Squire, E.J.Gray, W.Leupin, and S.Neidle (1996).
Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.
  Nucleic Acids Res, 24, 4882-4889.
PDB codes: 302d 303d
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