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PDBsum entry 1m6f
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dna_rna ligands metals links
DNA PDB id
1m6f

 

 

 

 

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Contents
DNA/RNA
Ligands
CGQ
Metals
_MG
Waters ×117
PDB id:
1m6f
Name: DNA
Title: Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove
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)
Resolution:
1.78Å     R-factor:   0.205     R-free:   0.277
Authors: B.Nguyen,M.P.H.Lee,D.Hamelberg,A.Joubert,C.Bailly,R.Brun,S.Neidle, W.D.Wilson
Key ref: B.Nguyen et al. (2002). Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove. J Am Chem Soc, 124, 13680-13681. PubMed id: 12431090 DOI: 10.1021/ja027953c
Date:
16-Jul-02     Release date:   15-Nov-02    
 Headers
 References

DNA/RNA chains
  C-G-C-G-A-A-T-T-C-G-C-G 12 bases
  C-G-C-G-A-A-T-T-C-G-C-G 12 bases

 

 
DOI no: 10.1021/ja027953c J Am Chem Soc 124:13680-13681 (2002)
PubMed id: 12431090  
 
 
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove.
B.Nguyen, M.P.Lee, D.Hamelberg, A.Joubert, C.Bailly, R.Brun, S.Neidle, W.D.Wilson.
 
  ABSTRACT  
 
A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21337433 M.Capela, N.J.Mosey, L.Xing, R.Wang, and A.Petitjean (2011).
Amine exchange in formamidines: an experimental and theoretical study.
  Chemistry, 17, 4598-4612.  
20179336 T.Moreno, J.Pous, J.A.Subirana, and J.L.Campos (2010).
Coiled-coil conformation of a pentamidine-DNA complex.
  Acta Crystallogr D Biol Crystallogr, 66, 251-257.
PDB code: 3ey0
18798655 B.Nguyen, S.Neidle, and W.D.Wilson (2009).
A role for water molecules in DNA-ligand minor groove recognition.
  Acc Chem Res, 42, 11-21.  
19445463 P.Athri, and W.D.Wilson (2009).
Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove.
  J Am Chem Soc, 131, 7618-7625.  
18343228 W.D.Wilson, F.A.Tanious, A.Mathis, D.Tevis, J.E.Hall, and D.W.Boykin (2008).
Antiparasitic compounds that target DNA.
  Biochimie, 90, 999.  
17219397 C.M.Baker, and G.H.Grant (2007).
Role of aromatic amino acids in protein-nucleic acid recognition.
  Biopolymers, 85, 456-470.  
17506529 F.A.Tanious, W.Laine, P.Peixoto, C.Bailly, K.D.Goodwin, M.A.Lewis, E.C.Long, M.M.Georgiadis, R.R.Tidwell, and W.D.Wilson (2007).
Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.
  Biochemistry, 46, 6944-6956.  
16299076 B.Nguyen, J.Stanek, and W.D.Wilson (2006).
Binding-linked protonation of a DNA minor-groove agent.
  Biophys J, 90, 1319-1328.  
16810657 C.H.Yang, K.C.Jeng, W.H.Yang, Y.L.Chen, C.C.Hung, J.W.Lin, S.T.Chen, S.Richardson, C.R.Martin, M.J.Waring, and L.Sheh (2006).
Unusually strong positive cooperativity in binding of peptides to latent membrane protein-1 DNA fragments of the Epstein-Barr viral gene.
  Chembiochem, 7, 1187-1196.  
16633568 N.Lomadze, H.J.Schneider, M.T.Albelda, E.García-España, and B.Verdejo (2006).
Dramatic selectivity differences in the association of DNA and RNA models with new ethylene- and propylene diamine derivatives and their copper complexes.
  Org Biomol Chem, 4, 1755-1759.  
16099661 M.A.Ismail, A.Batista-Parra, Y.Miao, W.D.Wilson, T.Wenzler, R.Brun, and D.W.Boykin (2005).
Dicationic near-linear biphenyl benzimidazole derivatives as DNA-targeted antiprotozoal agents.
  Bioorg Med Chem, 13, 6718-6726.  
16050790 M.N.Soeiro, E.M.De Souza, C.E.Stephens, and D.W.Boykin (2005).
Aromatic diamidines as antiparasitic agents.
  Expert Opin Investig Drugs, 14, 957-972.  
14747338 B.Nguyen, D.Hamelberg, C.Bailly, P.Colson, J.Stanek, R.Brun, S.Neidle, and W.D.Wilson (2004).
Characterization of a novel DNA minor-groove complex.
  Biophys J, 86, 1028-1041.  
15193317 T.E.Cheatham (2004).
Simulation and modeling of nucleic acid structure, dynamics and interactions.
  Curr Opin Struct Biol, 14, 360-367.  
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.  
14529286 C.Carrasco, A.Joubert, C.Tardy, N.Maestre, M.Cacho, M.F.Braña, and C.Bailly (2003).
DNA sequence recognition by bispyrazinonaphthalimides antitumor agents.
  Biochemistry, 42, 11751-11761.  
14732928 R.L.Rich, and D.G.Myszka (2003).
A survey of the year 2002 commercial optical biosensor literature.
  J Mol Recognit, 16, 351-382.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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