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PDBsum entry 129d
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DNA PDB id
129d

 

 

 

 

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Contents
DNA/RNA
Ligands
HT1
Waters ×64
PDB id:
129d
Name: DNA
Title: DNA (5'-d( Cp Gp Cp Gp Ap Ap Tp Tp Cp Gp Cp G)-3') complexed with hoechst 33342
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:
2.25Å     R-factor:   0.168    
Authors: M.Sriram,G.A.Van Der Marel,H.L.P.F.Roelen,J.H.Van Boom,A.H.-J.Wang
Key ref: M.Sriram et al. (1992). Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342. Embo J, 11, 225-232. PubMed id: 1371249
Date:
30-Jun-93     Release date:   15-Jan-94    
 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

 

 
Embo J 11:225-232 (1992)
PubMed id: 1371249  
 
 
Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342.
M.Sriram, G.A.van der Marel, H.L.Roelen, J.H.van Boom, A.H.Wang.
 
  ABSTRACT  
 
O6-ethyl-G (e6G) is an important DNA lesion, caused by the exposure of cells to alkylating agents such as N-ethyl-N-nitrosourea. A strong correlation exists between persistence of e6G lesion and subsequent carcinogenic conversion. We have determined the three-dimensional structure of a DNA molecule incorporating the e6G lesion by X-ray crystallography. The DNA dodecamer d(CGC[e6G]AATTCGCG), complexed to minor groove binding drugs Hoechst 33258 or Hoechst 33342, has been crystallized in the space group P212121, isomorphous to other related dodecamer DNA crystals. In addition, the native dodecamer d(CGCGAATTCGCG) was crystallized with Hoechst 33342. All three new structures were solved by the molecular replacement method and refined by the constrained least squares procedure to R-factors of approximately 16% at approximately 2.0 A resolution. In the structure of three Hoechst drug-dodecamer complexes in addition to the one published earlier [Teng et al. (1988) Nucleic Acids Res., 16, 2671-2690], the Hoechst molecule lies squarely at the central AATT site with the ends approaching the G4-C21 and the G16-C9 base pairs, consistent with other spectroscopic data, but not with another crystal structure reported [Pjura et al. (1987) J. Mol. Biol., 197, 257-271]. The two independent e6G-C base pairs in the DNA duplex adopt different base pairing schemes. The e6G4-C21 base pair has a configuration similar to a normal Watson-Crick base pair, except with bifurcated hydrogen bonds between e6G4 and C21, and the ethyl group is in the proximal orientation. In contrast, the e6G16-C9 base pair adopts a wobble configuration and the ethyl group is in the distal orientation.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21261999 L.J.Mah, C.Orlowski, K.Ververis, R.S.Vasireddy, A.El-Osta, and T.C.Karagiannis (2011).
Evaluation of the efficacy of radiation-modifying compounds using γH2AX as a molecular marker of DNA double-strand breaks.
  Genome Integr, 2, 3.  
20554855 E.C.Magat Juan, S.Shimizu, X.Ma, T.Kurose, T.Haraguchi, F.Zhang, M.Tsunoda, A.Ohkubo, M.Sekine, T.Shibata, C.L.Millington, D.M.Williams, and A.Takénaka (2010).
Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
  Nucleic Acids Res, 38, 6737-6745.
PDB codes: 3n4n 3n4o
  20976303 M.Tsunoda, T.Sakaue, S.Naito, T.Sunami, N.Abe, Y.Ueno, A.Matsuda, and A.Takénaka (2010).
Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil.
  J Nucleic Acids, 2010, 107289.
PDB codes: 3ajj 3ajk 3ajl
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.  
19145606 C.G.Yang, K.Garcia, and C.He (2009).
Damage detection and base flipping in direct DNA alkylation repair.
  Chembiochem, 10, 417-423.  
17950611 A.Inase-Hashimoto, S.Yoshikawa, Y.Kawasaki, T.S.Kodama, and S.Iwai (2008).
Characterization of distamycin A binding to damaged DNA.
  Bioorg Med Chem, 16, 164-170.  
17390724 L.S.Yasui, K.Chen, K.Wang, T.P.Jones, J.Caldwell, D.Guse, and A.I.Kassis (2007).
Using Hoechst 33342 to target radioactivity to the cell nucleus.
  Radiat Res, 167, 167-175.  
16204886 A.Adams, C.Leong, W.A.Denny, and J.M.Guss (2005).
Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 1348-1353.
PDB codes: 1zph 1zpi
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.  
14626657 S.G.Tarasov, J.R.Casas-Finet, W.M.Cholody, T.Kosakowska-Cholody, Z.K.Gryczynski, and C.J.Michejda (2003).
Bisimidazoacridones: 2. Steady-state and time-resolved fluorescence studies of their diverse interactions with DNA.
  Photochem Photobiol, 78, 313-322.  
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.  
11509372 B.Wellenzohn, W.Flader, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2001).
Significance of ligand tails for interaction with the minor groove of B-DNA.
  Biophys J, 81, 1588-1599.  
10666470 C.J.Squire, L.J.Baker, G.R.Clark, R.F.Martin, and J.White (2000).
Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design.
  Nucleic Acids Res, 28, 1252-1258.
PDB codes: 442d 443d 444d 445d 447d 448d 449d
10580832 B.S.Reddy, S.M.Sondhi, and J.W.Lown (1999).
Synthetic DNA minor groove-binding drugs.
  Pharmacol Ther, 84, 1.  
10391953 Y.Fujiwara, C.Masutani, T.Mizukoshi, J.Kondo, F.Hanaoka, and S.Iwai (1999).
Characterization of DNA recognition by the human UV-damaged DNA-binding protein.
  J Biol Chem, 274, 20027-20033.  
9692982 H.Robinson, Y.G.Gao, C.Bauer, C.Roberts, C.Switzer, and A.H.Wang (1998).
2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis.
  Biochemistry, 37, 10897-10905.
PDB codes: 1bhr 403d
9321660 C.J.Squire, G.R.Clark, and W.A.Denny (1997).
Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.
  Nucleic Acids Res, 25, 4072-4078.
PDB code: 328d
9591476 J.B.Chaires (1997).
Energetics of drug-DNA interactions.
  Biopolymers, 44, 201-215.  
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
8614632 J.M.Rydzewski, W.Leupin, and W.Chazin (1996).
The width of the minor groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA.
  Nucleic Acids Res, 24, 1287-1293.  
8811103 L.Tabernero, J.Bella, and C.Alemán (1996).
Hydrogen bond geometry in DNA-minor groove binding drug complexes.
  Nucleic Acids Res, 24, 3458-3466.  
8706743 M.C.Vega, M.Coll, and C.Alemán (1996).
Intrinsic conformational preferences of the Hoechst dye family and their influence of DNA binding.
  Eur J Biochem, 239, 376-383.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
7517864 M.C.Vega, I.García Sáez, J.Aymamí, R.Eritja, G.A.Van der Marel, J.H.Van Boom, A.Rich, and M.Coll (1994).
Three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258.
  Eur J Biochem, 222, 721-726.
PDB code: 264d
8092675 M.Sriram, D.Yang, Y.G.Gao, and A.H.Wang (1994).
Crystal and solution structures of d(CGC[e6G]AATTCGCG)-drug complexes reveal conformational polymorphism of O6-ethyl-guanine:cytosine base pair.
  Ann N Y Acad Sci, 726, 18.  
7515488 N.Spink, D.G.Brown, J.V.Skelly, and S.Neidle (1994).
Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.
  Nucleic Acids Res, 22, 1607-1612.
PDB code: 296d
7690125 C.Bailly, P.Colson, J.P.Hénichart, and C.Houssier (1993).
The different binding modes of Hoechst 33258 to DNA studied by electric linear dichroism.
  Nucleic Acids Res, 21, 3705-3709.  
8233777 J.A.Grasby, P.Jonathan, G.Butler, and M.J.Gait (1993).
The synthesis of oligoribonucleotides containing O6-methylguanosine: the role of conserved guanosine residues in hammerhead ribozyme cleavage.
  Nucleic Acids Res, 21, 4444-4450.  
1437563 J.C.Xuan, and I.T.Weber (1992).
Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.
  Nucleic Acids Res, 20, 5457-5464.
PDB code: 1d77
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 codes are shown on the right.

 

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