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PDBsum entry 261d
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dna_rna ligands links
DNA PDB id
261d

 

 

 

 

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Contents
DNA/RNA
Ligands
_NT
Waters ×85
PDB id:
261d
Name: DNA
Title: Crystal structure of the DNA decamer d(cgcaattgcg) complexed with the minor groove binding drug netropsin
Structure: DNA (5'-d( Cp Gp Cp Ap Ap Tp Tp Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.201    
Authors: C.M.Nunn,E.Garman,S.Neidle
Key ref:
C.M.Nunn et al. (1997). Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry, 36, 4792-4799. PubMed id: 9125500 DOI: 10.1021/bi9628228
Date:
08-Nov-96     Release date:   22-Apr-97    
 Headers
 References

DNA/RNA chains
  C-G-C-A-A-T-T-G-C-G 10 bases
  G-C-A-A-T-T-G-C-G 9 bases

 

 
DOI no: 10.1021/bi9628228 Biochemistry 36:4792-4799 (1997)
PubMed id: 9125500  
 
 
Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin.
C.M.Nunn, E.Garman, S.Neidle.
 
  ABSTRACT  
 
The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21335028 C.A.Andac, A.M.Miandji, U.Hornemann, and N.Noyanalpan (2011).
Use of the parmbsc0 force field and trajectory analysis to study the binding of netropsin to the DNA fragment (5'CCAATTGG)(2) in the presence of excess NaCl salt in aqueous solution.
  Int J Biol Macromol, 48, 531-539.  
19859703 L.Premvardhan, and J.C.Maurizot (2010).
Netropsin binding in five duplex-dimer DNA constructs as a function of size and distance between binding sites: circular dichroism and absorption spectroscopy.
  Eur Biophys J, 39, 781-787.  
19405506 L.S.Glass, B.Nguyen, K.D.Goodwin, C.Dardonville, W.D.Wilson, E.C.Long, and M.M.Georgiadis (2009).
Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA.
  Biochemistry, 48, 5943-5952.
PDB code: 3fsi
18937643 M.A.Grant, R.M.Baron, A.A.Macias, M.D.Layne, M.A.Perrella, and A.C.Rigby (2009).
Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter.
  Biochem J, 418, 103-112.  
17645660 S.McMasters, and L.A.Kelly (2007).
Sequence-dependent interactions of cationic naphthalimides and polynucleotides.
  Photochem Photobiol, 83, 889-896.  
17623435 Z.Shen, X.Liu, X.Zhou, A.Liang, D.Wu, L.Yu, Z.Dai, J.Qin, and B.Lin (2007).
Quantitative evaluation of the interaction between netropsin and double stranded oligodeoxynucleotides by microfabricated capillary array electrophoresis.
  J Sep Sci, 30, 1544-1548.  
16528102 W.A.Weihofen, A.Cicek, F.Pratto, J.C.Alonso, and W.Saenger (2006).
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
  Nucleic Acids Res, 34, 1450-1458.
PDB codes: 2bnw 2bnz 2cax
16049022 K.D.Goodwin, E.C.Long, and M.M.Georgiadis (2005).
A host-guest approach for determining drug-DNA interactions: an example using netropsin.
  Nucleic Acids Res, 33, 4106-4116.
PDB codes: 1ztt 1ztw
16008554 K.Van Hecke, P.C.Nam, M.T.Nguyen, and L.Van Meervelt (2005).
Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations.
  FEBS J, 272, 3531-3541.
PDB code: 1z8v
15623330 L.W.Roberts, and G.B.Schuster (2004).
Effect of netropsin on one-electron oxidation of duplex DNA.
  Photochem Photobiol, 80, 456-461.  
15039556 N.Valls, G.Wright, R.A.Steiner, G.N.Murshudov, and J.A.Subirana (2004).
DNA variability in five crystal structures of d(CGCAATTGCG).
  Acta Crystallogr D Biol Crystallogr, 60, 680-685.
PDB code: 1s23
12115142 B.Wellenzohn, W.Flader, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2001).
Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2.
  Biopolymers, 61, 276-286.  
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.  
11058124 A.Adams, J.M.Guss, C.A.Collyer, W.A.Denny, and L.P.Wakelin (2000).
A novel form of intercalation involving four DNA duplexes in an acridine-4-carboxamide complex of d(CGTACG)(2).
  Nucleic Acids Res, 28, 4244-4253.
PDB codes: 1fn1 1fn2
10871376 R.M.Brosh, J.K.Karow, E.J.White, N.D.Shaw, I.D.Hickson, and V.A.Bohr (2000).
Potent inhibition of werner and bloom helicases by DNA minor groove binding drugs.
  Nucleic Acids Res, 28, 2420-2430.  
10600105 D.Vlieghe, J.Sponer, and L.Van Meervelt (1999).
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode.
  Biochemistry, 38, 16443-16451.
PDB code: 432d
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
10455145 J.Liu, and J.A.Subirana (1999).
Structure of d(CGCGAATTCGCG) in the presence of Ca(2+) ions.
  J Biol Chem, 274, 24749-24752.
PDB code: 463d
9493396 S.Neidle, and C.M.Nunn (1998).
Crystal structures of nucleic acids and their drug complexes.
  Nat Prod Rep, 15, 1.  
9770648 A.Bell, L.Kittler, G.Löber, and C.Zimmer (1997).
DNA binding properties of minor groove binders and their influence on the topoisomerase II cleavage reaction.
  J Mol Recognit, 10, 245-255.  
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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