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PDBsum entry 1fd5
Go to PDB code: 
dna_rna ligands metals links
DNA PDB id
1fd5

 

 

 

 

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Contents
DNA/RNA
Ligands
B9A
Metals
_MG
_CO ×2
Waters ×74
PDB id:
1fd5
Name: DNA
Title: Binding of a macrocyclic bisacridine and ametantrone to cgtacg involves similar unusual intercalation platforms (bisacridine complex)
Structure: DNA (5'-d( Cp Gp Tp Ap Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: synthetic DNA moleclue
Biol. unit: Tetramer (from PQS)
Resolution:
1.10Å     R-factor:   0.168     R-free:   0.203
Authors: X.-L.Yang,H.Robinson,Y.-G.Gao,A.H.-J.Wang
Key ref:
X.L.Yang et al. (2000). Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms. Biochemistry, 39, 10950-10957. PubMed id: 10998231 DOI: 10.1021/bi001319z
Date:
19-Jul-00     Release date:   07-Aug-00    
 Headers
 References

DNA/RNA chains
  C-G-T-A-C-G 6 bases
  C-G-T-A-C-G 6 bases

 

 
DOI no: 10.1021/bi001319z Biochemistry 39:10950-10957 (2000)
PubMed id: 10998231  
 
 
Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms.
X.L.Yang, H.Robinson, Y.G.Gao, A.H.Wang.
 
  ABSTRACT  
 
The binding of a macrocyclic bisacridine and an antitumor intercalator ametantrone to DNA has been studied. We carried out X-ray diffraction analyses of the complexes between both intercalators and CGTACG. We have determined the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method, of bisacridine complexed with CGTA[br(5)C]G at 1.8 A resolution. The refined native crystal structure at 1.1 A resolution (space group C222, a = 29.58 A, b = 54.04 A, c = 40.22 A, and R-factor = 0.163) revealed that only one acridine of the bisacridine drug binds at the C5pG6 step of the DNA, with the other acridine plus both linkers completely disordered. Surprisingly, both terminal G.C base pairs are unraveled. The C1 nucleotide is disordered, and the G2 base is bridged to its own phosphate P2 through a hydrated Co(2+) ion. G12 is swung toward the minor groove with its base stacked over the backbone. The C7 nucleotide is flipped away from the duplex part and base paired to a 2-fold symmetry-related G6. The central four base pairs adopt the B-DNA conformation. An unusual intercalator platform is formed by bringing four complexes together (involving the 222 symmetry) such that the intercalator cavity is flanked by two sets of G x C base pairs (i.e., C5 x G8 and G6 x C7) on each side, joined together by G6 x G8 tertiary base pairing interactions. In the bisacridine-CGTACG complex, the intercalation platform is intercalated with two acridines, whereas in the ametantrone-CGTACG complex, only one ametantrone is bound. NMR titration of the bisacridine to AACGATCGTT suggests that the bisacridine prefers to bridge more than one DNA duplex by intercalating each acridine to different duplexes. The results may be relevant in understanding binding of certain intercalators to DNA structure associated with the quadruplet helix and Holliday junction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19321501 J.Viladoms, N.Escaja, M.Frieden, I.Gómez-Pinto, E.Pedroso, and C.González (2009).
Self-association of short DNA loops through minor groove C:G:G:C tetrads.
  Nucleic Acids Res, 37, 3264-3275.
PDB codes: 2k8z 2k90 2k97
17120074 A.R.Stettler, V.Chaurin, E.C.Constable, C.E.Housecroft, and M.A.Schwarz (2007).
Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I.
  J Biol Inorg Chem, 12, 194-203.  
17047882 J.O.Morley, and P.J.Furlong (2006).
Synthesis and calculated properties of some 1,4-bis(amino)anthracene-9,10-diones.
  Org Biomol Chem, 4, 4005-4014.  
17145714 N.H.Hopcroft, A.L.Brogden, M.Searcey, and C.J.Cardin (2006).
X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative.
  Nucleic Acids Res, 34, 6663-6672.
PDB code: 2gb9
15926069 N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, and J.A.Subirana (2005).
Variable role of ions in two drug intercalation complexes of DNA.
  J Biol Inorg Chem, 10, 476-482.
PDB codes: 1xcs 1xcu
15103127 A.Adams, J.M.Guss, W.A.Denny, and L.P.Wakelin (2004).
Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)(2): a comparison of structures of d(CGTACG)(2) complexed with intercalatorsin the presence of cobalt.
  Acta Crystallogr D Biol Crystallogr, 60, 823-828.
PDB code: 1rqy
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
15157277 S.M.Nelson, L.R.Ferguson, and W.A.Denny (2004).
DNA and the chromosome - varied targets for chemotherapy.
  Cell Chromosome, 3, 2.  
12598364 J.A.Subirana, and M.Soler-Lopez (2003).
Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.
  Annu Rev Biophys Biomol Struct, 32, 27-45.  
12560479 J.H.Thorpe, S.C.Teixeira, B.C.Gale, and C.J.Cardin (2003).
Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.
  Nucleic Acids Res, 31, 844-849.
PDB code: 1mf5
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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