PDBsum entry 1fn1

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dna_rna ligands metals links
_CO ×2
Waters ×19
PDB id:
Name: DNA
Title: Crystal structure of 9-amino-(n-(2-dimethylamino)butyl) acridine-4-carboxamide bound to d(cg(5br)uacg)2
Structure: DNA (5'-d(p Gp (Bro)up Ap Cp G)-3'). Chain: a. Engineered: yes. Other_details: known to be a good sequence for intercalation. DNA (5'-d( Cp Gp (Bro)up Ap Cp G)-3'). Chain: b. Engineered: yes. Other_details: known to be a good sequence for
Source: Synthetic: yes. Synthetic: yes
Biol. unit: Tetramer (from PQS)
1.60Å     R-factor:   0.230     R-free:   0.240
Authors: A.Adams,J.M.Guss,C.A.Collyer,W.A.Denny,L.P.G.Wakelin
Key ref: A.Adams et al. (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. PubMed id: 11058124 DOI: 10.1093/nar/28.21.4244
19-Aug-00     Release date:   30-Oct-00    


DOI no: 10.1093/nar/28.21.4244 Nucleic Acids Res 28:4244-4253 (2000)
PubMed id: 11058124  
A novel form of intercalation involving four DNA duplexes in an acridine-4-carboxamide complex of d(CGTACG)(2).
A.Adams, J.M.Guss, C.A.Collyer, W.A.Denny, L.P.Wakelin.
The structures of the complexes formed between 9-amino-[N:-(2-dimethyl-amino)butyl]acridine-4-carboxamide and d(CG(5Br)UACG)(2) and d(CGTACG)(2) have been solved by X-ray crystallography using MAD phasing methodology and refined to a resolution of 1.6 A. The complexes crystallised in space group C222. An asymmetric unit in the brominated complex comprises two strands of DNA, one disordered drug molecule, two cobalt (II) ions and 19 water molecules (31 in the native complex). Asymmetric units in the native complex also contain a sodium ion. The structures exhibit novel features not previously observed in crystals of DNA/drug complexes. The DNA helices stack in continuous columns with their central 4 bp adopting a B-like motif. However, despite being a palindromic sequence, the terminal GC base pairs engage in quite different interactions. At one end of the duplex there is a CpG dinucleotide overlap modified by ligand intercalation and terminal cytosine exchange between symmetry-related duplexes. A novel intercalation complex is formed involving four DNA duplexes, four ligand molecules and two pairs of base tetrads. The other end of the DNA is frayed with the terminal guanine lying in the minor groove of the next duplex in the column. The structure is stabilised by guanine N7/cobalt (II) coordination. We discuss our findings with respect to the effects of packing forces on DNA crystal structure, and the potential effects of intercalating agents on biochemical processes involving DNA quadruplexes and strand exchanges. NDB accession numbers: DD0032 (brominated) and DD0033 (native).

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
18175117 D.J.Bridewell, A.C.Porter, G.J.Finlay, and B.C.Baguley (2008).
The role of topoisomerases and RNA transcription in the action of the antitumour benzonaphthyridine derivative SN 28049.
  Cancer Chemother Pharmacol, 62, 753-762.  
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
15157277 S.M.Nelson, L.R.Ferguson, and W.A.Denny (2004).
DNA and the chromosome - varied targets for chemotherapy.
  Cell Chromosome, 3, 2.  
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
11809884 A.Adams, J.M.Guss, W.A.Denny, and L.P.Wakelin (2002).
Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide bound to d(CGTACG)2: implications for structure-activity relationships of acridinecarboxamide topoisomerase poisons.
  Nucleic Acids Res, 30, 719-725.
PDB code: 1kci
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