Primary Citation PubMed: 2991536
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A host-guest approach for determining drug-DNA interactions: an example using netropsin.
(2005) Nucleic Acids Res 33
PubMed: 16049022 | PubMedCentral: PMC1181240 | DOI: 10.1093/nar/gki717
Furthermore, we analyzed the previously reported DNA structure d(CGCGAATTCGCG) in the presence (PDB accession ID 6BNA) and absence (3BNA) of netropsin, and found that minor groove widths were the same... even though a number of structural changes were evident upon netropsin binding (data not shown) ( 13 , 27 ).
Publication Year: 2005
Nucleic acid visualization with UCSF Chimera.
(2006) Nucleic Acids Res 34
PubMed: 16478715 | PubMedCentral: PMC1368656 | DOI: 10.1093/nar/gnj031
Figure 5 Netropsin bound to double-stranded DNA ( 28 ) (PDB identifier 6bna).
Publication Year: 2006
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation.
(2008) Nucleic Acids Res 36
PubMed: 18039704 | PubMedCentral: PMC2241865 | DOI: 10.1093/nar/gkm892
Z-scores of the drug dataset and Z -scores of the available free PDB structures with the same DNA sequence as the drug-bound DNA Sequence Drug PDB Z PDB m Z m PDB M Z M N Z ave CCAATTGG Netropsin 1z8v... −2.85 431d −2.84 431d −2.84 1 −2.84 CCAGGCCTGG Imidazole-pyrrole 365d −2.68 1cw9 −3.16 1bd1 −1.77 5 −2.50 CGCATATTTGCG Tri-benzimidazole 459d −2.49 458d −2.00 458d −2.00 1 −2.00 CGCGAATTCGCG m -iodo Hoechst 443d −3.43 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG m -iodo Hoechst 449d −3.51 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Benzimidazole 453d −3.65 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Benzimidazole 1ftd −3.57 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Benzimidazole 1qv4 −3.33 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Thiophene diamidine 1vzk −3.67 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Propamidine 1prp −3.54 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Oxapentamidine 166d −3.52 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Netropsin 6bna −3.86 428d −4.18 270d −2.24 25 −3.33 CGCGAATTCGCG Netropsin 101d −3.54 428d −4.18 270d −2.24 25 −3.33 GCGCGC Triostin 0dac −2.78 1d97 −1.69 1d97 −1.69 1 −1.69 GCGTACGC Quinoxaline 1pfe −3.97 253d −2.43 253d −2.43 1 −2.43 GCGTACGC Echinomycin 1xvk −2.88 253d −2.43 253d −2.43 1 −2.43 GTATATAC Netropsin 473d 1.63 446d 1.77 446d 1.77 1 1.77 Notes : The columns PDB and Z show the PDB file name of the DNA-drug complex and the respective Z -score value; PDB m and Z m give the PDB file name of the free B-DNA crystal structure and the Z -score with the minimum Z -score value; PDB M and Z M show the PDB file name and Z -score value of the free B-DNA crystal structure with the maximum Z -score.
Publication Year: 2008
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