Fluorescent intercalator displacement analyses of DNA binding by the peptide-derived natural products netropsin, actinomycin, and bleomycin.
The response of the high-throughput fluorescent intercalator displacement (HT-FID) assay reported recently by Boger et al. to peptide-based DNA binding intercalators and metal complexes was examined through the study of actinomycin and Co(III).bleomycin-B2. Along with a validation of netropsin that illustrated the good laboratory-to-laboratory reproducibility of the assay, our examination of actinomycin revealed results for a four base pair cassette library of DNA hairpins that paralleled the known DNA site-selectivity of this agent and also indicated the involvement of the flanking sequences of the hairpin oligonucleotide. In addition, for Co(III).bleomycin-B2 the established cleavage site-selectivity for 5'-GT and 5'-GC sites was correlated to drug-DNA association in this binding-only assay; our results also suggest a tetranucleotide site-selectivity for metallobleomycin involving cross-strand, 'back-to-back' 5'-GT and 5'-GC sites such as 5'-ACGT and 5'-ACGC.
Lewis
Mark A
MA
Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, USA.
Long
Eric C
EC
D000900:Anti-Bacterial Agents / Q000737:chemistry; D000903:Antibiotics, Antineoplastic / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D001761:Bleomycin / Q000737:chemistry*; D003035:Cobalt / Q000737:chemistry; D003609:Dactinomycin / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009429:Netropsin / Q000737:chemistry*; D009942:Organometallic Compounds / Q000737:chemistry; D013050:Spectrometry, Fluorescence / Q000379:methods
D000900:Anti-Bacterial Agents; D000903:Antibiotics, Antineoplastic; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D009942:Organometallic Compounds; D001761:Bleomycin; D003609:Dactinomycin; D003035:Cobalt; D009429:Netropsin