title: DNA sequence recognition by the indolocarbazole antitumor antibiotic AT2433-B1 and its diastereoisomer.
abstract: The antibiotic AT2433-B1 belongs to a therapeutically important class of antitumor agents. This natural product contains an indolocarbazole aglycone connected to a unique disaccharide consisting of a methoxyglucose and an amino sugar subunit, 2,4-dideoxy-4-methylamino-L-xylose. The configuration of the amino sugar distinguishes AT2433-B1 from its diastereoisomer iso-AT2433-B1. Here we have investigated the interaction of these two disaccharide indolocarbazole derivatives with different DNA sequences by means of DNase I footprinting and surface plasmon resonance (SPR). Accurate binding measurements performed at 4 and 25 degrees C using the BIAcore SPR method revealed that AT2433-B1 binds considerably more tightly to a hairpin oligomer containing a [CG](4) block than to an oligomer with a central [AT](4) tract. The kinetic analysis shows that the antibiotic dissociates much more slowly from the GC sequence compared to the AT one. Preferential binding of AT2433-B1 to GC-rich sequences in DNA was independently confirmed by DNase I footprinting experiments performed with a 117 bp DNA restriction fragment. The specific binding sequence 5'-AACGCCAG identified from the footprints was then converted into a biotin-labeled DNA hairpin duplex and compound interactions with this specific sequence were characterized by high resolution BIAcore SPR experiments. Such a combined approach provided a detailed understanding of the molecular basis of DNA recognition. The discovery that the glycosyl antibiotic AT2433-B1 preferentially recognizes defined sequences offers novel opportunities for the future design of sequence-specific DNA-reading small molecules.
authors.affiliation: Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret and INSERM U-524, IRCL, Place de Verdun, 59045 Lille, France.
authors.forename: Carolina
authors.initials: C
authors.lastname: Carrasco
authors.forename: Michaël
authors.initials: M
authors.lastname: Facompré
authors.forename: John D
authors.initials: JD
authors.lastname: Chisholm
authors.forename: David L
authors.initials: DL
authors.lastname: Van Vranken
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: Christian
authors.initials: C
authors.lastname: Bailly
mesh_terms: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism*; D000903:Antibiotics, Antineoplastic / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002227:Carbazoles; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting; D020862:GC Rich Sequence; D007211:Indoles; D007700:Kinetics; D008969:Molecular Sequence Data; D013237:Stereoisomerism; D020349:Surface Plasmon Resonance
chemical_list: D000617:Aminoglycosides; D000900:Anti-Bacterial Agents; D000903:Antibiotics, Antineoplastic; D002227:Carbazoles; D007211:Indoles; C061863:AT 2433-B1; D004247:DNA