Molecular recognition of B-DNA by Hoechst 33258.
The binding sites of Hoechst 33258, netropsin and distamycin on three DNA restriction fragments from plasmid pBR322 were compared by footprinting with methidiumpropyl-EDTA X Fe(II) [MPE X Fe(II)]. Hoechst, netropsin and distamycin share common binding sites that are five +/- one bp in size and rich in A X T DNA base pairs. The five base pair protection patterns for Hoechst may result from a central three base pair recognition site bound by two bisbenzimidazole NHs forming a bridge on the floor of the minor groove between adjacent adenine N3 and thymine O2 atoms on opposite helix strands. Hydrophobic interaction of the flanking phenol and N-methylpiperazine rings would afford a steric blockade of one additional base pair on each side.
K D
KD
Harshman
P B
PB
Dervan
D001483:Base Sequence; D001562:Benzimidazoles / Q000494:pharmacology*; D001665:Binding Sites; D006690:Bisbenzimidazole / Q000494:pharmacology*; D004247:DNA; D004214:Distamycins / Q000494:pharmacology; D009429:Netropsin / Q000494:pharmacology
D001562:Benzimidazoles; D004214:Distamycins; D009429:Netropsin; D004247:DNA; D006690:Bisbenzimidazole