title: Effects of a hairpin polyamide on DNA melting: comparison with distamycin and Hoechst 33258.
abstract: We have used DNase I footprinting and fluorescence melting studies to study the interaction of the hairpin polyamide Im-Py-Py-Py-(R)H2Ngamma-Im-Py-Py-Py-beta-Dp with its preferred binding sites (5'-WGWWCW; W=A or T) and other sequences. DNase I footprinting confirmed that the ligand binds to the sequence AGAACA at nanomolar concentrations and that changing the terminal A to G causes a dramatic decrease in affinity, while there was no interaction with the reverse sequence WCWWGW. Fluorescence melting studies with 11-mer duplexes showed that the polyamide had very different effects on the forward (TGWWCT) and reverse (TCTAGT) sequences. At low concentrations, the polyamide produced biphasic melting curves with TGATCT, TGTACT and TGAACT, suggesting a strong interaction. In contrast, the melting profiles with TCTAGT were always monophasic and showed much smaller concentration dependent changes in Tm. The polyamide also showed weak binding to the sequence TGATCT when one of the central AT pairs was replaced with an AC mismatch. These melting profiles were compared with those produced by the AT-selective minor groove binding agents distamycin and Hoechst 33258 at the same sites and at similar sequences containing A5 and (AT)3, which are expected to bind distamycin in the 1:1 and 2:1 modes, respectively. These ligands produced simple monophasic melting curves in which the Tm steadily increased as the ligand concentration was raised.
authors.affiliation: Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
authors.forename: Peter L
authors.initials: PL
authors.lastname: James
authors.forename: Loic
authors.initials: L
authors.lastname: Le Strat
authors.forename: Ulf
authors.initials: U
authors.lastname: Ellervik
authors.forename: Christina
authors.initials: C
authors.lastname: Bratwall
authors.forename: Bengt
authors.initials: B
authors.lastname: Nordén
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D001665:Binding Sites; D006690:Bisbenzimidazole / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D018983:DNA Footprinting; D003850:Deoxyribonuclease I; D004214:Distamycins / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D008024:Ligands; D015394:Molecular Structure; D009691:Nucleic Acid Denaturation; D011758:Pyrroles / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004214:Distamycins; D005456:Fluorescent Dyes; C500729:Im-Py-Py-Py-(R)(H2N)gamma-Im-Py-Py-Py-beta-Dp; D008024:Ligands; D011758:Pyrroles; C030000:stallimycin; D004247:DNA; D003850:Deoxyribonuclease I; D006690:Bisbenzimidazole