Effects of a hairpin polyamide on DNA melting: comparison with distamycin and Hoechst 33258.

Journal article

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 ...

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Authors: James, P; Le Strat, L; Ellervik, U; Bratwall, C; Nordén, B

• Publication status: Published
• Journal: Biophysical chemistry
• Volume: 111
• Issue: 3
• Pages: 205-212
• Publication date: 2004-11-01
• DOI: 10.1016/j.bpc.2004.06.001
• EISSN: 1873-4200
• ISSN: 0301-4622
• Language: English
• Keywords: Ligands; DNA; Deoxyribonuclease I; Base Pair Mismatch; DNA Footprinting; Fluorescent Dyes; Nucleic Acid Denaturation; Molecular Structure; Binding Sites; Base Sequence; Thermodynamics; Pyrroles; Bisbenzimidazole; Distamycins