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We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted thiazole polyamide, to DNA. In one fragment, which contains every tetranucleotide sequence, sub-micromolar concentrations of the ligand generate a single footprint at the sequence ACTAGT. This sequence preference is confirmed in melting experiments with fluorescently labelled oligonucleotides. Experiments with DNA fragments that contain variants of this sequence suggest that the ligand also binds, with slightly lower affinity, to sequences of the type XCYRGZ, where X is any base except C, and Z is any base except G.

Original publication

DOI

10.1093/nar/gkh666

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

2004

Volume

32

Pages

3410 - 3417

Keywords

Base Sequence, Binding Sites, DNA, DNA Footprinting, Molecular Sequence Data, Nucleic Acid Denaturation, Spectrometry, Fluorescence, Thiazoles