Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z junction.
Equilibrium binding studies are reported that describe the interaction of the simple intercalator ethidium with a hexadecadeoxynucleotide (BZ-1) that contains a stable B-Z junction. The transition of BZ-1 from its low-salt right-handed form to its high-salt hybrid form containing the junction between left- and right-handed DNA was found to greatly facilitate ethidium binding. Ethidium binding to all conformational forms of BZ-1 was found to be complex and highly cooperative, a result that indicates an unusually robust conformational mobility in the molecule. Binding results were quantitatively analyzed by using an allosteric model that provides a description of energetics of the conformational transitions in BZ-1, in addition to estimates of the binding constants for ethidium binding to the different conformations. These results provide a quantitative description of a structurally specific intercalator-DNA interaction.
Suh
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Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505.
Sheardy
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RD
Chaires
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JB
D001483:Base Sequence; D001665:Binding Sites / Q000187:drug effects; D004996:Ethidium / Q000378:metabolism*; D007364:Intercalating Agents / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D012965:Sodium Chloride / Q000494:pharmacology; D013050:Spectrometry, Fluorescence
D007364:Intercalating Agents; D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D004996:Ethidium