Environments of ethidium binding to allosteric Dna: II. Accessibility, mobility and mode of binding.
DNA binding compounds were previously shown to bind to the right-handed DNA forms and hybrid B-Z forms in a highly cooperative manner and indicate that structural specificity plays a key role in a ligand binding to DNA. In this study, the modes of binding and structural specificity of agents to unusual DNA are examined by a variety of fluorescence techniques (intensity, polarization and quenching, etc.) to explore a reliable method to detect the association environment of ligands to deoxyoligonucleotides initially containing a B-Z junction between the left-handed Z-DNA and right-handed B-DNA. The results of fluorescence energy transfer measurement demonstrated that the ligand molecules bind to the allosterically converted DNA structures by intercalation. In the absence of high-resolution structural data, this fluorescence energy transfer measurement allowed reliable measures and infer the binding environment of ligands to the allosteric DNA structures.
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Department of Biochemistry, School of Medicine, Pochon CHA University, Kyungki-Do, Korea. DCSuh@hanmail.net
D000494:Allosteric Regulation; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004735:Energy Transfer; D004996:Ethidium / Q000378:metabolism*; D005090:Exodeoxyribonucleases / Q000378:metabolism; D008024:Ligands; D009038:Motion; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*
D008024:Ligands; D009838:Oligodeoxyribonucleotides; D004247:DNA; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III; D004996:Ethidium