Exp Mol Med.  2000 Dec;32(4):204-209.

Environments of ethidium binding to allosteric Dna: II. Accessibility, mobility and mode of binding

• Suh DC

Abstract

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.

Keyword

allosteric DNA; fluorescence energy transfer; fluorescence polarization; fluorescence quenching; mode of binding

MeSH Terms

Allosteric Regulation
Circular Dichroism
DNA/*chemistry/*metabolism
Energy Transfer
Ethidium/*metabolism
Exodeoxyribonucleases/metabolism
Ligands
Motion
Nucleic Acid Conformation
Oligodeoxyribonucleotides/*metabolism