title: Selective inhibition of restriction endonuclease cleavage by DNA intercalators.
abstract: The preferred dye binding sites and the microenvironment of known nucleotide sequences within mitochondrial and plasmid pBR322 DNA was probed in a gross fashion with restriction endonucleases. The intercalating dyes, ethidium bromide and propidium iodide, do not inhibit a given restriction endonuclease equally at all of the restriction sites within a DNA molecule. The selective inhibition may be explained, in part, by the potential B to Z conformation transition of DNA flanking the restriction site and by preferred dye binding sites. Propidium iodide was found to be a more potent inhibitor than ethidium bromide and the inhibition is independent of the type of cut made by the enzyme.
mesh_terms: D000818:Animals; D001665:Binding Sites; D006224:Cricetinae; D004262:DNA Restriction Enzymes / Q000037:antagonists & inhibitors*; D004272:DNA, Mitochondrial / Q000378:metabolism; D004587:Electrophoresis, Agar Gel; D004996:Ethidium / Q000494:pharmacology; D007364:Intercalating Agents / Q000494:pharmacology*; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011419:Propidium / Q000494:pharmacology
chemical_list: D004272:DNA, Mitochondrial; D007364:Intercalating Agents; D011419:Propidium; D004262:DNA Restriction Enzymes; D004996:Ethidium