Binding of ethidium bromide to 5-S ribosomal RNA

Abstract

The nature of the complex formed between the polycyclic drug, ethidium bromide and 5-S rRNA's of Escherichia coli and of Bacillus stearothermophilus has been examined by fluorescence and absorption spectroscopy. This complex has properties similar to the complex formed with other highly base-paired nucleic acids. In E. coli 5-S rRNA 12–13 ethidium bromide molecules are bound per molecule of 5-S rRNA while B. stearothermophilus 5-S rRNA binds 9–10 ethidium bromide molecules per molecule of 5-S rRNA. This difference may be explained by E. coli having longer base-paired regions than has B. stearothermophilus 5-S rRNA. Thermal denaturation and ORD studies also indicate that the long base-paired regions in E. coli 5-S rRNA are primarily composed of G · C runs rather than heterogeneous stretches of G · C and A · U pairs. B. stearothermophilus 5-S rRNA, which has a base content and degree of helicity similar to that of E. coli, has paired regions which are composed of more equal amounts of G · C and A · U base pairs. The comparative studies on E. coli and B. stearothermophilus 5-S rRNA indicate that there is probably not a common conformation for 5-S rRNA in all species.