Conformational studies of Escherichia coli ribosomes with the use of acridine orange as a probe

Journal of Biochemistry
K HorieH Fukutome

Abstract

The interaction of E. coli vacant ribosomes with acridine orange (AO) was studied, to obtain conformational information about rRNAs in ribosomes. Acridine orange binds to an RNA in two different modes: cooperative outside binding with stacking of bound AO's and intercalation between nucleotide bases. Free 16S and 23S rRNAs have almost identical affinities to AO. At 1 mM Mg2+, AO can achieve stacking binding on about 40% of rRNA phosphate groups. The number of stacking binding sites falls to about 1/3 in the 30S subunit in comparison with free 16S rRNA. In the 50S subunit, the number of stacking binding sites is only 1/5 in comparison with free 23S rRNA. Mg2+ ions are more inhibitory for the binding of AO to ribosomes than to free rRNAs. The strength of stacking binding appears to be more markedly reduced by Mg2+ in active ribosomes than in rRNAs. "Tight couple" 70S particles are less accessible for stacking binding than free subunits. The 30S subunits that have irreversibly lost the capability for 70S formation under low Mg2+ conditions have an affinity to AO that is very different from that of active 30S but similar to that of free rRNA, though the number of stacking binding sites is little changed by the inactivation. 70S and...Continue Reading

Citations

Dec 18, 2009·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Masami UetaAkira Wada
May 15, 2013·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Masami UetaAkira Wada
Aug 3, 2013·Nucleic Acids Research·Yok Hian ChionhPeter C Dedon
Jan 28, 2009·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Hideji YoshidaAkira Wada
Aug 25, 2010·The Journal of Cell Biology·Julio O OrtizWolfgang Baumeister
Jun 20, 2020·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Masami UetaAkira Wada
Apr 7, 2004·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Hideji YoshidaAkira Wada
Dec 6, 2005·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Masami UetaAkira Wada
Jan 5, 2008·Journal of Biochemistry·Masami UetaAkira Wada
Aug 28, 1999·Journal of Bacteriology·T I MeierG Zhao
Mar 1, 1984·Biophysical Chemistry·H HagiharaH Fukutome

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