Cleavage of a 23S rRNA pseudoknot by phenanthroline-Cu(II)

Studying the intricate folding of rRNA within the ribosome remains a comple x problem. Phenanthroline-Cu(II) complexes cleave phosphodiester bonds in r RNA in specific regions, apparently especially where the rRNA structure is constrained in some fashion. We have introduced phenanthroline-copper compl exes into 50S Escherichia coli ribosomal subunits and shown specific cleava ges in the regions containing nucleotides 60-66 and 87-100. This specificit y of cleavage is reduced when the ribosome is heated to 80 degrees C and re duced to background when the ribosomal proteins are extracted and the cleav age repeated on protein-free 23S rRNA, It has been suggested that nucleotid es 60-66 and 87-95 in E.coli 23S rRNA are involved in a putative pseudoknot structure, which is supported by covariance data. The paired cleavages of nearly equal intensity of these two regions, when in the ribosome, may furt her support the existence of a pseudoknot structure in the 100 region of 23 S rRNA.