PROBING THE STRUCTURE OF MOUSE EHRLICH ASCITES CELL 5.8S, 18S AND 28SRIBOSOMAL-RNA IN-SITU

The secondary structure of mouse Ehrlich ascites 18S, 5.8S and 28S rib osomal RNA in situ was investigated by chemical modification using dim ethyl sulphate and 1-cyclohexyl-3-(morpholinoethyl) carbodiimide metho -p-toluene sulphonate. These reagents specifically modify unpaired bas es in the RNA. The reactive bases were localized by primer extension f ollowed by gel electrophoresis. The three rRNA species were equally ac cessible for modification i.e. approximately 10% of the nucleotides we re reactive. The experimental data support the theoretical secondary s tructure models proposed for 18S and 5.8/28S rRNA as almost all modifi ed bases were located in putative single-strand regions of the rRNAs o r in helical regions that could be expected to undergo dynamic breathi ng. However, deviations from the suggested models were found in both 1 8S and 28S rRNA. In 18S rRNA some putative helices in the 5'-domain we re extensively modified by the single-strand specific reagents as was one of the suggested helices in domain III of 28S rRNA. Of the four eu karyote specific expansion segments present in mouse Ehrlich ascites c ell 28S rRNA, segments I and III were only partly available for modifi cation while segments II and IV showed average to high modification.