Spatial Arrangement of the RNAs in Situ

For the elucidation of the spatial arrangement of the 16 S and 23 S RNA strands within their cognate ribosomal subunits, several approaches have been used. Two of them, namely (immune) electron microscopy and RNA-RNA cross-links, will be described here. 

Several attempts have been made to elucidate the shape of the isolated 5 S RNA (Tesche et al, 1980 Sieber et al, 1980), the 16 S RNA (Vasiliev et al., 1978 Sieber et al., 1980 Edlind and Bassel, 1980 Boublik et al., 1982), and the 23 S RNA (Sieber et al., 1980 Edlind and Bassel, 1980 Vasiliev and Zalite, 1980 Boublik et al., 1982) by direct visualization in the electron microscope. In some studies (Vasiliev et al., 1978 Vasiliev and Zalite, 1980), both the 16 S and the 23 S RNAs have been seen in a specific and compact structure. According to these results, the isolated 16 S RNA has a V-like structure, and the isolated 23 S RNA has a size and shape which can be accommodated within the 50 S subunit. However, the conclusion that the shape and size of the in situ RNA and of the isolated RNA are very similar has been questioned by other electron microscopy results (Boublik et al., 1982), and it is also in disagreement with physical studies (Tam et al, 1981a,b Robakis and Boublik, 1981). 

The locations of several characteristic regions of the ribosomal RNA strands within their subunits have been mapped by immune electron microscopy. In this way the positions of the following regions on the 16 S RNA were determined (Fig. 4) its 5 end (Mochalova et al., 1982), the 

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