Secondary structure mapping experiments using SI nuclease, RNase Th and diethyl pyrocarbonate as conformational probes have identified those regions in mouse 5.8S rRNA containing major sites of interaction with 28S rRNA. One site encompasses the 3'-terminal 20 nucleotides and corresponds to the region identified previously as a component of an RNase-resistant 5.8S/28S rRNA junction complex. A second site, located at the 5’ terminus, has not been defined precisely but is believed to involve approximately 20-30 nucleotides. The existence of these sites of interaction is supported by comparing sequences of eukaryotic 5.8S and 28S rRNA with those of the prokaryotic 23S rRNA. Evidence for the occurrence of at least three helical regions in the central portion of the mouse 5.8S rRNA molecule is also presented.
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