Determining the polarity of the map of crosslinked interactions in Escherichia coli 16 S ribosomal RNA.

Hydroxymethyltrimethylpsoralen crosslinked 16 S rRNA from Escherichia coli has been R loop hybridized to two plasmid DNAs containing different sections of the 16 S ribosomal gene. It is possible to identify crosslinked features in the part of the RNA that is not complementary to the DNA. Crosslinked features can be aligned into a relative map of interactions. Crosslinked loops that correspond to features located, originally arbitrarily, in the left part of this map are seen in the 5′ half of the 16 S rRNA in one hybrid and loops that correspond to features in the right part of the map are seen in the 3′ two-thirds of the 16 S rRNA in the other hybrid. These results confirm the relative orientations of the crosslinked loops and establish that the left end of the map corresponds to the 5′ end of the molecule.