Structure and topology of 16S ribosomal RNA. An analysis of the pattern of psoralen crosslinking

Abstract

All of the eleven psoralen crosslinking features previously mapped by electron microscopy of the 16S rRNA can be matched by energetically stable duplex regions found by a computer search of the sequence. One additional particularly stable duplex found in the sequence has subsequently been seen in the microscope. There is no indication that a best or unique fit of the sequence to the crosslinking data has been found. However, it is encouraging that all twelve assignments involve non-overlapping regions of the sequence which allows their simultaneous construction. The resulting general pattern of secondary structure is very different from previous suggestions for rRNAs or other complex RNAs. It is an RNA chain folded in space much like a typical protein chain. Because of the interwound nature of double helices, base pairing between distant regions of the sequence might result in topologically knotted structures. However, examination of available electron microscopic data suggests that the 16S rRNA does not contain any knots.