Results Overview of the motif The K-turn is a two-stranded, helix?internal loop?helix motif comprising 15 nucleotides (Figures 1 and 2). The first helical stem, the ∑canonical stem∏ or ∑C-stem∏, ends at the internal loop with two Watson?Crick base pairs, typically C?Gs, while the second helical stem, the ∑non-canonical stem∏ or ∑NC-stem∏, which follows the internal loop, starts with two non-Watson?Crick base pairs, typically sheared G?A base pairs. The internal loop between the helical stems is always asymmetrical, and usually has three unpaired nucleotides on one strand and none on the other (Figure 1). The 5'-most nucleotide in the long strand of the loop stacks on the C-stem, the second extends to stack on the NC-stem, and the third protrudes into solution. Because of the kink in the phosphodiester backbone in this strand, the orientation of the axes of the C-stem and the NC-stem differ by 120‰. The K-turn occurs six times in H.marismortui 23S rRNA, and twice in T.thermophilus 16S rRNA. Each one is designated ∑KT-#∏, with KT standing for kink-turn and the number indicating the helix of rRNA in which it is found (Leffers et al., 1987). Although these eight K-turns vary somewhat in sequence, each has essentially the same distinctive three-dimensional form, and a consensus sequence can be derived (Figure 1). next