Figure 1

RNA secondary structures. Double lines between nucleotides indicate a strong Watson-Crick interaction between C and G; single lines indicate a weaker interaction between A and U. Nucleotides are colored as follows: blue, involved in Watson-Crick pairs; yellow, unpaired; red, involved in non-Watson-Crick pairs; green, the bulging G. The non-Watson-Crick pairs are named after the edges forming the H-bonded pairs and are indicated by: circle, Watson-Crick edge; square, Hoogsteen edge; triangle, Sugar edge. These symbols are blank when the two nucleotides approach in the trans orientation and dark when they approach in the cis orientation. Each panel shows the sequence with only Watson-Crick pairing on the left, the secondary structure with non-Watson-Crick pairing in the middle and the resulting three-dimensional structure on the right. (a) A G-bulged or loop E module completes a hairpin structure by forming non-Watson-Crick pairs within an internal loop. The sequential order of the usually observed set of non-Watson-Crick pairs is maintained, thereby defining a module. The structure of the G-bulged module shown is from helix H11 of the 23S rRNA of Escherichia coli (Protein DataBank (PDB) code 2AW4) [10]. (b) A G-bulged module organizes a three-way junction, leading to a rough co-axiality between two helical stems. The structure of the G-bulged module shown is the one at the junction of helices H16-H21-H22 from the 23S rRNA of Escherichia coli (PDB code 2AW4) [10]. Drawings courtesy of Jose Almeida Cruz.