FIG. 5.
A three-dimensional model for the wild-type pseudoknot structure. Modeling was performed using miniCarlo as described in Materials and Methods. (A) A ribbon representation (three different views). Stem 1 is shown in blue, Watson-Crick strands of stem 2 are colored in brown (purine-rich strand) and yellow (pyrimidine-rich strand), and the third oligo(U) strand is colored in cyan. Bulged-out U959 is shown in magenta; unpaired residues C861, C877, and C957 underneath the last triple are in red; and the Watson-Crick pair C878-G956 terminating stem 2 are in gray. (B) A schematic representation of base-pairing in the pseudoknot. Vertical lines represent Watson-Crick interactions; tilted lines, Hoogsteen interactions; and the asterisk, a G·U wobble pair. Note that if protonated, C861 has a potential to form a base triple (C878-G956·C861+).