Figure 2.

MC-SYM script for the human prion pseudoknot. The arrows represent nucleotide relations. The arrows start from the reference to the placed nucleotide. For instance, C230 is the global reference nucleotide. It was used to stack A231 and to pair G257, A231 was used to pair U256, and so on. Unlabeled arrows indicate the ‘connect’ relation, which includes ‘stack’ and ‘bulged out’ relations, except in stems, where they indicate helical stacking. The label ‘pair’ indicates that all hydrogen bonding patterns were tentatively assigned for the given pair of nucleotides. The nucleotides are colored following the rules of Figure 1.