Predicting structures and stabilities for H-type pseudoknots with interhelix loops

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FIGURE 1.
FIGURE 1.

(A) An RNA pseudoknot with an interhelix loop L3. (B) Traditional two-vector virtual bond model for RNA nucleotides involves two bonds, P–C4–P. To describe the base orientation, we introduce a third virtual bond model, C4–N1 (pyrimidine) or C4–N9 (purine). (C) A virtual bond representation for a pseudoknot motif with S1 = 8 bp, S2 = 6 bp, L1 = 4 nt, L2 = 4 nt, and L3 = 2 nt.

This Article

  1. Published in Advance February 23, 2009, doi: 10.1261/rna.1429009 RNA 15: 696-706

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