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[Preprint]. 2022 Jan 4:rs.3.rs-1160075. [Version 1] doi: 10.21203/rs.3.rs-1160075/v1

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Figure 6: — Alternative 3_3 and 3_5 conformations. (Top) The 77 and 87-nt 3_3 pseudoknot structures (iFoldRNA). For 77-nt, two residues in the 3′ end (purple), which are involved in the 3_6 and 3_5 Stem 2, form triplets with the 3_3 Stem 2. For 87-nt, the 5′ and 3′ end bind to form flanking stem SF, and the same two 3′ end residues (purple) are locked around Stem 3 by a downstream triplet. (Bottom) The 3_5 junction 77-nt MD model (SimRNA). The Stem 2 helix formed by the 5′ and 3′ ends is stabilized around Stem 3 by multiple hydrogen bonds.