(A) Sequence and secondary structure representation of the 54 nt part of CopA (green box) and the corresponding 47 nt CopT (blue box) counterpart used in our simulation study. The three central residues of the hairpins (CCG/GGC) are the initial interaction site (marked in orange). (B) Fold-A and Fold-B of DsrA from Wu et al. (2017) in 2D structure representation. We label the stem–loops SL1–SL3 and the LR between SL1 and SL2. Fold-B opens the entire region from SL1 up to C40. (C) 2D DsrA consensus structure representation based on Rfam and predicted by the ViennaRNA package. The orange lines in (B) and (C) mark potential initial sites used later. (D) Sequence and dot-bracket representation of the HIV-1 DIS stem–loop interaction with the 6 nt kissing hairpin interaction marked in orange, and the conserved, unbounded, noncomplimentary nucleotides marked in red. The 3D representation below (visualized with PyMOL [Schrödinger 2022]) represents both: the individual nucleotides and the associated secondary structure in Ernwin-style, represented as cylinders. Thus, the green cylinders stand for the respective intramolecular stem in each chain, the orange one for the interaction, and the small red ones for the unbounded nucleotides. All 2D representations in this figure are generated with forna (Kerpedjiev et al. 2015a).
