EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame
Fig 2
The 6 strategies included in the SAP.
(A) The original state of the puzzle before SAP. This represents a puzzle initiated with an arbitrary sequence of nucleotides; panel displays the target structure, where mismatched nucleotides (C-A) are highlighted. (B) The first step of the SAP is to correct mismatched pairs. Here, the cytosine nucleotides are switched to uracil to pair with adenine. (C) Changing end pairs to G-C. Changing base pairs that are at the edges of stems and flank loops to G-C pairs lowers the free energy of the molecule. (D) G-internal loop boost. The first nucleotide in an internal loop on either side is switched to a guanine. (E) U-G-U-G super boost. In an internal loop with 2 unpaired bases on either side, the 2 bases are changed to uracil and guanine, in that order, on either side. (F) G-hairpin boost. The first nucleotide in each strand of a hairpin loop is changed to a guanine. (G) Reorienting base pairs. Target base pairs that are not predicted to be folded correctly are ‘flipped’ to lower the energy of the structure. Here, alternating the A-U pairs lowers the energy of the stack. The 5’ end of each puzzle is at the top left, with the puzzle drawn counter-clockwise from that point.