Table 1.

FSE systems studied in this work. For each motif (3_6, 3_3, and 3_5) and length (77, 87, and 144-nt) combination, we use five 3D prediction programs (R for RNAComposer, S for SimRNA, I for iFoldRNA, V for Vfold3D, and F for Farfar2) to generate starting models.

All FSE systems considered (37) and validated (30)
Length	WT 3_6	WT 3_3	WT 3_5	M 3_6	M 3_3	M 3_5
77-nt	*R1, S2, *I3, V4	R, S10, *I11, V12	R16, S17, *I18, *V19	R${}^{1^{\prime }}$, *S${}^{2^{\prime }}$, I${}^{3^{\prime }}$, V${}^{4^{\prime }}$	*I${}^{11^{\prime }}$	R${}^{16^{\prime }}$, S${}^{17^{\prime }}$, *I${}^{18^{\prime }}$, V${}^{19^{\prime }}$
87-nt	*R5, S, *I6, V	R, S, *I13, V	N/A	N/A	N/A	N/A
144-nt	R7, I8, F9	R, I14, F15	N/A	*R${}^{7^{\prime }}$, I${}^{8^{\prime }}$	N/A	N/A

The 19 convergent and validated wildtype MD trajectories and the 11 mutant trajectories are numbered as indicated by the superscript. Representative trajectories for the Results section are marked with asterisks.