Ab initio models of pre-mRNA and docking analysis. (A) Ab initio structures corresponding to wt (i) and mutated (ii) pre-mRNA sequences generated on iFold. The structure is depicted in stick format and shown in cyan. The mutated residue location is depicted in blue and marked with a lavender-shaded area. Hydrogen bonds are depicted as magenta dots throughout panels A-C. The backbone of the region corresponding to residues that bind to U1 snRNA is red, whereas the bases are yellow. This region is also marked by the lavender-shaded area. (B) Region corresponding to U1 snRNA binding for the wt (i) and mutated (ii) pre-mRNA models at a closer view. Color coding is as observed in panel A. The residues that bind to U1 snRNA are numbered in the mutated sequence structure model. In the wt sequence model, the unbound residues corresponding to U1 snRNA binding are marked with lavender-shaded regions. (C) Coarse-grained depiction of the dock of U1 snRNA over the wt (i) and mutated (ii) pre-mRNA sequence structure. Because the depiction is coarse-grained, the entire model is depicted only as a beaded trace. The trace is blue for the pre-mRNA sequence, with only the region corresponding to U1 snRNA binding shown in red. The different putative U1 snRNA docked structures are colored differently. Because only 1 putative dock was observed for the wt sequence, U1 snRNA is shown as light green in the dock between the U1 snRNA and wt pre-mRNA structures. The inset images provide a closer view of the U1 snRNA binding region on the pre-mRNA structures. The proximal regions in the U1 snRNA and wt pre-mRNA structures are marked by the lavender-shaded area.