Fig. 3
From: Programming molecular topologies from single-stranded nucleic acids
Optimization of the folding pathway for ssDNA knots. a A designed model shows the selected best folding pathway (from one to seven) for the three-square structure with 23 crossings, by following our optimization rules. The red to gray color scale as well as the number one to seven represent the order of the paranemic cohesion interaction strengths on the edges from high to low (one to seven), based on the number and length of the paranemic cohesions involved as shown in b. c The paranemic interaction regions can be designed with lengths of 4 bp or 6 bp with distinct expected binding strengths (6 bp > 4 bp). Therefore, one is able to guide the folding order of the knot structure by controlling the sequences and lengths of the paranemic interactions in each individual edge. We compared the folding efficiency of the known structures by using different folding pathways before and after optimization (d). The AFM images revealed a dramatic increase in the folding yield of well-form structures from 0.9% (N = 221) to 57.9% (N = 214) (e). The scale bars are 200 nm
