Figure 4.

Conformational transitions and dynamic structural properties of therapeutic 22-mer, 25-mer, and 30-mer PMOs

(A) Extended conformation of the 22-mer PMO (see Figure 1) and three representative partially folded conformations formed in the course of three independent MD runs. The extended and partially folded conformations are displayed in the twister representation (for the backbone; blue line) and in the PaperChain representation (for nucleic bases). (B and C) Time profiles of the structural properties of the 22-mer (red curves), 25-mer (green curves), and 30-mer (black curves) PMOs from structure snapshots extracted from these simulations at every 5-ns time interval. (B) Evolution of the end-to-end distance $X$ (solid curves; left $y$ axis) and radius of gyration $R_g$ (dashed curves; right $y$ axis) from a 1-μs MD simulation run. (C) Number of base-stacking interactions $N_{BS}$ (solid curves; left $y$ axis) and base-pairing interactions $N_{BP}$ (dashed curves; right $y$ axis).