Figure 3.
Minimum free energy (MFE) structures and base availabilities for select fuel strands and the substrate backbone. (a) MFE structures of the original fuel strand and fuel modifications A1A2, G1T2, G1G2, and C24 calculated by NUPACK. The Gibbs free energy of each structure is provided in units of kcal/mol. (b) Base availabilities for the original fuel and fuel modifications A1A2, G1T2, and G1G2 (upper plot) and the differrence in base availabilities (ΔA) for each modification relative to the original fuel (lower plot). (c) Base availabilities for the original fuel and fuel modification C24 (upper plot) and the difference in availability relative to the original fuel (lower plot). (d) MFE structure of the substrate calculated by NUPACK. (e) Availability of each base in the backbone strand of the substrate. Because the fuel strand hybridizes with the backbone strand on the substrate, the base positions of the backbone strand were plotted on the x axis and labeled to correspond to the complement of the fuel strand.