Figure 2.

(a) Sequence and domain representation of the substrate with fraying locations highlighted. (b) Sequence and domain representation of the original fuel strand. Corresponding to the fraying locations of the substrate, the locations of fuel base mismatches are numbered, highlighted, and shown in bold font. They are 5′ end (bases 1 and 2), nick (bases 24 and 25), and 3′ end (bases 43 and 44). (c) Leakage rate constants for fuel modifications. The concentrations for leakage reactions are fuel (1300 nM), substrate (14 nM), and reporter (20 nM). The black bar represents the leakage rate with the original fuel strand. Pink, orange, and blue bars represent leakage rates for fuels with 1 and 2 nt modifications at 5′, nick, and 3′ locations, respectively. The rates are labeled by the identity of the modified base and its location on the fuel (see panel (b) for locations and originial base idenities). For example, G₁T₂ indicates that base 1 was changed from C to G and base 2 was changed to C to T. Error bars show the standard deviation from the mean for select samples in triplicate to estimate experimental error.