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. Author manuscript; available in PMC: 2015 May 13.
Published in final edited form as: Methods Enzymol. 2015 Jan 5;550:215–249. doi: 10.1016/bs.mie.2014.10.049

Figure 2.

Figure 2

Sequence-specific activation of Spinach.ST molecular beacon by toehold-mediated strand displacement. Sequences of the invariant (aptamer-derived) domains 6*, 6.1, and 6.2 are shown, while the variable (target-derived) domains 2 and 5 (and their complementary domains 2* and 5*) are depicted as strings of “N.” (A) Trigger toehold domain 2* initiates strand displacement upon binding to its complementary domain 2 in Spinach.ST. (B) Toehold hybridization initiates branch migration leading to contiguous hybridization of the trigger domains 2*, 5*, and 6* to the Spinach.ST 3′-end extended domains 2, 5, and 6.2, respectively. The ensuing conformational rearrangement restores the Spinach 24-2-min aptamer structure, including the basal stem formed by base pairing between domain 6* and 6.1. All structures were generated using NUPACK.